US20040161741A1 - Novel compositions and processes for analyte detection, quantification and amplification - Google Patents

Novel compositions and processes for analyte detection, quantification and amplification Download PDF

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US20040161741A1
US20040161741A1 US09/896,897 US89689701A US2004161741A1 US 20040161741 A1 US20040161741 A1 US 20040161741A1 US 89689701 A US89689701 A US 89689701A US 2004161741 A1 US2004161741 A1 US 2004161741A1
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nucleic acid
group
nucleic acids
analytes
primers
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Elazar Rabani
Jannis Stavrianopoulos
James Donegan
Jack Coleman
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Enzo Life Sciences Inc
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Enzo Life Sciences Inc
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Priority to US09/896,897 priority Critical patent/US20040161741A1/en
Priority to CA2841389A priority patent/CA2841389C/en
Priority to CA2841397A priority patent/CA2841397C/en
Priority to CA2714119A priority patent/CA2714119C/en
Priority to CA2390141A priority patent/CA2390141C/en
Priority to IL210626A priority patent/IL210626A/en
Priority to IL210621A priority patent/IL210621A/en
Priority to IL210636A priority patent/IL210636A/en
Priority to IL210628A priority patent/IL210628A/en
Priority to IL210624A priority patent/IL210624A/en
Priority to IL210627A priority patent/IL210627A/en
Priority to IL210619A priority patent/IL210619A/en
Priority to IL210629A priority patent/IL210629A/en
Priority to IL210633A priority patent/IL210633A/en
Priority to IL210625A priority patent/IL210625A/en
Priority to IL210622A priority patent/IL210622A/en
Priority to IL210631A priority patent/IL210631A/en
Priority to IL210635A priority patent/IL210635A/en
Priority to IL150226A priority patent/IL150226A/en
Priority to IL210634A priority patent/IL210634A/en
Priority to IL210620A priority patent/IL210620A/en
Priority to IL201151A priority patent/IL201151A/en
Priority to IL201150A priority patent/IL201150A/en
Priority to IL210630A priority patent/IL210630A/en
Priority to IL210637A priority patent/IL210637A/en
Priority to IL210632A priority patent/IL210632A/en
Priority to IL210623A priority patent/IL210623A/en
Priority to EP10182828A priority patent/EP2360273A1/en
Priority to EP10182825.9A priority patent/EP2366797B1/en
Priority to EP10182833.3A priority patent/EP2361992B1/en
Priority to EP10182831A priority patent/EP2360274A1/en
Priority to EP16200296.8A priority patent/EP3208346A1/en
Priority to EP02014087.7A priority patent/EP1275737B1/en
Priority to JP2002192771A priority patent/JP2003088390A/ja
Assigned to ENZO LIFE SCIENCES, INC. reassignment ENZO LIFE SCIENCES, INC. ASSIGNMENT OF ASSIGNORS INTEREST (SEE DOCUMENT FOR DETAILS). Assignors: RABBANI, ELAZAR, COLEMAN, JACK, DONEGAN, JAMES J., STAVRIANOPOULOS, JANNIS G.
Priority to US10/693,481 priority patent/US20060057583A1/en
Priority to US10/900,452 priority patent/US20050233343A1/en
Priority to US10/900,455 priority patent/US9790621B2/en
Priority to US10/900,453 priority patent/US9309563B2/en
Priority to US10/900,009 priority patent/US20070196828A1/en
Priority to US10/900,454 priority patent/US9234234B2/en
Priority to US10/900,451 priority patent/US8557522B2/en
Priority to US10/902,640 priority patent/US9279147B2/en
Priority to US10/902,567 priority patent/US8597888B2/en
Priority to US10/902,564 priority patent/US9163280B2/en
Priority to US10/902,587 priority patent/US9057100B2/en
Priority to US10/902,682 priority patent/US9428797B2/en
Priority to US10/902,629 priority patent/US7807352B2/en
Priority to US10/902,597 priority patent/US9434984B2/en
Priority to US10/902,641 priority patent/US9234235B2/en
Priority to US10/902,586 priority patent/US9487821B2/en
Publication of US20040161741A1 publication Critical patent/US20040161741A1/en
Priority to US11/403,117 priority patent/US20060257906A1/en
Priority to US11/444,151 priority patent/US9777312B2/en
Priority to JP2007241620A priority patent/JP2008017853A/ja
Priority to JP2009050273A priority patent/JP2009112317A/ja
Priority to US14/055,547 priority patent/US9528146B2/en
Priority to US14/812,449 priority patent/US9777406B2/en
Priority to US14/812,254 priority patent/US9637778B2/en
Priority to US14/812,388 priority patent/US9745619B2/en
Priority to US14/812,487 priority patent/US9765387B2/en
Priority to US14/812,332 priority patent/US9650666B2/en
Priority to US14/812,293 priority patent/US9617584B2/en
Priority to US14/849,993 priority patent/US9873956B2/en
Priority to US15/075,495 priority patent/US9611508B2/en
Priority to US15/076,063 priority patent/US9617585B2/en
Priority to US15/285,749 priority patent/US9771667B2/en
Priority to US15/689,120 priority patent/US20170362641A1/en
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Definitions

  • This invention relates to the field of analyte detection, quantification and amplification, including compositions and processes directed thereto.
  • RNA expression provides major insights into analysis of cellular metabolism, function, growth and interactions. Although individual RNA species have historically been the subject of these studies, more interest is currently being shown in analysis of the patterns of the simultaneous expression of multiple RNA species of both known and unknown function. This approach allows comparative studies on the patterns of expression between different populations of cells, thereby serving as an indicator of the differences in biochemical activities taking place within these populations. For instance, a single group of cells can be divided up into two or more populations where one group serves as a control and the other part is exposed to drugs, metabolites or different physical conditions. In this way, although the majority of the various species of mRNA show little or no differences in expression levels, certain mRNA species may show dramatic increased or decreased levels of expression compared to the untreated or normal control.
  • HMEC human mammary epithelial cells
  • the first element is concerned with the preparation of the bank of probes that will be used to bind or capture labeled material that is derived from the mRNAs that are being analyzed.
  • the purpose of these arrays is to provide a multiplicity of individual probes where each probe is located in a discrete spatially defined position. After hybridization of the sample is carried out, the particular amount of sample is measured for each site giving a relative measurement of how much material is present in the sample that has homology with the particular probe that is located at that site.
  • the two most commonly used methods for array assembly operate on two very different scales for synthesis of arrays.
  • discrete nucleic acids are affixed to solid matrixes such as glass slides or nylon membranes in a process that is very similar to that employed by ink jet printers (For example, see Okamoto et al., 2000, Nature Biotechnology 18; 438-441).
  • the nature of the probe deposited on the matrix can range from small synthetic oligonucleotides to large nucleic acid segments from clones.
  • Preparation of a cloned segment to be used in this form of array assembly can range from E. coli colonies containing individual clones that are lysed and fixed directly onto a matrix or more elaborately by using individual plasmids as templates for preparation of PCR amplified material.
  • the latter method is preferred due to the higher purity of the nucleic acid product.
  • the choice of a particular probe to be used in the assembly can be directed in the sense that the function and sequence is known. This of course will always be true when oligonucleotides are used as the probes since they must be synthesized artificially.
  • the probes when they are derived from larger cloned segments of DNA, they can be used irrespective of knowledge of sequence or function. For instance, a bank of probes that represent the entire yeast genome was used in the studies cited earlier on differential expression during cell cycle progression. For human sequences, the burgeoning growth of the human sequencing project has provided a wealth of sequence information that is constantly expanding.
  • An advantage of this system is that instead of a single probe for a particular gene product, a number of probes from different segments can be synthesized and incorporated into the design of the array. This provides a redundancy of information, establishing that changes in levels of a particular transcript are due to fluctuations in the intended target rather than by transcripts with one or more similar sequences.
  • biochips are commercially available as well as the hardware and software required to read them.
  • the second element involved in array analysis is the means by which the presence and amount of labeled nucleic acids bound to the various probes of the array will be detected.
  • the native RNA itself can be labeled. This has been carried out enzymatically by phosphorylation of fragmented RNA followed by T4 RNA ligase mediated addition of a biotinylated oligomer to the 5′ ends (Lockhart et al, 1996). This method has the limitation that it entails an overnight incubation to insure adequate joining of labels to the RNA.
  • the fragments can be labeled with psoralen that has been linked to biotin (Lockhart et al, 1996).
  • This method has the disadvantage that the crosslinking that joins the label to the RNA can also lead to intrastrand crosslinking of target molecules reducing the amount of hybridizable material.
  • the RNA is used as a template to synthesize cDNA copies by the use of either random primers or by oligo dT primers.
  • Extension of the primers by reverse transcriptase can be carried out in the presence of modified nucleotides, thereby labeling all of the nascent cDNA copies.
  • the modified nucleotides can have moieties attached that generate signals in themselves or they may have moieties suitable for attachment of other moieties capable of generation of signals. Examples of groups that have been used for direct signal generation have been radioactive compounds and fluorescent compounds such as fluorescein, Texas red, Cy3 and Cy 5.
  • Direct signal generation has the advantage of simplicity but has the limitation that in many cases there is reduced efficiency for incorporation of the labeled nucleotides by a polymerase.
  • groups that have been used for indirect signal generation in arrays are dinitrophenol (DNP) or biotin ligands. Their presence is detected later by the use of labeled molecules that have affinities for these ligands.
  • Avidin or strepavidin specifically bind to biotin moieties and antibodies can be used that are specific for DNP or biotin. These proteins can be labeled themselves or serve as targets for secondary bindings with labeled compounds.
  • post-synthetic modification can be carried out by a chemical addition of a suitably labeled ester.
  • a cDNA copy from an mRNA template essentially results in a one to one molar ratio of labeled product compared to starting material. In some cases there may be limiting amounts of the mRNA being analyzed and for these cases, some amplification of the nucleic acid sequences in the sample may be desirable. This has led to the use of the third approach, where the cDNA copy derived from the original mRNA template is in itself used as a template for further synthesis.
  • TAS Transcription Amplification System
  • a target specific oligonucleotide is used to generate a cDNA copy and a second target specific oligonucleotide is used to convert the single stranded DNA into double-stranded form.
  • a T7 promoter sequence is included in the first oligonucleotide, the double-stranded molecule can be used to make multiple transcription products that are complementary to the original mRNA of interest.
  • the purpose of this system was for amplification of a discrete sequence from a pool of various RNA species. No suggestion or appreciation of such a system for the use of non-discrete primer sequences for general amplification was described in this work.
  • RNA transcript copies homologous to the original RNA population has been disclosed by van Gelder et al. in U.S. Pat. No. 5,891,636 where specific reference is given to the utility of such a system for creating a library of various gene products in addition to discrete sequences. Since each individual mRNA molecule has the potential for ultimately being the source of a large number of complementary transcripts, this system enjoys the advantages of linear amplification such that smaller amounts of starting material are necessary compared to direct labeling of the original mRNA or its cDNA copy.
  • the first method has a limitation that RNase H has to be added after the completion of the cDNA synthesis reaction and a balance of RNase H activity has to be determined to provide sufficient nicking without total degradation of potential RNA primers.
  • the second method requires an extra step of incubation a different polymerase besides the Reverse Transcriptase and also S1 nuclease has to be added to eliminate the loop in the hairpin structure.
  • the formation and extension by foldback is a poorly understood system that does not operate at high efficiency where sequences and amounts of cDNA copies may act as random factors.
  • PCR has been included in some protocols to carry out synthesis of a library through the use of common primer binding sites at each end of individual sequences (Endege et al., 1999 Biotechniques 26; 542-550, Ying et al., 1999 Biotechniques 27; 410-414). These methods share the necessity for a machine dedicated to thermal cycling.
  • the nucleic acids on an array can use the analytes as templates for primer extension reactions.
  • SNP's Single Nucleotide Polymorphisms
  • determination of Single Nucleotide Polymorphisms, (SNP's) has been carried out by the use of a set of primers at different sites on the array that exhibit sequence variations from each other (Pastinen et al., 2000, Genome Research 10; 1031-1042).
  • SNP's Single Nucleotide Polymorphisms
  • the ability or inability of a template to be used for primer extension by each set of primers is an indication of the particular sequence variations within the analytes.
  • More complex series of reactions have also been carried out by the use of arrays as platforms for localized amplification as described in U.S. Pat. No.
  • PCR and SDA were carried out by providing a pair of unique primers for each individual nucleic acid target at each locus of the array.
  • the presence or absence of amplification at each locus of the array served as an indicator of the presence or absence of the corresponding target sequences in the analyte samples.
  • Protein arrays have also been used for high throughput ELISA assays (Mendoza et al., (1999) Biotechniques 27; 778-788) and for the detection of individual proteins in complex solutions (Haab, et al.; (2001) Genome Biology 2; 1-13).
  • DNA is extremely robust and can be immobilized on a solid matrix, dried and rehydrated without any loss of activity or function. Proteins, however, are far more difficult to utilize in array formats.
  • One of the main problems of using proteins in an array format is the difficulty of applying the protein to a solid matrix in a form that would allow the protein to be accessible and reactive without denaturing or otherwise altering the peptide or protein. Also, many proteins cannot be dehydrated and must be kept in solution at all times, creating further difficulties for use in arrays.
  • Some methods which have been used to prepare protein arrays include placing the proteins on a polyacrylamide gel matrix on a glass slide that has been activated by treatment with glutaraldehyde or other reagents (Arenkov, op. cit.). Another method has been the addition of proteins to aldehyde coated glass slides, followed by blocking of the remaining aldehyde sites with BSA after the attachment of the desired protein. This method, however, could not be used for small proteins because the BSA obscured the protein. Peptides and small proteins have been placed on slides by coating the slides with BSA and then activating the BSA with N,N′-disuccinimidyl carbonate (Taton et al., (2000) Science 2789, 1760-1763).
  • Protein arrays have also been prepared on poly-L-Lysine coated glass slides (Haab et al., op. cit.) and agarose coated glass slides (Afanassiev et al., (2000) Nucleic Acids Research 28, e66). “Protein Chips” are also commercially available from Ciphergen (Fremont, Calif.) for a process where proteins are captured onto solid surfaces and analyzed by mass spectroscopy.
  • oligonucleotides as ‘hooks’ or ‘tags’ as identifiers for non-nucleic acid molecules has been described in the literature. For instance, a library of peptides has been made where each peptide is attached to a discrete nucleic acid portion and members of the library are tested for their ability to bind to a particular analyte. After isolation of the peptides that have binding affinities, identification was carried out by PCR to “decode” the peptide sequence (Brenner. and Lerner, (1992) Proc. Nat. Acad. Sci. USA 89; 5381-5383, Needels et al., (1993) Proc. Nat. Acad. Sci.
  • Nuceleic acid sequences have also been used as tags in arrays where selected oligonucleotide sequences were added to primers used for single nucleotide polymorphism genotyping (Hirschhorn, et al., (2000) Proc. Natl. Acad. Sc. USA, 97; 12164-12169). However, in this case the ‘tag’ is actually part of the primer design and it is used specifically for SNP detection using a single base extension assay.
  • a patent application filed by Lohse, et al., (WO 00/32823) has disclosed the use of DNA-protein fusions for protein arrays.
  • the protein is synthesized from RNA transcripts which are then reverse transcribed to give the DNA sequences attached to the corresponding protein.
  • This system lacks flexibility since the technology specifically relates only to chimeric molecules that comprise a nucleic acid and a peptide or protein.
  • the protein is directly derived from the RNA sequence so that the resultant DNA sequence is also dictated by the protein sequence.
  • every protein that is to be used in an array requires the use of an in vitro translation system made from cell extracts, a costly and inefficient system for large scale synthesis of multiple probes.
  • This invention provides a composition of matter that comprises a library of analytes, the analytes being hybridized to an array of nucleic acids, the nucleic acids being fixed or immobilized to a solid support, wherein the analytes comprise an inherent universal detection target (UDT), and a universal detection element (UDE) attached to the UDT, wherein the UDE generates a signal indicating the presence or quantity of the analytes, or the attachment of UDE to UDT.
  • UDT inherent universal detection target
  • UDE universal detection element
  • This invention also provides a composition of matter that comprises a library of analytes, such analytes being hybridized to an array of nucleic acids, and such nucleic acids being fixed or immobilized to a solid support, wherein the analytes comprise a non-inherent universal detection target (UDT) and a universal detection element (UDE) hybridized to the UDT, and wherein the UDE generates a signal directly or indirectly to detect the presence or quantity of such analytes.
  • UDT non-inherent universal detection target
  • UDE universal detection element
  • the present invention further provides a composition of matter that comprises a library of analytes, such analytes being hybridized to an array of nucleic acids, and such nucleic acids being fixed or immobilized to a solid support, wherein the hybridization between the analytes and the nucleic acids generate a domain for complex formation, and the composition further comprises a signaling entity complexed to the domain.
  • the present invention yet further provides a process for detecting or quantifying more than one nucleic acid of interest in a library comprising the steps of: a) providing: (i) an array of fixed or immobilized nucleic acids complementary to the nucleic acids of interest; (ii) a library of nucleic acid analytes which may contain the nucleic acids of interest sought to be detected or quantified, wherein each of the nucleic acids of interest comprise at least one inherent universal detection target (UDT); and (iii) universal detection elements (UDE) which generates a signal directly or indirectly; b) hybridizing the library (ii) with the array of nucleic acids (i) to form hybrids if the nucleic acids of interest are present; c) contacting the UDEs with the UDTs to form a complex bound to the array; d) detecting or quantifying the more than one nucleic acid of interest by detecting or measuring the amount of signal generated from UDEs bound to the array.
  • Also provided by this invention is a process for detecting or quantifying more than one nucleic acid of interest in a library comprising the steps of a) providing: (i) an array of fixed or immobilized nucleic acids complementary to the nucleic acids of interest; (ii) a library of nucleic acid analytes which may contain the nucleic acids of interest sought to be detected or quantified, wherein each of the nucleic acids of interest comprise at least one inherent universal detection target (UDT); and (iii) universal detection elements (UDE) which generates a signal directly or indirectly; b) contacting the UDEs with the UDTs in the library of nucleic acid analytes to form one or more complexes; c) hybridizing the library of nucleic acid analytes with the array of nucleic acids (i) to form hybrids if such nucleic acids of interest are present; d) detecting or quantifying the more than one nucleic acid of interest by detecting or measuring the amount of signal generated from UDT
  • Also provided herein is a process for detecting or quantifying more than one nucleic acid of interest in a library comprising the steps of a) providing (i) an array of fixed or immobilized nucleic acids complementary to the nucleic acids of interest; (ii) a library of nucleic acid analytes which may contain the nucleic acids of interest sought to be detected or quantified, wherein each of the nucleic acids of interest comprise at least one non-inherent universal detection target (UDT), wherein the non-inherent UDT is attached to the nucleic acid analytes; and (iii) universal detection elements (UDE) which generate a signal directly or indirectly; b) hybridizing the library (ii) with the array of nucleic acids (i) to form hybrids if the nucleic acids of interest are present; c) contacting the UDEs with the UDTs to form a complex bound to the array; d) detecting or quantifying the more than one nucleic acid of interest by detecting or
  • Another aspect provided by this invention is a process for detecting or quantifying more than one nucleic acid of interest in a library comprising the steps of a) providing (i) an array of fixed or immobilized nucleic acids complementary to the nucleic acids of interest; (ii) a library of nucleic acid analytes which may contain the nucleic acids of interest sought to be detected or quantified, wherein each of such nucleic acids of interest comprise at least one non-inherent universal detection target (UDT), wherein the non-inherent UDTs are attached to the nucleic acid analytes; and (iii) universal detection elements (UDE) which generate a signal directly or indirectly; b) contacting the UDEs with the UDTs in the library of nucleic acid analytes to form one or more complexes; c) hybridizing the library (ii) with the array of nucleic acids (i) to form hybrids if such nucleic acids of interest are present; d) detecting or quantifying
  • Another aspect provided by this invention is a process for detecting or quantifying more than one nucleic acid of interest in a library comprising the steps of a) providing (i) an array of fixed or immobilized nucleic acids complementary to the nucleic acids of interest; (ii) a library of nucleic acid analytes which may contain the nucleic acids of interest sought to be detected or quantified; (iii) means for attaching one or more universal detection targets (UDT) to a nucleic acid; (iv) universal detection elements (UDE) which generates a signal directly or indirectly; b) attaching such UDTs (iii) to the library of nucleic acid analytes (ii); c) hybridizing the library (ii) with the array of nucleic acids (i) to form hybrids if such nucleic acids of interest are present; d) contacting the UDEs with the UDTs to form a complex bound to the array; e) detecting or quantifying the more than one nucle
  • Still another feature is process for detecting or quantifying more than one nucleic acid of interest in a library comprising the steps of a) providing (i) an array of fixed or immobilized nucleic acids complementary to the nucleic acids of interest; (ii) a library of nucleic acid analytes which may contain the nucleic acids of interest sought to be detected or quantified; (iii) means for attaching one or more universal detection targets (UDT) to a nucleic acid; (iv) universal detection elements (UDE) which generate a signal directly or indirectly; b) attaching the UDTs (iii) to the library of nucleic acid analytes (ii); c) contacting the UDEs with the UDTs in the library of nucleic acid analytes to form one or more complexes; d) hybridizing the library (ii) with the array of nucleic acids (i) to form hybrids if such nucleic acids of interest are present; e) detecting or quantifying the
  • the present invention provides additionally a process for detecting or quantifying more than one nucleic acid of interest in a library comprising the steps of a) providing (i) an array of fixed or immobilized nucleic acids complementary to the nucleic acids of interest; (ii) a library of nucleic acid analytes which may contain the nucleic acids of interest sought to be detected or quantified; and (iii) universal detection elements (UDEs) which bind to a domain formed by nucleic acid hybrids for complex formation and generate a signal directly or indirectly; b) hybridizing the library (ii) with the array of nucleic acids (i) to form hybrids if such nucleic acids of interest are present, wherein any formed hybrids generate a domain for complex formation; c) contacting the UDEs with any hybrids to form a complex bound to the array; d) detecting or quantifying the more than one nucleic acid of interest by detecting or measuring the amount of signal generated from UDEs bound to the array.
  • UDEs universal
  • composition of matter comprising a library of first nucleic acid analyte copies, such first nucleic acid copies being hybridized to an array of nucleic acids, those nucleic acids being fixed or immobilized to a solid support, wherein such first nucleic acid copies comprise an inherent universal detection target (UDT) and a universal detection element (UDE) attached to the UDT, wherein the UDE generates a signal directly or indirectly to detect the presence or quantity of any analytes.
  • UDT inherent universal detection target
  • UDE universal detection element
  • Another embodiment of this invention is a composition of matter comprising a library of first nucleic acid analyte copies, such first nucleic acid copies being hybridized to an array of nucleic acids, the nucleic acids being fixed or immobilized to a solid support, wherein such first nucleic acid copies comprise one or more non-inherent universal detection targets (UDTs) and one or more universal detection elements (UDEs) attached to the UDTs, wherein the UDEs generate a signal directly or indirectly to detect the presence or quantity of any analytes, and wherein the UDTs are either: (i) at the 5′ ends of the first nucleic acid copies and not adjacent to an oligot segment or sequence, or (ii) at the 3′ ends of the first nucleic acid copies, or (iii) both (i) and (ii).
  • UDTs non-inherent universal detection targets
  • UEs universal detection elements
  • This invention also concerns a process for detecting or quantifying more than one nucleic acid of interest in a library comprising the steps of a) providing (i) an array of fixed or immobilized nucleic acids identical in part or whole to the nucleic acids of interest; (ii) a library of nucleic acid analytes which may contain the nucleic acids of interest sought to be detected or quantified, wherein each of such nucleic acids of interest comprise at least one inherent universal detection target (UDT); (iii) universal detection elements (UDE) which generate a signal directly or indirectly; and (iv) polymerizing means for synthesizing nucleic acid copies of the nucleic acids of analytes; b) synthesizing one or more first nucleic acid copies which are complementary to all or part of the nucleic acid analytes and synthesizing sequences which are complementary to all or part of the UDT to form a complementary UDT; c) hybridizing such first nucleic acid copies with the array of nucleic acid
  • Another embodiment provided by this invention is a process for detecting or quantifying more than one nucleic acid of interest in a library comprising the steps of a) providing (i) an array of fixed or immobilized nucleic acids identical in part or whole to the nucleic acids of interest; (ii) a library of nucleic acid analytes which may contain the nucleic acids of interest sought to be detected or quantified, wherein each of such nucleic acids of interest comprise at least one inherent universal detection target (UDT); (iii) universal detection elements (UDE) which generate a signal directly or indirectly; and (iv) polymerizing means for synthesizing nucleic acid copies of such nucleic acid analytes; b) synthesizing one or more first nucleic acid copies of such nucleic acid analytes; c) contacting the UDEs with the UDTs in the first nucleic acid copies to form one or more complexes; d) hybridizing such first nucleic acid copies with the array of nucle
  • An additional aspect of the present invention is a process for detecting or quantifying more than one nucleic acid of interest in a library comprising the steps of a) providing (i) an array of fixed or immobilized nucleic acids identical in part or whole to the nucleic acids of interest; (ii) a library of nucleic acid analytes which may contain the nucleic acids of interest sought to be detected or quantified; (iii) means for attaching one or more non-inherent universal detection targets (UDT) to a nucleic acid; (iv) universal detection elements (UDE) which generate a signal directly or indirectly; and (v) polymerizing means for synthesizing nucleic acid copies of the nucleic acid analytes; b) attaching the non-inherent UDTs to either the 3′ ends of the nucleic acid analytes, the 5′ ends of the first nucleic acid analytes, or both the 3′ ends and the 5′ ends of the nucleic acid analytes
  • Also provided herein is a process for detecting or quantifying more than one nucleic acid of interest in a library comprising the steps of a) providing (i) an array of fixed or immobilized nucleic acids identical in part or whole to the nucleic acids of interest; (ii) a library of nucleic acid analytes which may contain the nucleic acids of interest sought to be detected or quantified; (iii) means for attaching one or more non-inherent universal detection targets (UDT) to a nucleic acid; (iv) universal detection elements (UDE) which generate a signal directly or indirectly; and (v) polymerizing means for synthesizing nucleic acid copies of the nucleic acid analytes; b) attaching such non-inherent UDTs to either the 3′ ends of the nucleic acid analytes, the 5′ ends of the first nucleic acid analytes, or both the 3′ ends and the 5′ ends of the nucleic acid analytes; c
  • Another embodiment provided herein is a process for detecting or quantifying more than one nucleic acid of interest in a library comprising the steps of a) providing (i) an array of fixed or immobilized nucleic acids identical in part or whole to such nucleic acids of interest; (ii) a library of nucleic acid analytes which may contain the nucleic acids of interest sought to be detected or quantified; (iii) means for attaching one or more non-inherent universal detection targets (UDT) to a nucleic acid; (iv) universal detection elements (UDE) which generate a signal directly or indirectly; and (v) polymerizing means for synthesizing nucleic acid copies of the nucleic acid analytes; b) synthesizing one or more first nucleic acid copies of the nucleic acid analytes; c) attaching the non-inherent UDTs to either the 3′ ends of the first nucleic acid copies, the 5′ ends of the first nucleic acid copies, or
  • Another process provided by this invention is for detecting or quantifying more than one nucleic acid of interest in a library comprising the steps of a) providing (i) an array of fixed or immobilized nucleic acids identical in part or whole to the nucleic acids of interest; (ii) a library of nucleic acid analytes which may contain the nucleic acids of interest sought to be detected or quantified; (iii) means for attaching one or more non-inherent universal detection targets (UDT) to a nucleic acid; (iv) universal detection elements (UDE) which generate a signal directly or indirectly; and (v) polymerizing means for synthesizing nucleic acid copies of the nucleic acid analytes; b) synthesizing one or more first nucleic acid copies of the nucleic acid analytes; c) attaching the non-inherent UDTs to either the 3′ ends of the first nucleic acid copies, the 5′ ends of the first nucleic acid copies, or both the
  • a process for detecting or quantifying more than one nucleic acid of interest in a library comprising the steps of a) providing (i) an array of fixed or immobilized nucleic acids complementary to the nucleic acids of interest; (ii) a library of nucleic acid analytes which may contain the nucleic acids of interest sought to be detected or quantified; (iii) universal detection elements (UDEs) which bind to a domain for complex formation formed by nucleic acid hybrids and generate a signal directly or indirectly; and (iv) polymerizing means for synthesizing nucleic acid copies of the nucleic acid analytes; b) synthesizing one or more nucleic acid copies of the nucleic acid analytes; c) hybridizing the first nucleic acid copies with the array of nucleic acids (i) to form hybrids if any nucleic acids of interest are present, wherein any formed hybrids generate a domain for complex formation; d) contacting the UDE
  • Another aspect provided by this invention is a composition of matter comprising a library of double-stranded nucleic acids substantially incapable of in vivo replication and free of non-inherent homopolymeric sequences, the nucleic acids comprising sequences complementary or identical in part or whole to inherent sequences of a library obtained from a sample, wherein the double-stranded nucleic acids comprise at least one inherent universal detection target (UDT) proximate to one end of the double strand and at least one non-inherent production center proximate to the other end of the double strand.
  • UDT inherent universal detection target
  • Yet another aspect of this invention concerns a composition of matter comprising a library of double-stranded nucleic acids substantially incapable of in vivo replication, such nucleic acids comprising sequences complementary or identical in part or whole to inherent sequences of a library obtained from a sample, wherein the double-stranded nucleic acids comprise at least four (4) non-inherent nucleotides proximate to one end of the double strand and a non-inherent production center proximate to the other end of the double strand.
  • composition of matter comprising a library of double-stranded nucleic acids fixed to a solid support, those nucleic acids comprising sequences complementary or identical in part or whole to inherent sequences of a library obtained from a sample and the nucleic acids further comprising at least one first sequence segment of non-inherent nucleotides proximate to one end of the double strand and at least one second sequence segment proximate to the other end of the double strand, the second sequence segment comprising at least one production center.
  • Another feature of this invention is a composition of matter comprising a library of double-stranded nucleic acids attached to a solid support, the nucleic acids comprising sequences complementary or identical in part or whole to inherent sequences of a library obtained from a sample, wherein the double-stranded nucleic acids comprise at least one inherent universal detection target (UDT) proximate to one end of the double strand and at least one non-inherent production center proximate to the other end of the double strand.
  • UDT inherent universal detection target
  • the invention herein also provides a process for detecting or quantifying more than one nucleic acid of interest in a library comprising the steps of a) providing (i) an array of fixed or immobilized nucleic acids identical or complementary in part or whole to sequences of the nucleic acids of interest; (ii) a library of nucleic acid analytes which may contain the nucleic acids of interest sought to be detected or quantified; and (iii) polymerizing means for synthesizing nucleic acid copies of the nucleic acid analytes, the polymerizing means comprising a first set of primers and a second set of primers, wherein the second set of primers comprises at least two segments, the first segment at the 3′ end comprising random sequences, and the second segment comprising at least one production center; (iv) means for synthesizing nucleic acid copies under isothermal or isostatic conditions; b) contacting the library of nucleic acid analytes with the first set of primers to form more than
  • Also provided by this invention is a process for detecting or quantifying more than one nucleic acid of interest in a library comprising the steps of a) providing (i) an array of fixed or immobilized nucleic acids identical or complementary in part or whole to sequences of the nucleic acids of interest; (ii) a library of nucleic acid analytes which may contain the nucleic acids of interest sought to be detected or quantified; (iii) polymerizing means for synthesizing nucleic acid copies of the nucleic acid analytes, such polymerizing means comprising a first set of primers and a second set of primers, wherein the first set of primers comprise at least one production center; and (iv) means for synthesizing nucleic acid copies under isothermal or isostatic conditions; b) contacting the library of nucleic acid analytes with the first set of primers to form more than one first bound entity; c) extending the bound first set of primers by means of template sequences provided by
  • Another feature of this invention is a process for detecting or quantifying more than one nucleic acid of interest in a library comprising the steps of a) providing (i) an array of fixed or immobilized nucleic acids identical or complementary in part or whole to sequences of the nucleic acids of interest; (ii) a library of nucleic acid analytes which may contain the nucleic acids of interest sought to be detected or quantified; (iii) polymerizing means for synthesizing nucleic acid copies of the nucleic acid analytes, such polymerizing means comprising a first set of primers and a second set of primers, wherein the first set comprises at least one production center; (iv) a set of oligonucleotides or polynucleotides complementary to at least one segment or sequence of the second set of primers; and(v) means for ligating the set of oligonucleotides or polynucleotides (iv); b) contacting the library of nucleic acid
  • this invention provides a process for detecting or quantifying more than one nucleic acid of interest in a library comprising the steps of a) providing (i) an array of fixed or immobilized nucleic acids identical or complementary in part or whole to sequences of the nucleic acids of interest; (ii) a library of nucleic acid analytes which may contain the nucleic acids of interest sought to be detected or quantified; (iii) polymerizing means for synthesizing nucleic acid copies of the nucleic acid analytes, such polymerizing means comprising a first set of primers and a second set of primers, wherein the second set comprises at least one production center; (iv) a set of oligonucleotides or polynucleotides complementary to at least one segment or sequence of the second set of primers; and (v) means for ligating the set of oligonucleotides or polynucleotides (iv); b) contacting the library of nucleic acid analy
  • Still yet further provided by this invention is a process for detecting or quantifying more than one nucleic acid of interest in a library comprising the steps of a) providing (i) an array of fixed or immobilized nucleic acids identical or complementary in part or whole to sequences of the nucleic acids of interest; (ii) a library of nucleic acid analytes which may contain the nucleic acids of interest sought to be detected or quantified; and (iii) polymerizing means for synthesizing nucleic acid copies of the nucleic acid analytes, such polymerizing means comprising a first set of primers, a second set of primers and a third set of primers wherein the third set comprises at least one production center; and b) contacting the library of nucleic acid analytes with the first set of primers to form a first set of bound primers; c) extending the first set of bound primers by means of template sequences provided by the nucleic acid analytes to form first copies of the an
  • Also uniquely provided in this invention is a process for detecting or quantifying more than one nucleic acid of interest in a library comprising the steps of a) providing (i) an array of fixed or immobilized nucleic acids identical or complementary in part or whole to sequences of the nucleic acids of interest; (ii) a library of nucleic acid analytes which may contain the nucleic acids of interest sought to be detected or quantified; and (iii) polymerizing means for synthesizing nucleic acid copies of the nucleic acid analytes, such polymerizing means comprising a first set of primers and a second set of primers, wherein the first set of primers are fixed or immobilized to a solid support, and wherein the second set of primers comprises at least two segments, the first segment at the 3′ end comprising random sequences, and the second segment comprising at least one production center; (iv) means for synthesizing nucleic acid copies under isothermal or isostatic conditions; b) contacting
  • Another significant aspect of this invention is a process for detecting or quantifying more than one nucleic acid of interest in a library comprising the steps of a) providing (i) an array of fixed or immobilized nucleic acids identical or complementary in part or whole to sequences of the nucleic acids of interest; (ii) a library of nucleic acid analytes which may contain the nucleic acids of interest sought to be detected or quantified; (iii) polymerizing means for synthesizing nucleic acid copies of the nucleic acid analytes, such polymerizing means comprising a first set of primers and a second set of primers, wherein the first set of primers are fixed or immobilized to a solid support, and wherein the first set of primers comprise at least one production center; and (iv) means for synthesizing nucleic acid copies under isothermal or isostatic conditions; b) contacting the library of nucleic acid analytes with the first set of primers to form more than one first bound
  • Also provided in accordance with the present invention is a process for detecting or quantifying more than one nucleic acid of interest in a library comprising the steps of a) providing (i) an array of fixed or immobilized nucleic acids identical or complementary in part or whole to sequences of the nucleic acids of interest; (ii) a library of nucleic acid analytes which may contain the nucleic acids of interest sought to be detected or quantified; (iii) polymerizing means for synthesizing nucleic acid copies of the nucleic acid analytes, such polymerizing means comprising a first set of primers and a second set of primers, wherein the first set of primers are fixed or immobilized to a solid support, and wherein the first set comprises at least one production center; (iv) a set of oligonucleotides or polynucleotides complementary to at least one segment or sequence of the second set of primers; and (v) means for ligating the set of oligonu
  • Another feature of the present invention concerns a process for detecting or quantifying more than one nucleic acid of interest in a library comprising the steps of a) providing (i) an array of fixed or immobilized nucleic acids identical or complementary in part or whole to sequences of the nucleic acids of interest; (ii) a library of nucleic acid analytes which may contain the nucleic acids of interest sought to be detected or quantified; (iii) polymerizing means for synthesizing nucleic acid copies of the nucleic acid analytes, such polymerizing means comprising a first set of primers and a second set of primers, wherein the first set of primers are fixed or immobilized to a solid support, and wherein the second set i;:;; comprises at least one production center; (iv) a set of oligonucleotides or polynucleotides complementary to at least one segment or sequence of the second set of primers; and (v) means for ligating the set of a library of
  • Yet another process is provided by this invention, the process being one for detecting or quantifying more than one nucleic acid of interest in a library and comprising the steps of a) providing (i) an array of fixed or immobilized nucleic acids identical or complementary in part or whole to sequences of the nucleic acids of interest; (ii) a library of nucleic acid analytes which may contain the nucleic acids of interest sought to be detected or quantified; and (iii) polymerizing means for synthesizing nucleic acid copies of the nucleic acid analytes, such polymerizing means comprising a first set of primers, a second set of primers and a third set of primers, wherein the first set of primers are fixed or immobilized to a solid support, and wherein the third set comprises at least one production center; and b) contacting the library of nucleic acid analytes with the first set of primers to form more than one first bound entity; c) extending the bound first set of primers by
  • Another significant embodiment provided herein is a process for detecting or quantifying more than one nucleic acid of interest in a library comprising the steps of a) providing (i) an array of fixed or immobilized nucleic acids identical in part or whole to sequences of the nucleic acids of interest; (ii) a library of nucleic acid analytes which may contain the nucleic acids of interest sought to be detected or quantified; and (iii) polymerizing means for synthesizing nucleic acid copies of the nucleic acid analytes, such polymerizing means comprising a first set of primers; b) contacting the nucleic acid analytes with the first set of primers to form a first bound entity; c) extending the bound set of first set of primers by means of template sequences provided by the nucleic acid analytes to form first nucleic acid copies of the analytes; d) separating the first nucleic acid copies from the analytes; e) repeating steps
  • the invention described herein also provides a process for detecting or quantifying more than one nucleic acid of interest in a library comprising the steps of a) providing (i) an array of fixed or immobilized nucleic acids identical in part or whole to sequences of the nucleic acids of interest; (ii) a library of nucleic acid analytes which may contain the nucleic acids of interest sought to be detected or quantified; (iii) polymerizing means for synthesizing nucleic acid copies of the nucleic acid analytes, such polymerizing means comprising a first set of primers and a second set of primers; (iv) means for addition of sequences to the 3′ end of nucleic acids; b) contacting the nucleic acid analytes with the first set of primer to form a first bound entity; c) extending the bound set of first set of primers by means of template sequences provided by the nucleic acid analytes to form first nucleic acid copies of the analytes
  • compositions provided by the present invention is a composition of matter that comprises an array of solid surfaces comprising discrete areas, wherein at least two of the discrete areas each comprises a first set of nucleic acid primers; and a second set of nucleic acid primers; wherein the nucleotide sequences in the first set of nucleic acid primers are different from the nucleotide sequences in the second set of nucleic acid primers; wherein the nucleotide sequences of a first set of nucleic acid primers of a first discrete area and the nucleotide sequences of a first set of nucleic acid primers of a second -discrete area differ from each other by at least one base; and wherein the nucleotide sequences of the second set of nucleic acid primers of a first discrete area and the nucleotide sequences of the second set of nucleic acid primers of a second discrete area are substantially the same or identical.
  • a related composition of this invention concerns a composition of matter that comprises an array of solid surfaces comprising a plurality of discrete areas; wherein at least two of the discrete areas each comprises a first set of nucleic acid primers; and a second set of nucleic acid primers; wherein the nucleotide sequences in the first set of nucleic acid primers are different from the nucleotide sequences in the second set of nucleic acid primers; wherein the nucleotide sequences of a first set of nucleic acid primers of a first discrete area and the nucleotide sequences of a first set of nucleic acid primers of a second discrete area differ substantially from each other; and wherein the nucleotide sequences of the second set of nucleic acid primers of a first discrete area and the nucleotide sequences of the second set of nucleic acid primers of a second discrete area are substantially the same or identical.
  • compositions for producing two or more copies of nucleic acids of interest in a library comprising the steps of a) providing (i) an array of solid surfaces comprising a plurality of discrete areas; wherein at least two of the discrete areas each comprises: (1) a first set of nucleic acid primers; and (2) a second set of nucleic acid primers; wherein the nucleotide sequences in the first set of nucleic acid primers are different from the nucleotide sequences in the second set of nucleic acid primers; wherein the nucleotide sequences of a first set of nucleic acid primers of a first discrete area and the nucleotide sequences of a first set of nucleic acid primers of a second discrete area differ from each other by at least one base; and wherein the nucleotide sequences of the second set of nucleic acid primers of a first discrete area and the nucleotide sequences of the second set
  • Another related process of the present invention is useful for detecting or quantifying more than one nucleic acid of interest in a library comprising the steps of a) providing (i) an array of solid surfaces comprising a plurality of discrete areas; wherein at least two of such discrete areas each comprises: (1) a first set of nucleic acid primers; and (2) a second set of nucleic acid primers; wherein the nucleotide sequences in the first set of nucleic acid primers are different from the nucleotide sequences in the second set of nucleic acid primers; wherein the nucleotide sequences of a first set of nucleic acid primers of a first discrete area and the nucleotide sequences of a first set of nucleic acid primers of a second discrete area differ from each other by at least one base; and wherein the nucleotide sequences of the second set of nucleic acid primers of a first discrete area and the nucleotide sequences of the second set of nu
  • composition of matter that comprises an array of solid surfaces comprising a plurality of discrete areas, wherein at least two of such discrete areas comprise: a chimeric composition comprising a nucleic acid portion; and a non-nucleic acid portion, wherein the nucleic acid portion of a first discrete area has the same sequence as the nucleic acid portion of a second discrete area, and wherein the non-nucleic acid portion has a binding affinity for analytes of interest.
  • composition of matter that comprises an array of solid surfaces comprising a plurality of discrete areas; wherein at least two of the discrete areas comprise a chimeric composition hybridized to complementary sequences of nucleic acids fixed or immobilized to the discrete areas, wherein the chimeric composition comprises a nucleic acid portion, and a non-nucleic acid portion, the nucleic acid portion comprising at least one sequence, wherein the non-nucleic acid portion has a binding affinity for analytes of interest, and wherein when the non-nucleic acid portion is a peptide or protein, the nucleic acid portion does not comprises sequences which are either identical or complementary to sequences that code for such peptide or protein.
  • Also provided as a significant aspect of the present invention is a process for detecting or quantifying analytes of interest, the process comprising the steps of 1) providing a) an array of solid surfaces comprising a plurality of discrete areas, wherein at least two of such discrete areas comprise a chimeric composition comprising a nucleic acid portion, and a non-nucleic acid portion; wherein the nucleic acid portion of a first discrete area has the same sequence as the nucleic acid portion of a second discrete area; and wherein the non-nucleic acid portion has a binding affinity for analytes of interest; b) a sample containing or suspected of containing one or more of the analytes of interest; and c) signal generating means; 2) contacting the array a) with the sample b) under conditions permissive of binding the analytes to the non-nucleic acid portion; 3) contacting the bound analytes with the signal generating means; and 4) detecting or quantifying the
  • Another feature provided by the present invention is a process for detecting or quantifying analytes of interest, this process comprising the steps of 1) providing a) an array of solid surfaces comprising a plurality of discrete areas; wherein at least two of such discrete areas comprise a chimeric composition comprising a nucleic acid portion; and a non-nucleic acid portion; wherein the nucleic acid portion of a first discrete area has the same sequence as the nucleic acid portion of a second discrete area; and wherein the non-nucleic acid portion has a binding affinity for analytes of interest; b) a sample containing or suspected of containing one or more of the analytes of interest; and c) signal generating means; 2) labeling the analytes of interest with the signal generating means; 3) contacting the array a) with the labeled analytes under conditions permissive of binding the labeled analytes to the non-nucleic acid portion; and 4) detecting or
  • Also provided by the present invention is a process for detecting or quantifying analytes of interest, the process comprising the steps of 1) providing a) an array of solid surfaces comprising a plurality of discrete areas; wherein at least two of such discrete areas comprise nucleic acids fixed or immobilized to such discrete areas, b) chimeric compositions comprising: i) a nucleic acid portion; and ii) a non-nucleic acid portion; the nucleic acid portion comprising at least one sequence, wherein the non-nucleic acid portion has a binding affinity for analytes of interest, and wherein when the non-nucleic acid portion is a peptide or protein, the nucleic acid portion does not comprise sequences which are either identical or complementary to sequences that code for the peptide or protein; c) a sample containing or suspected of containing the analytes of interest; and d) signal generating means; 2) contacting the array with the chimeric compositions to hybridize the nu
  • this invention provides a process for detecting or quantifying analytes of interest, the process comprising the steps of 1) providing a) an array of solid surfaces comprising a plurality of discrete areas; wherein at least two of the discrete areas comprise nucleic acids fixed or immobilized to the discrete areas, b) chimeric compositions comprising i) a nucleic acid portion; and ii) a non-nucleic acid portion, the nucleic acid portion comprising at least one sequence, wherein the non-nucleic acid portion has a binding affinity for analytes of interest, and wherein when the non-nucleic acid portion is a peptide or protein, the nucleic acid portion does not comprise sequences which are either identical or complementary to sequences that code for the peptide or protein; c) a sample containing or suspected of containing the analytes of interest; and d) signal generating means; 2) contacting the chimeric compositions with the sample b) under conditions permissive of
  • Another useful provision of the invention herein is a process for detecting or quantifying analytes of interest, such process comprising the steps of 1) providing a) an array of solid surfaces comprising a plurality of discrete areas; wherein at least two of the discrete areas comprise nucleic acids fixed or immobilized to the discrete areas, b) chimeric compositions comprising i) a nucleic acid portion; and ii) a non-nucleic acid portion; the nucleic acid portion comprising at least one sequence, wherein the non-nucleic acid portion has a binding affinity for analytes of interest, and wherein when the non-nucleic acid portion is a peptide or protein, the nucleic acid portion does not comprise sequences which are either identical or complementary to sequences that code for the peptide or protein; c) a sample containing or suspected of containing the analytes of interest; and d) signal generating means; 2) contacting the array with the chimeric compositions to hybridize the
  • a process for detecting or quantifying analytes of interest comprising the steps of 1) providing a) an array of solid surfaces comprising a plurality of discrete areas; wherein at least two of the discrete areas comprise nucleic acids fixed or immobilized to the discrete areas, b) chimeric compositions comprising: i) a nucleic acid portion; and ii) a non-nucleic acid portion; the nucleic acid portion comprising at least one sequence, wherein the non-nucleic acid portion has a binding affinity for analytes of interest, and wherein when the non-nucleic acid portion is a peptide or protein, such nucleic acid portion does not comprise sequences which are either identical or complementary to sequences that code for the peptide or protein; c) a sample containing or suspected of containing the analytes of interest; and d) signal generating means; 2) contacting the array with the chimeric compositions to hybridize the
  • FIG. 1 shows an array with mRNA from a library of analytes with UDTs.
  • FIG. 2 shows fragmentation of analytes followed by addition of non-inherent UDTs to analytes.
  • FIG. 3 depicts the incorporation of a non-inherent UDT to a 1st cNA copy by means of a primer.
  • FIG. 4 illustrates the use of Random Primers with Production Centers for 2 nd strand synthesis.
  • FIG. 5 relates to the same process as FIG. 4 wherein the Production Centers are double-stranded.
  • FIG. 6 illustrates 2nd cNA strand priming at terminal and internal sites.
  • FIG. 7 illustrates 2nd cNA strand priming after Terminal transferase addition of homopolymeric sequences.
  • FIG. 8 shows the addition of primer binding sites by ligation.
  • FIG. 9 illustrates multiple additions of primer binding sites.
  • FIG. 10 shows 1 st strand synthesis by extension of an oligo dT primer bound to a bead followed by 2nd cNA strand synthesis with random primers having production centers.
  • FIG. 11 illustrates 1st strand synthesis from poly T primer indirectly bound to a bead followed by 2nd strand synthesis with random primers having production center.
  • FIG. 12 shows the incorporation of a promoter during 3rd strand synthesis.
  • FIG. 13 illustrates the synthesis of an amplicon for isothermal amplification of a library of analytes.
  • FIG. 14 shows the synthesis of an amplicon for SDA amplification.
  • FIG. 15 shows the ligation of a primer binding site for isothermal amplification.
  • FIG. 16 shows the binding of an analyte to an array with SPEs and UPEs for solid phase amplification.
  • FIG. 17 shows the extension of an SPE on an array during solid phase amplification.
  • FIG. 18 shows the binding of an UPE to an extended SPE followed by extension of the UPE during solid phase amplification.
  • FIG. 19 shows solid phase amplification in which binding of extended SPEs and UPEs to unextended SPEs and UPEs occur.
  • FIG. 20 depicts an amplification array for comparative analysis.
  • FIG. 21 illustrates the use of an array with SPEs and UPEs for SNP analysis.
  • FIG. 22 relates to binding of analytes to SPEs on an array.
  • FIG. 23 shows the binding of primers to extended SPEs on an array.
  • FIG. 24 demonstrates the binding of primers and extended primers to SPEs on an array.
  • FIG. 25 shows the extension of primers and SPEs on an array in accordance with amplification disclosed in this invention.
  • FIG. 26 depicts the binding of nucleic acid portions of chimeric compositions to complementary sequences on an array
  • FIG. 27 is a gel analysis illustrating the dependency on Reverse Transcriptase for the amplification of a library in accordance with this invention and Example 3 below.
  • FIG. 28 is a gel analysis that demonstrates transcription after multiple rounds of 2nd strand synthesis as described further below in Example 4.
  • FIG. 29 is also a gel analysis that shows second round of RNA transcription from a library as described in Example 5 below.
  • FIG. 30 is a gel analysis also shows transcription from library made after poly dG tailing in accordance with the present invention and Example 6 below.
  • FIG. 31 is a gel analysis that shows RNA transcription after a series of reactions one of which was 2nd strand synthesis by thermostable DNA polymerases as described in Example 9 below.
  • FIG. 32 is a gel analysis that shows transcription from libraries made from sequential synthesis of 2nd strands as further described in Example 10 below.
  • FIG. 33 is also a gel analysis of amplification of a library of analytes using various reverse transcriptases for 1st stand synthesis.
  • the present invention discloses novel methods, compositions and kits that can be used in making and analyzing a library of nucleic acids.
  • the nucleic acids in the sample being tested can be used directly for signal generation or they can be used as templates to provide one or more nucleic acid copies that comprise sequences that are either identical or complementary to the original sequences.
  • An analyte is a biological polymer or ligand that is isolated or derived from biological sources such as organs, tissues or cells, or non-biological sources by synthetic or enzymatic means or processes.
  • biological polymers can include but are not limited to oligonucleotides, polynucleotides, oligopeptides, polypeptides, oligosaccharides, polysaccharides and lipids.
  • ligands can include but are not necessarily limited to non-peptide antigens, hormones, enzyme substrates, vitamins, drugs, and non-peptide signal molecules.
  • a library is a diverse collection of nucleic acids that comprises: a) analytes; b) nucleic acids derived from analytes that comprise sequences that are complementary to sequences in the analytes; c) nucleic acids derived from analytes that comprise sequences that are identical to sequences in the analytes; and d) any combination of the foregoing.
  • a label is any moiety that is capable of directly or indirectly generating a signal.
  • a production center is a segment of a nucleic acid or analogue thereof that is capable of producing more than one copy of a sequence that is identical or complementary to sequences that are operably linked to the production center.
  • UDTs Universal Detection Targets
  • the UDTs may be intrinsic or they may be artificially incorporated into nucleic acids.
  • Examples of inherent UDTs can comprise but not be limited to 3′ poly A segments, 5′ caps, secondary structures and consensus sequences.
  • Examples of inherent consensus sequences that might find use in the present invention can comprise but not be limited to signal sites for poly A addition, splicing elements and multicopy repeats such as Alu sequences.
  • UDTs may also be artificially incorporated into nucleic acids by an addition to the original analyte nucleic acid or during synthesis of nucleic acids that comprise sequences that are identical or complementary to the sequences of the original analytes. Artificially added UDTs may be labeled themselves or they may serve as binding partners.
  • UDEs Universal Detection Elements
  • first segment that is capable of acting as a binding partner for a UDT
  • second segment that is either labeled or otherwise capable of generating a detectable signal.
  • first and second segments can be overlapping or even comprise the same segments.
  • UDEs When UDEs are labeled, they may comprise a single signal moiety or they may comprise more than one signal entity. Segments of UDEs involved in binding to UDTs or signal generation may comprise but not be limited to polymeric substances such as nucleic acids, nucleic acid analogues, polypeptides, polysacharides or synthetic polymers.
  • the present invention discloses the use of UDTs and UDEs for the purpose of array analysis.
  • the present invention also discloses novel methods for incorporation of production centers into nucleic acid libraries that may be used in array analysis. These production centers may provide amplification of sequences that are identical or complementary to sequences in the original diverse nucleic acid analytes. The products derived from these production centers may be labeled themselves or UDTs may be incorporated for detection purposes.
  • Nucleic acids that may be of use in the present invention can comprise or be derived from DNA or RNA.
  • the original population of nucleic acids may comprise but not be limited to genomic DNA, unspliced RNA, mRNA, rRNA and snRNA.
  • This invention provides a composition of matter that comprises a library of analytes, the analytes being hybridized to an array of nucleic acids, the nucleic acids being fixed or immobilized to a solid support, wherein the analytes comprise an inherent universal detection target (UDT), and a universal detection element (UDE) attached to the UDT, wherein the UDE generates a signal indicating the presence or quantity of the analytes, or the attachment of UDE to UDT.
  • the library of analytes can be derived from a biological source selected from the group consisting of organs, tissues and cells, or they may be from non-natural sources as discussed in the definitions section above.
  • Biological analytes can be selected from the group consisting of genomic DNA, episomal DNA, unspliced RNA, mRNA, rRNA, snRNA and a combination of any of the foregoing.
  • the nucleic acid array can be selected from the group consisting of DNA, RNA and analogs thereof, an example of the latter being PNA. Such nucleic acids or analogs can be modified on any one of the sugar, phosphate or base moieties.
  • the solid support can take a number of different forms, including being porous or non-porous.
  • a porous solid support can be selected from the group consisting of polyacrylamide and agarose.
  • a non-porous solid support may comprise glass or plastic.
  • the solid support can also be transparent, translucent, opaque or reflective.
  • Nucleic acids can be directly or indirectly fixed or immobilized to the solid support. In terms of indirect attachment, the nucleic acids can be indirectly fixed or immobilized to the solid support by means of a chemical linker or linkage arm.
  • the inherent UDT can selected from the group consisting of 3′ polyA segments, 5′ caps, secondary structures, consensus sequences and a combination of any of the foregoing.
  • the consensus sequences can be selected from the group consisting of signal sequences for polyA addition, splicing elements, multicopy repeats and a combination of any of the foregoing.
  • the UDEs can be selected from the group consisting of nucleic acids, nucleic acid analogs, polypeptides, polysaccharides, synthetic polymers and a combination of any of the foregoing. As mentioned previously, such analogs can take the form of PNA.
  • the UDE generates a signal directly or indirectly.
  • Direct signal generation can take any number of forms and can be selected from the group consisting of a fluorescent compound, a phosphorescent compound, a chemiluminescent compound, a chelating compound, an electron dense compound, a magnetic compound, an intercalating compound, an energy transfer compound and a combination of any of the foregoing.
  • indirect signal generation can take a number of different forms and in this regard can be selected from the group consisting of an antibody, an antigen, a hapten, a receptor, a hormone, a ligand, an enzyme and a combination of any of the foregoing.
  • suitable enzymes which can be indirectly detected these would include enzymes which catalyze any reaction selected from the group consisting of a fluorogenic reaction, a chromogenic reaction and a chemiluminescent reaction.
  • This invention also provides a composition of matter that comprises a library of analytes, such analytes being hybridized to an array of nucleic acids, and such nucleic acids being fixed or immobilized to a solid support, wherein the analytes comprise a non-inherent universal detection target (UDT) and a universal detection element (UDE) hybridized to the UDT, and wherein the UDE generates a signal directly or indirectly to detect the presence or quantity of such analytes.
  • the nature of the analyte, the nucleic acid array, modifications, solid support are as described in the preceding paragraphs above.
  • the non-inherent universal detection targets (UDTs) can comprise homopolymeric sequences or heteropolymeric sequences.
  • the universal detection elements (UDEs) can be selected from the group consisting of nucleic acids, nucleic acid analogs and modified forms thereof. The UDEs generate a signal directly or indirectly, such direct and indirect signal generation also being discussed in the paragraphs just above.
  • the present invention further provides a composition of matter that comprises a library of analytes, such analytes being hybridized to an array of nucleic acids, and such nucleic acids being fixed or immobilized to a solid support, wherein the hybridization between the analytes and the nucleic acids generate a domain for complex formation, and the composition further comprises a signaling entity complexed to the domain.
  • the domain for complex formation can be selected from the group consisting of DNA-DNA hybrids, DNA-RNA hybrids, RNA-RNA hybrids, DNA-PNA hybrids and RNA-PNA hybrids.
  • the signaling entity that is complexed to the domain can be selected from the group consisting of proteins and intercalators.
  • proteins can comprise nucleic acid binding proteins which bind preferentially to double-stranded nucleic acid, the latter comprising antibodies, for example. These antibodies are specific for nucleic acid hybrids and are selected from the group consisting of DNA-DNA hybrids, DNA-RNA hybrids, RNA-RNA hybrids, DNA-PNA hybrids and RNA-PNA hybrids.
  • useful intercalators can be selected from the group consisting of ethidium bromide, diethidium bromide, acridine orange and SYBR Green.
  • the proteins When employed in accordance with the present invention, the proteins generate a signal directly or indirectly. Such forms and manner of direct and indirect signal generation are as described elsewhere in this disclosure, particularly in several paragraphs above.
  • the present invention thus provides a process for detecting or quantifying more than one nucleic acid of interest in a library comprising the steps of: a) providing: (i) an array of fixed or immobilized nucleic acids complementary to the nucleic acids of interest; (ii) a library of nucleic acid analytes which may contain the nucleic acids of interest sought to be detected or quantified, wherein each of the nucleic acids of interest comprise at least one inherent universal detection target (UDT); and (iii) universal detection elements (UDE) which generates a signal directly or indirectly; b) hybridizing the library (ii) with the array of nucleic acids (i) to form hybrids if the nucleic acids of interest are present; c) contacting the UDEs with the UDTs to form a complex bound to the array; d) detecting or quantifying the more than one nucleic acid of interest by detecting or measuring the amount of signal generated from UDEs bound
  • the nucleic acid array can be selected from the group consisting of DNA, RNA and analogs thereof, the latter comprising PNA. Modifications to these nucleic acids and analogs can be usefully carried out to any one of the sugar, phosphate or base moieties.
  • the solid support can be porous, e.g., polyacrylamide and agarose, or non-porous, e.g., glass or plastic.
  • the solid support can also be transparent, translucent, opaque or reflective.
  • Nucleic acids are directly or indirectly fixed or immobilized to the solid support. Indirect fixation or immobilization to the solid support can be carried out by means of a chemical linker or linkage arm.
  • the library of analytes can be derived from a biological source selected from the group consisting of organs, tissues and cells, or they may be from non-natural or more synthetic or man-made sources.
  • biological analytes are those selected from the group consisting of genomic DNA, episomal DNA, unspliced RNA, mRNA, rRNA, snRNA and a combination of any of the foregoing.
  • the inherent UDT used in the above process can be selected from the group consisting of 3′ polyA segments, 5′ caps, secondary structures, consensus sequences, and a combination of any of the foregoing.
  • consensus sequences can be selected from the group consisting of signal sequences for polyA addition, splicing elements, multicopy repeats, and a combination of any of the foregoing.
  • UDEs can be selected from the group consisting of nucleic acids, nucleic acid analogs, e.g., PNA, polypeptides, polysaccharides, synthetic polymers and a combination of any of the foregoing.
  • UDEs generate a signal directly or indirectly.
  • Direct signal generation can be various and may be selected from the group consisting of a fluorescent compound, a phosphorescent compound, a chemiluminescent compound, a chelating compound, an electron dense compound, a magnetic compound, an intercalating compound, an energy transfer compound and a combination of any of the foregoing.
  • Indirect signal generation can also be various and may be selected from the group members consisting of an antibody, an antigen, a hapten, a receptor, a hormone, a ligand, an enzyme and a combination of any of the foregoing.
  • an enzyme catalyzes a reaction selected from the group consisting of a fluorogenic reaction, a chromogenic reaction and a chemiluminescent reaction.
  • the above-described process can further comprise one or more washing steps.
  • This invention provides another such process for detecting or quantifying more than one nucleic acid of interest in a library comprising the steps of a) providing: (i) an array of fixed or immobilized nucleic acids complementary to the nucleic acids of interest; (ii) a library of nucleic acid analytes which may contain the nucleic acids of interest sought to be detected or quantified, wherein each of the nucleic acids of interest comprise at least one inherent universal detection target (UDT); and (iii) universal detection elements (UDE) which generates a signal directly or indirectly; b) contacting the UDEs with the UDTs in the library of nucleic acid analytes to form one or more complexes; c) hybridizing the library of nucleic acid analytes with the array of nucleic acids (i) to form hybrids if such nucleic acids of interest are present; d) detecting or quantifying the more than one nucleic acid of interest by detecting or measuring the amount of signal generated from UDEs bound
  • nucleic acid array modifications, solid support, direct/indirect fixation or immobilization, library of analytes, inherent UDT, UDE, direct/indirect signal generation, and the like, are as described elsewhere in this disclosure, including more particularly the last several paragraphs above. Furthermore, this process can comprise one or more conventional washing steps.
  • Another process for detecting or quantifying more than one nucleic acid of interest in a library comprises the steps of a) providing (i) an array of fixed or immobilized nucleic acids complementary to the nucleic acids of interest; (ii) a library of nucleic acid analytes which may contain the nucleic acids of interest sought to be detected or quantified, wherein each of the nucleic acids of interest comprise at least one non-inherent universal detection target (UDT), wherein the non-inherent UDT is attached to the nucleic acid analytes; and (iii) universal detection elements (UDE) which generate a signal directly or indirectly; b) hybridizing the library (ii) with the array of nucleic acids (i) to form hybrids if the nucleic acids of interest are present; c) contacting the UDEs with the UDTs to form a complex bound to the array; d) detecting or quantifying the more than one nucleic acid of interest by detecting or measuring the amount of signal generated from
  • nucleic acid array modifications to nucleic acid and nucleic acid analogs, the solid support, direct and indirectfixation/immobilization to the solid support, the library of analytes, direct and indirect signal generation, and the like, are as described elsewhere in this disclosure.
  • non-inherent universal detection targets UDTs
  • heteropolymeric sequences UDTs
  • universal detection elements UAEs
  • One or more washing steps can be included in this last process.
  • Another process for detecting or quantifying more than one nucleic acid of interest in a library comprises the steps of a) providing (i) an array of fixed or immobilized nucleic acids complementary to the nucleic acids of interest; (ii) a library of nucleic acid analytes which may contain the nucleic acids of interest sought to be detected or quantified, wherein each of such nucleic acids of interest comprise at least one non-inherent universal detection target (UDT), wherein the non-inherent UDTs are attached to the nucleic acid analytes; and (iii) universal detection elements (UDE) which generate a signal directly or indirectly; b) contacting the UDEs with the UDTs in the library of nucleic acid analytes to form one or more complexes; c) hybridizing the library (ii) with the array of nucleic acids (i) to form hybrids if such nucleic acids of interest are present; d) detecting or quantifying the more than one nucleic acid of
  • nucleic acid array modifications, solid support, direct/indirect fixation or immobilization to the solid support, the library of analytes, the non-inherent universal detection targets (UDTs), the universal detection elements (UDEs), direct/indirect signal generation, inclusion of washing steps, and the like, are found elsewhere in this disclosure and are equally applicable to this last described process.
  • Another process for detecting or quantifying more than one nucleic acid of interest in a library comprises the steps of a) providing (i) an array of fixed or immobilized nucleic acids complementary to the nucleic acids of interest; (ii) a library of nucleic acid analytes which may contain the nucleic acids of interest sought to be detected or quantified; (iii) means for attaching one or more universal detection targets (UDT) to a nucleic acid; (iv) universal detection elements (UDE) which generates a signal directly or indirectly; b) attaching such UDTs (iii) to the library of nucleic acid analytes (ii); c) hybridizing the library (ii) with the array of nucleic acids (i) to form hybrids if such nucleic acids of interest are present; d) contacting the UDEs with the UDTs to form a complex bound to the array; e) detecting or quantifying the more than one nucleic acid of interest by detecting or measuring
  • attaching means which add homopolymeric sequences through various enzymes, e.g., poly A polymerase and terminal transferase.
  • Other attaching means can be used for adding homopolymeric or heteropolymeric sequences, and these include enzymatic means and enzymes selected from DNA ligase and RNA ligase.
  • Still another process for detecting or quantifying more than one nucleic acid of interest in a library comprises the steps of a) providing (i) an array of fixed or immobilized nucleic acids complementary to the nucleic acids of interest; (ii) a library of nucleic acid analytes which may contain the nucleic acids of interest sought to be detected or quantified; (iii) means for attaching one or more universal detection targets (UDT) to a nucleic acid; (iv) universal detection elements (UDE) which generate a signal directly or indirectly; b) attaching the UDTs (iii) to the library of nucleic acid analytes (ii); c) contacting the UDEs with the UDTs in the library of nucleic acid analytes to form one or more complexes; d) hybridizing the library (ii) with the array of nucleic acids (i) to form hybrids if such nucleic acids of interest are present; e) detecting or quantifying the more than one
  • Another process for detecting or quantifying more than one nucleic acid of interest in a library comprises the steps of a) providing (i) an array of fixed or immobilized nucleic acids complementary to the nucleic acids of interest; (ii) a library of nucleic acid analytes which may contain the nucleic acids of interest sought to be detected or quantified; and (iii) universal detection elements (UDEs) which bind to a domain formed by nucleic acid hybrids for complex formation and generate a signal directly or indirectly; b) hybridizing the library (ii) with the array of nucleic acids (i) to form hybrids if such nucleic acids of interest are present, wherein any formed hybrids generate a domain for complex formation; c) contacting the UDEs with any hybrids to form a complex bound to the array; d) detecting or quantifying the more than one nucleic acid of interest by detecting or measuring the amount of signal generated from UDEs bound to the array.
  • UDEs universal detection elements
  • nucleic acid array nucleic acid array
  • nucleic acid analogs e.g., PNA, modifications (sugar, base and phosphate moieties), the solid support, fixation/immobilization, the library of analytes, the domain for complex formation, direct/indirect signal generation from signaling proteins, washing steps, and the like
  • PNA nucleic acid analogs
  • modifications sucrose, base and phosphate moieties
  • the solid support fixation/immobilization
  • the library of analytes the domain for complex formation
  • direct/indirect signal generation from signaling proteins, washing steps, and the like have already been given above and are equally applicable to this last mentioned process.
  • the signaling entity is complexed to the domain for complex formation, such signaling entity being selected from proteins and intercalators.
  • Such proteins can include nucleic acid binding proteins which bind preferentially to double-stranded nucleic acids, e.g., antibodies, particularly such antibodies which are specific for nucleic acid hybrids, e.g., DNA-DNA hybrids, DNA-RNA hybrids, RNA-RNA hybrids, DNA-PNA hybrids and RNA-PNA hybrids.
  • Intercalators have also been previously described in this disclosure and can be selected from ethidium bromide, diethidium bromide, acridine orange and SYBR Green.
  • compositions of matter are provided by this invention.
  • One such composition comprises a library of first nucleic acid analyte copies, such first nucleic acid copies being hybridized to an array of nucleic acids, those nucleic acids being fixed or immobilized to a solid support, wherein such first nucleic acid copies comprise an inherent universal detection target (UDT) and a universal detection element (UDE) attached to the UDT, wherein the UDE generates a signal directly or indirectly to detect the presence or quantity of any analytes.
  • UDT inherent universal detection target
  • UDE universal detection element
  • analytes e.g., biological sources
  • examples of such analytes e.g., genomic DNA, episomal DNA, unspliced RNA, mRNA, rRNA, snRNA and a combination of any of the foregoing
  • the nucleic acid array has been already described, including, for example, DNA, RNA and analogs thereof, e.g., PNA.
  • nucleic acids and analogs sucrose, phosphate, base
  • features of the solid support porous/non-porous, transparent, translucent, opaque, reflective
  • fixation/immobilization to the solid support the inherent UDT, the UDE, direct/indirect signal generation from UDEs have been described above and apply equally to this last composition.
  • composition of matter comprises a library of first nucleic acid analyte copies, such first nucleic acid copies being hybridized to an array of nucleic acids, the nucleic acids being fixed or immobilized to a solid support, wherein such first nucleic acid copies comprise one or more non-inherent universal detection targets (UDTs) and one or more universal detection elements (UDEs) attached to the UDTs, wherein the UDEs generate a signal directly or indirectly to detect the presence or quantity of any analytes, and wherein the UDTs are either: (i) at the 5′ ends of the first nucleic acid copies and not adjacent to an oligoT segment or sequence, or (ii) at the 3′ ends of the first nucleic acid copies, or (iii) both (i) and (ii).
  • UDTs non-inherent universal detection targets
  • UEs universal detection elements
  • UDTs e.g., heteropolymeric sequences
  • UDEs e.g., nucleic acids, nucleic acid analogs, polypeptides, polysaccharides, synthetic polymers, etc
  • Another process for detecting or quantifying more than one nucleic acid of interest in a library comprises the steps of a) providing (i) an array of fixed or immobilized nucleic acids identical in part or whole to the nucleic acids of interest; (ii) a library of nucleic acid analytes which may contain the nucleic acids of interest sought to be detected or quantified, wherein each of such nucleic acids of interest comprise at least one inherent universal detection target (UDT); (iii) universal detection elements (UDE) which generate a signal directly or indirectly; and (iv) polymerizing means for synthesizing nucleic acid copies of the nucleic acids of analytes; b) synthesizing one or more first nucleic acid copies which are complementary to all or part of the nucleic acid analytes and synthesizing sequences which are complementary to all or part of the UDT to form a complementary UDT; c) hybridizing such first nucleic acid copies with the array of nucleic acids (i) to form
  • nucleic acid array modifications, solid support, fixation/immobilization, the library of analytes, inherent UDTs, e.g., consensus sequences, UDEs, direct/indirect signal generation from UDEs, have been given above and are equally applicable to this last process.
  • polymerizing means which can be selected from E. coli DNA Pol I, Klenow fragment of E.
  • coli DNA Pol I Bst DNA polymerase, Bca DNA polymerase, Taq DNA polymerase, Tth DNA Polymerase, T4 DNA polymerase, ALV reverse transcriptase, MuLV reverse transcriptase, RSV reverse transcriptase, HIV-1 reverse transcriptase, HIV-2 reverse transcriptase, Sensiscript and Omniscript.
  • Another embodiment provided by this invention is a process for detecting or quantifying more than one nucleic acid of interest in a library comprising the steps of a) providing (i) an array of fixed or immobilized nucleic acids identical in part or whole to the nucleic acids of interest; (ii) a library of nucleic acid analytes which may contain the nucleic acids of interest sought to be detected or quantified, wherein each of such nucleic acids of interest comprise at least one inherent universal detection target (UDT); (iii) universal detection elements (UDE) which generate a signal directly or indirectly; and (iv) polymerizing means for synthesizing nucleic acid copies of such nucleic acid analytes; b) synthesizing one or more first nucleic acid copies of such nucleic acid analytes; c) contacting the UDEs with the UDTs in the first nucleic acid copies to form one or more complexes; d) hybridizing such first nucleic acid copies with the array of nucle
  • nucleic acid array nucleic acid modifications, the solid support, fixation/immobilization (direct and indirect), the library of analytes, inherent UDTs, UDEs, signal generation from UDEs (direct/indirect), polymerizing means, have been described above. Such descriptions are equally applicable to this last process.
  • Another process for detecting or quantifying more than one nucleic acid of interest in a library comprises the steps of a) providing (i) an array of fixed or immobilized nucleic acids identical in part or whole to the nucleic acids of interest; (ii) a library of nucleic acid analytes which may contain the nucleic acids of interest sought to be detected or quantified; (iii) means for attaching one or more non-inherent universal detection targets (UDT) to a nucleic acid; (iv) universal detection elements (UDE) which generate a signal directly or indirectly; and (v) polymerizing means for synthesizing nucleic acid copies of the nucleic acid analytes; b) attaching the non-inherent UDTs to either the 3′ ends of the nucleic acid analytes, the 5′ ends of the first nucleic acid analytes, or both the 3′ ends and the 5′ ends of the nucleic acid analytes; c) synthesizing one or
  • nucleic acid array modifications, the solid support, fixation/immobilization, the library of analytes, attaching means, UDEs, direct/indirect signal generation from UDEs, polymerizing means, and the like.
  • Yet another process for detecting or quantifying more than one nucleic acid of interest in a library comprises the steps of a) providing (i) an array of fixed or immobilized nucleic acids identical in part or whole to the nucleic acids of interest; (ii) a library of nucleic acid analytes which may contain the nucleic acids of interest sought to be detected or quantified; (iii) means for attaching one or more non-inherent universal detection targets (UDT) to a nucleic acid; (iv) universal detection elements (UDE) which generate a signal directly or indirectly; and (v) polymerizing means for synthesizing nucleic acid copies of the nucleic acid analytes; b) attaching such non-inherent UDTs to either the 3′ ends of the nucleic acid analytes, the 5′ ends of the first nucleic acid analytes, or both the 3′ ends and the 5′ ends of the nucleic acid analytes; c) synthesizing one
  • nucleic acid array modifications, the solid support, direct/indirect fixation/immobilization, the library of analytes, attachment means, UDEs, signal generation from UDEs, direct/indirect signal generation, polymerizing means, and the like, have already been described. Such descriptions are equally applicable to this last-described process.
  • Another process for detecting or quantifying more than one nucleic acid of interest in a library comprises the steps of a) providing (i) an array of fixed or immobilized nucleic acids identical in part or whole to such nucleic acids of interest; (ii) a library of nucleic acid analytes which may contain the nucleic acids of interest sought to be detected or quantified; (iii) means for attaching one or more non-inherent universal detection targets (UDT) to a nucleic acid; (iv) universal detection elements (UDE) which generate a signal directly or indirectly; and (v) polymerizing means for synthesizing nucleic acid copies of the nucleic acid analytes; b) synthesizing one or more first nucleic acid copies of the nucleic acid analytes; c) attaching the non-inherent UDTs to either the 3′ ends of the first nucleic acid copies, the 5′ ends of the first nucleic acid copies, or both the 3′ ends and the 5
  • Yet another process for detecting or quantifying more than one nucleic acid of interest in a library comprises the steps of a) providing (i) an array of fixed or immobilized nucleic acids complementary to the nucleic acids of interest; (ii) a library of nucleic acid analytes which may contain the nucleic acids of interest sought to be detected or quantified; (iii) universal detection elements (UDEs) which bind to a domain for complex formation formed by nucleic acid hybrids and generate a signal directly or indirectly; and (iv) polymerizing means for synthesizing nucleic acid copies of the nucleic acid analytes; b) synthesizing one or more nucleic acid copies of the nucleic acid analytes; c) hybridizing the first nucleic acid copies with the array of nucleic acids (i) to form hybrids if any nucleic acids of interest are present, wherein any formed hybrids generate a domain for complex formation; d) contacting the UDEs with the hybrids
  • One aspect of the present invention discloses methods that eliminate the necessity for enzymatic incorporation of labeled nucleotides by an end user.
  • common or conserved features present in a diverse population of nucleic acid analytes are used to assay the extent of hybridization of the analytes to discrete target elements in an array format.
  • These common or conserved features are Universal Detection Targets (UDTs) which can provide signal generation by binding of Universal Detection Elements (UDEs).
  • Examples of UDTs that may be inherently present in a population of diverse nucleic acid analytes can comprise but not be limited to 3′ poly A segments, 5′ caps, secondary structures and consensus sequences.
  • Examples of consensus sites that might find use in the present invention can comprise but not be limited to signal sites for poly A addition, splicing elements and multicopy repeats such as Alu sequences.
  • UDEs may be directly or indirectly labeled.
  • directly labels can comprise but not be limited to any members of a group consisting of a fluorescent compound, a phosphorescent compound, a chemiluminescent compound, a chelating compound, an electron dense compound, a magnetic compound, an intercalating compound, an energy transfer compound and a combination of any of the foregoing.
  • Examples of indirect labels can comprise but not be limited to any members of a group consisting of an antibody, an antigen, a hapten, a receptor, a hormone, a ligand, an enzyme and a combination of any of the foregoing.
  • enzymes are any enzymes which catalyze reactions_selected from the group consisting of a fluorogenic reaction, a chromogenic reaction and a chemiluminescent reaction.
  • RNA and DNA polymerases sometimes have difficulty in accepting labeled nucleotides as substrates for polymerization.
  • this shortcoming can result in the production of a labeled library that consists of short strands with few signal generating entities. Limitations caused by such inefficient incorporation can be partially compensated for by increasing the amount of labeled precursors in the reaction mixtures.
  • this method achieves only a moderate improvement and entails a higher cost and waste of labeled reagents.
  • this particular aspect of the present invention discloses means by which diverse nucleic acids in a library can be hybridized in an array format in their native form without the need of any manipulations or modifications and then be detected by the presence of UDTs bound to the array.
  • FIG. 1 An illustrative depiction of this process is given in FIG. 1. Although there are multiple unique species of mRNA that can make up a diverse population of nucleic acids in a sample, the common elements that are shared by these nucleic acids can be used as UDTs. Hybridization of the mRNA to an array permits the localization of individual species to discrete locations on the array. The determination of the amount of sample that is bound to each locus of an array is then carried out by detection of the amount of UDT present at each locus by binding of the appropriate UDE. Thus, in FIG. 1, locus 1 and 3 would be capable of generating an amount of signal that would be proportionate to the amount of mRNA bound to each of those sites.
  • a single labeled species of mostly or completely poly T or U could be used as a UDE to quantify the amount of poly A tails of the various species of eucaryotic mRNA in FIG. 1.
  • a single universal species of labeled material is synthesized for use as a UDE thereby providing an inexpensive and efficient means of indirectly labeling the RNA molecules being quantified.
  • a nucleic acid UDE can be prepared either chemically or enzymatically.
  • oligonucleotide synthesizers are commercially available that can produce a UDE consisting of labeled poly T/U sequences for detection of the poly A UDT described above. Both the amount and placement of labeled moieties can be tightly controlled by this method. Also, since this is a homopolymeric product, probes that are shorter by one or more bases will still be effective such that the net yield of usable product will be higher than one that requires a discrete specific sequence. On the other hand, methods of synthesizing such sequences enzymatically are also well known to those versed in the art.
  • a tetramer of dT is used as a primer for addition of poly T or poly U by terminal transferase.
  • Each base can be modified to be capable of signal generation or a mixture of labeled and unlabeled bases can be used.
  • a Poly A UDT has been described in the example above, when different sequences are used as UDTs, the synthesis of the corresponding UDEs can be carried out by the same chemical and enzymatic methodologies described above. It is also contemplated that analogues of DNA can also be used to synthesize the UDEs. For instance, instead of using DNA, labeled RNA or PNA (peptide nucleic acids) may also be used.
  • Detection and quantification of the amount of UDTs bound to particular loci can also be carried out by the use of an antibody acting as a UDE.
  • antibody specificities that are useful for UDEs can comprise but not be limited to recognition of the cap element at the 5′ end of mature mRNAs or the homopolymeric poly A sequence.
  • hybridization between nucleic acids is an event that in and of itself is capable of generating a UDT that can be recognized by antibody UDEs. For example, when a library of diverse RNA species are bound to an array, the RNA, DNA or PNA target elements in the array will generate RNA/RNA, RNA/DNA or RNA/PNA hybrids at each of the loci that has homology with the particular RNA species being quantified.
  • each of the sites has a discrete sequence
  • universal detection and quantification can be carried out by antibodies that recognize the change in physical structure produced by such hybridization events.
  • the hybridization between a UDE and the complementary UDT of a nucleic acid bound to the target elements of the array can be detected by an appropriate antibody.
  • the antibodies that are specific for the UDEs described above can be labeled themselves or secondary labeled antibodies can be used to enhance the signal.
  • binding of a UDE to a UDT may take place before or after hybridization of the RNA to an array of detection probes.
  • the particular order of events will depend upon the nature and stability of the binding partners.
  • binding of each UDE to a binding partner is preferably carried out prior to hybridization of the RNA to an array of target elements such that each library is differentially labeled.
  • comparisons are typically carried out between two libraries, any number of comparisons can be made simultaneously as long as each library is capable of generating a signal that can be distinguished from the other libraries.
  • the arrays can be used in a parallel or sequential fashion. In this format, hybridization and detection is carried out separately for each library and the analysis of the results is compared afterwards relative to normalized controls of steady state genes.
  • UDTs or UDEs are artificially incorporated into the diverse nucleic acids of the library.
  • Enzymes that find particular use with RNA analytes may comprise but not be limited to Poly A polymerase which specifically adds Adenine ribonucleotides to the 3′ end of RNA and RNA ligase which can add an oligonucleotide or polynucleotide to either the 5′ or 3′ end of an RNA analyte.
  • Poly A polymerase which specifically adds Adenine ribonucleotides to the 3′ end of RNA
  • RNA ligase which can add an oligonucleotide or polynucleotide to either the 5′ or 3′ end of an RNA analyte.
  • Enzymes that find particular use with DNA analytes may comprise but not be limited to Terminal Transferase for addition to 3′ ends and DNA ligase for addition to either 3′ or 5′ ends.
  • the sequences that are introduced into the nucleic acid analytes can be labeled during synthesis or addition of a UDE or conversely unlabeled UDTs can be synthesized or added that are detected later by corresponding labeled UDEs.
  • This aspect enjoys special utility when unspliced RNA, snRNA, or rRNA are used as analytes since they may be lacking inherent elements that are present in mRNA that have previously cited as being useful as UDTs.
  • This aspect of the present invention will also find use with procaryotic mRNA since the poly A additions, 5′ caps and splicing elements which have been previously cited as potential UDTs of mRNA are intrinsically lacking in procaryotes.
  • RNA molecules from eucaryotic organisms can be very large even after processing events have taken place. This size factor can hinder hybridization or allow scissions between the segment used for binding to a target element in the array and the UDT that is being used for signal generation. Additionally, a fragmentation step may also reduce the amount of secondary structure present in RNA. Therefore, in this aspect of the present invention, RNA can be fragmented into smaller sized pieces either by physical or enzymatic followed by addition of sequences that can act as UDTs or UDEs. Examples of physical means for fragmentation of nucleic acids can include but not be limited to shearing or alkali treatment. Examples of enzymatic means can include but not be limited to a partial nuclease or RNase digestion.
  • DNA from most sources will also be extremely large in its native form.
  • DNA analytes may also be fragmented by suitable physical or enzymatic means.
  • a particularly useful enzymatic means would be the use of restriction enzymes where the nature of the recognition sequence for the restriction enzyme will determine the average size of the fragments.
  • most restriction enzymes require double-stranded DNA as templates, some enzymes such as Hha I, Hin P1 I and MnI I cleave single-stranded DNA efficiently (2000-2001 catalog, New England BioLabs, Beverly, Mass., p214).
  • Hha I Hin P1 I
  • MnI I cleave single-stranded DNA efficiently (2000-2001 catalog, New England BioLabs, Beverly, Mass., p214).
  • the diverse nucleic acids in a library are used as templates for synthesis of complementary nucleic acid copies instead of using the analytes directly for array analysis.
  • the analyte templates may have intrinsic UDTs present or they may have UDTs artificially incorporated by the means cited earlier.
  • the UDTs do not have to be present in the analyte templates and incorporation of artificial UDTs can take place either during or after synthesis of nucleic acid copies.
  • Examples of enzymes that may be used for making copies of DNA templates can comprise but not be limited to DNA polymerases for synthesis of DNA copies and RNA polymerases for the synthesis of RNA copies.
  • DNA polymerases that may have use in the present invention for synthesis of DNA copies from DNA templates can include but not be limited to E.coli DNA Pol I, the Klenow fragment of E. coli DNA Pol I, Bst DNA polymerase, Bca DNA polymerase, Taq DNA polymerase, Tth DNA polymerase, T4 DNA polymerase, T7 DNA polymerase, ALV Reverse Transcriptase, RSV Reverse Transcriptase, HIV-1 Reverse Transcriptase, HIV-2 Reverse Transcriptase, Sensiscript, Omniscript and various mutated or otherwise altered forms of the foregoing.
  • RNA polymerases that may have use in the present invention for synthesis of RNA copies from DNA templates can include but not be limited to bacteriophage T3 RNA polymerase, bacteriophage T7 RNA polymerase and bacteriophage SP6 RNA polymerase.
  • enzymes that may have use in the present invention for making DNA copies of RNA templates can comprise but not be limited to ALV Reverse Transcriptase, RSV Reverse Transcriptase, HIV-1 Reverse Transcriptase, HIV-2 Reverse Transcriptase, Sensiscript, Omniscript, Bst DNA polymerase, Bca DNA polymerase, Tth DNA polymerase and various mutated or otherwise altered forms of the foregoing.
  • Examples of enzymes that may have use in the present invention for making RNA copies of RNA templates can comprise but not be RNA dependent RNA polymerases (Koonin, 1991 J. Gen Virol. 72; 2197-2206, incorporated herein by reference).
  • Efficient synthesis of complementary copies of analyte templates require the presence of a promoter for efficient synthesis by DNA dependent RNA polymerases while the other cited exemplary enzymes require primers.
  • Incorporation of a UDT into a DNA analyte that will be transcribed by a DNA dependent RNA polymerase can comprise but not be limited to ligation of a UDT sequence and a promoter sequence by the action of DNA ligase. This process is depicted below:
  • DNA analyte+UDT-Promoter DNA Analyte-UDT-Promoter
  • One means of carrying out this particular aspect of the present invention is digestion of a library of diverse double-stranded DNA analytes by a restriction enzyme followed by ligation of a double-stranded DNA segment comprising an RNA promoter sequence. Subsequent transcription of the transcription units can synthesize either labeled or unlabeled transcripts. The unlabeled transcripts can be detected by the presence of either inherent or synthetically added UDTs.
  • the primers can comprise random sequences or selected sequences for binding to the analyte templates. Random primers that have commonly been used for priming events have ranged from hexamers to dodecamers. Selected sequences that are useful as primers can be complementary to inherent sequences or to non-inherent sequences that have been introduced into the analyte templates. Examples of inherent sequences can include but not be limited to consensus sequences or homopolymeric sequences. Consensus sequences can be derived from elements that are retained in a large portion of the population being studied.
  • Non-inherent homopolymeric or unique sequences that can be used for primer binding may be introduced into RNA templates by means that can include but not be limited to poly A polymerase or RNA ligase.
  • Non-inherent homopolymeric or unique sequences that can be used for primer binding may be introduced into DNA templates by means that can include but not be limited to Terminal Transferase and DNA ligase.
  • the artificial binding sites can be introduced into intact nucleic acid templates or fragmentation processes may be carried out as described previously.
  • the library can be subdivided by the use of primers that have been synthesized with 1 or more additional discrete bases at the 3′ end.
  • primers that have been synthesized with 1 or more additional discrete bases at the 3′ end.
  • an oligonucleotide primer that has the formula 5′-T n dC-3′ would preferentially prime mRNAs whose last base was a G before the poly A tail rather than priming the entire population of mRNA's with poly A tails.
  • 5′-T n dG-3′ or 5′-T n dA-3′ primers are used.
  • oligonucleotides would have either dC, dG, dA or dT as the last base at the 3′ end and dC, dG or dA in the penultimate position and the remaining portion comprising a poly T segment. This would create the potential for 12 separate pools from the original population. Further provision of discrete bases at the 3 rd nucleotide position from the 3′ end would provide a separation into 48 different subpopulations if desired and so on.
  • subpopulations may have utility in providing RNA with lower complexity thereby simplifying analysis later on.
  • the use of discrete bases at the 3′ end would limit the size of poly T tails at the end of the cDNA copies since significant amounts of priming events will only take place at the junction of the poly A addition site. This may reduce background hybridization caused by extensive polyT or PolyA tracts. Also it may increase yields of labeled products by decreasing stalling or premature terminations caused by long homopolymeric tracts.
  • the cDNA molecules synthesized from the pool of RNA templates also comprise UDTs or UDEs.
  • these UDTs can be inherently present or they may be non-inherent sequences that are artificially incorporated during synthesis of cDNA.
  • synthesis of the complementary copy creates a sequence that can also be used as a UDT.
  • the poly A sequence at the 3′ end of eucaryotic mRNA was previously described as a potential UDT.
  • the poly T segment of the cDNA copy can function as a UDT.
  • the destruction or separation of the RNA templates from the cDNA would allow the poly T at the 5′ end of the cDNA to act as a UDT by binding of a labeled poly A UDE.
  • UDTs or UDEs can also be incorporated into cDNA copies by inclusion of nucleic acid segments that don't participate in primer binding into the 5′ tails of either random, homopolymeric, or specific sequence primers.
  • the particular sequence of the additional nucleic acid segments used as UDTs are of arbitrary nature since they aren't needed for primer binding.
  • the choice of sequence for these UDTs can range in complexity from homopolymeric sequences to specific unique sequences. Their nature is also arbitrary, and either the primer or the UDT can comprise PNA's or other nucleic acid homologues. In addition, they may be other polymeric entities besides nucleic acids that provide recognition for UDEs.
  • the present invention allows simple differentiation between libraries that are being compared. For instance, one population that is being studied can be extended by homopolymeric or random primers and hybridized with a UDE labeled with Cy 3. A second population that is being compared can be extended by homopolymeric or random primers and hybridized with UDEs that have Cy 5 incorporated into them.
  • the other end of the cDNA is also available for use with UDEs. For example, after synthesis of cDNA copies by reverse transcriptase, the 3′ ends can be extended further by the non-template directed addition of nucleotides by Terminal Transferase. An illustration of this particular aspect of the present invention is included in FIG. 3.
  • Detection of the presence of UDTs or UDEs in the library or libraries of various nucleic acids can be carried out by any of the means that have been described previously for UDTs. If only a single library is being analyzed, binding of a probe or antibody to a 5′ or 3′ UDT or UDE may take place before or after hybridization of nucleic acids to the detection elements of the array. The particular order of events will depend upon the nature and stability of the binding partners. On the other hand, when each population incorporates a different UDT or UDE, binding of labeled moieties to the UDTs can take place either before or after hybridization of the copies of the analyte to an array. However, as described previously, the same UDT or UDE can be used for each population if parallel or sequential hybridizations are carried out.
  • signal can be generated in cDNA copies by a labeled primer being extended in the presence of labeled nucleotides.
  • the signal generated by such a method would be a summation of the signal generated by the original primer and whatever labeled nucleotides were incorporated during strand extension.
  • a combination of methodologies would generate a signal that would be higher than the amount that would be achieved by either method alone.
  • the other methods that are disclosed in the present invention can also be used in various combinations.
  • the entire population or a subset of the population of nucleic acids analytes is used to synthesize 1 st strand nucleic acid copies.
  • this product is considered to be a cNA since it represents a nucleic acid copy of the analyte.
  • Synthesis of the 1 st strand nucleic acid copies can be carried out as described previously by using discrete primers, random primers, homopolymers, or homopolymers with one or more discrete bases at their 3′ ends.
  • priming with homopolymers with one or more discrete bases at their 3′ ends may also increase the efficiency of amplification since resources such as primers and substrates will be directed only towards amplification of a discrete subpopulation derived from the 1 st cNA synthesis reaction.
  • a primer binding site on a nucleic acid analyte is used multiple times by separation of a 1 st cNA copy from its template followed by reinitiation of a new 1 st cNA copy. Separation can be carried out by exposure of the reaction mix to high temperature. If the enzyme used for nucleic acid synthesis is Taq polymerase, Tth polymerase or some other heat stable polymerase the multiple reactions can be carried out by thermocycling of the reaction without the addition of any other reactions.
  • Amplification is a significant aspect of this invention.
  • compositions and processes are devoted and directed to amplification.
  • a composition of matter comprising a library of double-stranded nucleic acids substantially incapable of in vivo replication and free of non-inherent homopolymeric sequences, the nucleic acids comprising sequences complementary or identical in part or whole to inherent sequences of a library obtained from a sample, wherein the double-stranded nucleic acids comprise at least one inherent universal detection target (UDT) proximate to one end of the double strand and at least one non-inherent production center proximate to the other end of the double strand.
  • UDT inherent universal detection target
  • the sample from which the inherent sequences of the library are obtained can comprise biological sources, e.g., organs, tissues and cells.
  • the library of nucleic acids can be derived from genomic DNA, episomal DNA, unspliced RNA, mRNA, rRNA, snRNA and a combination of any of the foregoing.
  • Inherent UDTs can be selected from the group consisting of 3′ polyA segments, consensus sequences, or both.
  • consensus sequences can be selected from the group consisting of signal sequences for poly A addition, splicing elements, multicopy repeats, and a combination of any of the foregoing.
  • the production center which can be selected from the group consisting of primer binding sites, RNA promoters, or a combination of both.
  • Such RNA promoters can comprise phage promoters, e.g., T3, T7 and SP6.
  • composition of matter for amplification purposes comprises a library of double-stranded nucleic acids substantially incapable of in vivo replication, such nucleic acids comprising sequences complementary or identical in part or whole to inherent sequences of a library obtained from a sample, wherein the double-stranded nucleic acids comprise at least four (4) non-inherent nucleotides proximate to one end of the double strand and a non-inherent production center proximate to the other end of the double strand.
  • RNA promoters e.g., phage promoters (T3, T7 and SP6) are given elsewhere in this disclosure and are equally applicable to this last composition.
  • composition of matter for amplification comprises a library of double-stranded nucleic acids fixed to a solid support, those nucleic acids comprising sequences complementary or identical in part or whole to inherent sequences of a library obtained from a sample and the nucleic acids further comprising at least one first sequence segment of non-inherent nucleotides proximate to one end of the double strand and at least one second sequence segment proximate to the other end of the double strand, the second sequence segment comprising at least one production center.
  • beads as the solid support, particularly beads and magnetic beads.
  • Yet another amplification type composition of matter comprises a library of double-stranded nucleic acids attached to a solid support, the nucleic acids comprising sequences complementary or identical in part or whole to inherent sequences of a library obtained from a sample, wherein the double-stranded nucleic acids comprise at least one inherent universal detection target (UDT) proximate to one end of the double strand and at least one non-inherent production center proximate to the other end of the double strand.
  • UDT inherent universal detection target
  • RNA promoters solid support, beads, magnetic beads, sample, library of nucleic acids, inherent UDTs, consensus sequences, production centers, RNA promoters, phage promoters, e.g., T3, T7 and SP6, have been described above.
  • one such process of the present invention comprises the steps of a) providing (i) an array of fixed or immobilized nucleic acids identical or complementary in part or whole to sequences of the nucleic acids of interest; (ii) a library of nucleic acid analytes which may contain the nucleic acids of interest sought to be detected or quantified; and (iii) polymerizing means for synthesizing nucleic acid copies of the nucleic acid analytes, the polymerizing means comprising a first set of primers and a second set of primers, wherein the second set of primers comprises at least two segments, the first segment at the 3′ end comprising random sequences, and the second segment comprising at least one production center; (iv) means for synthesizing nucleic acid copies under isothermal or isostatic conditions; b) contacting the library of nucleic acid analytes with the first set of primers to form
  • the first set of primers which are complementary to inherent UDTs.
  • the hybridized nucleic acids can comprise one or more signaling entities attached or incorporated thereto. As described variously above, signal detection can be carried out directly or indirectly. Mention is also made that the process can further comprise the step of separating the first copies obtained from step c) from their templates and repeating step b). Other steps can also be included such as the step of separating the extended second set of primers obtained from step f) from their templates and repeating step e). Step g) can also be carried out repeatedly, a feature provided by this invention and this last-described process.
  • means for synthesizing nucleic acid copies under isothermal or isostatic conditions is carried out by one or more members selected from the group consisting of RNA transcription, strand displacement amplification and secondary structure amplification. These are all contemplated for use of this process.
  • Another process for detecting or quantifying more than one nucleic acid of interest in a library comprises the steps of a) providing (i) an array of fixed or immobilized nucleic acids identical or complementary in part or whole to sequences of the nucleic acids of interest; (ii) a library of nucleic acid analytes which may contain the nucleic acids of interest sought to be detected or quantified; (iii) polymerizing means for synthesizing nucleic acid copies of the nucleic acid analytes, such polymerizing means comprising a first set of primers and a second set of primers, wherein the first set of primers comprise at least one production center; and (iv) means for synthesizing nucleic acid copies under isothermal or isostatic conditions; b) contacting the library of nucleic acid analytes with the first set of primers to form more than one first bound entity; c) extending the bound first set of primers by means of template sequences provided by the nucleic acid analy
  • step d) wherein the four or more non-inherent homopolymeric nucleotides are themselves added.
  • Elements and subelements of this process are described above. Special mention is made of certain aspects of this process.
  • means for synthesizing nucleic acid copies under isothermal or isostatic conditions can be carried out by one or more members selected from the group consisting of RNA transcription, strand displacement amplification and secondary structure amplification.
  • the step of separating the first copies obtained from step c) from their templates and repeating step b) can be added to this process.
  • the extended second set of primers obtained from step f) can be separated from their templates and then step e) can be repeated as necessary or desired. In fact, step g) can be repeated as often as desired or deemed necessary.
  • a process for detecting or quantifying more than one nucleic acid of interest in a library comprises the steps of a) providing (i) an array of fixed or immobilized nucleic acids identical or complementary in part or whole to sequences of the nucleic acids of interest; (ii) a library of nucleic acid analytes which may contain the nucleic acids of interest sought to be detected or quantified; (iii) polymerizing means for synthesizing nucleic acid copies of the nucleic acid analytes, such polymerizing means comprising a first set of primers and a second set of primers, wherein the first set comprises at least one production center; (iv) a set of oligonucleotides or polynucleotides complementary to at least one segment or sequence of the second set of primers; and(v) means for ligating the set of oligonucleotides or polynucleotides (iv); b) contacting the library of nucleic acid analytes with
  • Another process for detecting or quantifying more than one nucleic acid of interest in a library comprises the steps of a) providing (i) an array of fixed or immobilized nucleic acids identical or complementary in part or whole to sequences of the nucleic acids of interest; (ii) a library of nucleic acid analytes which may contain the nucleic acids of interest sought to be detected or quantified; (iii) polymerizing means for synthesizing nucleic acid copies of the nucleic acid analytes, such polymerizing means comprising a first set of primers and a second set of primers, wherein the second set comprises at least one production center; (iv) a set of oligonucleotides or polynucleotides complementary to at least one segment or sequence of the second set of primers; and (v) means for ligating the set of oligonucleotides or polynucleotides (iv); b) contacting the library of nucleic acid analytes with
  • the process wherein the first set of primers comprise one or more sequences which are complementary to inherent UDTs.
  • the hybridized nucleic acid copies can further comprise one or more signaling entities attached or incorporate thereto. If so, previously described embodiments for signal generation and detection, e.g., direct and indirect generation and detection, are applicable to this process.
  • additional steps can be carried out. For example, the step of separating the first copies obtained from step c) from their templates and then repeating step b) can be carried out. A further step of separating the extended second set of primers obtained from step f) from their templates and then repeating step e) can be carried out. Also, step g) can be carried out repeatedly.
  • Another process for detecting or quantifying more than one nucleic acid of interest in a library comprises the steps of a) providing (i) an array of fixed or immobilized nucleic acids identical or complementary in part or whole to sequences of the nucleic acids of interest; (ii) a library of nucleic acid analytes which may contain the nucleic acids of interest sought to be detected or quantified; and (iii) polymerizing means for synthesizing nucleic acid copies of the nucleic acid analytes, such polymerizing means comprising a first set of primers, a second set of primers and a third set of primers wherein the third set comprises at least one production center; and b) contacting the library of nucleic acid analytes with the first set of primers to form a first set of bound primers; c) extending the first set of bound primers by means of template sequences provided by the nucleic acid analytes to form first copies of the analytes; d) contacting the
  • the second set of primers can be complementary to the primer binding site where the process comprises an additional step c′) of including a primer binding site after carrying out step c).
  • the primer binding site can be added by means of T4 DNA ligase or terminal transferase. Other aspects or variations of this process can be made or carried out.
  • the further step of separating the extended second set of primers obtained from step f) from their templates and then repeating step e) can be made.
  • Step g) can also be carried out repeatedly.
  • An additional step f′) of separating the extended second set of primers obtained in step e) can be carried out. Also, the step of separating the first copies obtained from step c) from their templates and then repeating step b) can be carried out. Further, the step of separating the extended second set of primers obtained from step f) from their templates and then repeating step e) can be carried out. Step g) can also be carried out repeatedly.
  • the second set of primers can comprise at least one production center which differs in nucleotide sequence from the production center in the third set of primers.
  • Still another process for detecting or quantifying more than one nucleic acid of interest in a library comprises the steps of a) providing (i) an array of fixed or immobilized nucleic acids identical or complementary in part or whole to sequences of the nucleic acids of interest; (ii) a library of nucleic acid analytes which may contain the nucleic acids of interest sought to be detected or quantified; and (iii) polymerizing means for synthesizing nucleic acid copies of the nucleic acid analytes, such polymerizing means comprising a first set of primers and a second set of primers, wherein the first set of primers are fixed or immobilized to a solid support, and wherein the second set of primers comprises at least two segments, the first segment at the 3′ end comprising random sequences, and the second segment comprising at least one production center; (iv) means for synthesizing nucleic acid copies under isothermal or isostatic conditions; b) contacting the library of nucleic acid an
  • Another significant process worth discussion is one for detecting or quantifying more than one nucleic acid of interest in a library.
  • This process comprises the steps of a) providing (i) an array of fixed or immobilized nucleic acids identical or complementary in part or whole to sequences of the nucleic acids of interest; (ii) a library of nucleic acid analytes which may contain the nucleic acids of interest sought to be detected or quantified; (iii) polymerizing means for synthesizing nucleic acid copies of the nucleic acid analytes, such polymerizing means comprising a first set of primers and a second set of primers, wherein the first set of primers are fixed or immobilized to a solid support, and wherein the first set of primers comprise at least one production center; and (iv) means for synthesizing nucleic acid copies under isothermal or isostatic conditions; b) contacting the library of nucleic acid analytes with the first set of primers to form more than one first bound entity
  • Another process for detecting or quantifying more than one nucleic acid of interest in a library comprises the steps of a) providing (i) an array of fixed or immobilized nucleic acids identical or complementary in part or whole to sequences of the nucleic acids of interest; (ii) a library of nucleic acid analytes which may contain the nucleic acids of interest sought to be detected or quantified; (iii) polymerizing means for synthesizing nucleic acid copies of the nucleic acid analytes, such polymerizing means comprising a first set of primers and a second set of primers, wherein the first set of primers are fixed or immobilized to a solid support, and wherein the first set comprises at least one production center; (iv) a set of oligonucleotides or polynucleotides complementary to at least one segment or sequence of the second set of primers; and (v) means for ligating the set of oligonucleotides or polynucleotides
  • Another process for detecting or quantifying more than one nucleic acid of interest in a library comprises the steps of a) providing (i) an array of fixed or immobilized nucleic acids identical or complementary in part or whole to sequences of the nucleic acids of interest; (ii) a library of nucleic acid analytes which may contain the nucleic acids of interest sought to be detected or quantified; (iii) polymerizing means for synthesizing nucleic acid copies of the nucleic acid analytes, such polymerizing means comprising a first set of primers and a second set of primers, wherein the first set of primers are fixed or immobilized to a solid support, and wherein the second set comprises at least one production center; (iv) a set of oligonucleotides or polynucleotides complementary to at least one segment or sequence of the second set of primers; and (v) means for ligating the set of oligonucleotides or polynucleotides
  • Another process for detecting or quantifying more than one nucleic acid of interest in a library comprises the steps of a) providing (i) an array of fixed or immobilized nucleic acids identical or complementary in part or whole to sequences of the nucleic acids of interest; (ii) a library of nucleic acid analytes which may contain the nucleic acids of interest sought to be detected or quantified; and (iii) polymerizing means for synthesizing nucleic acid copies of the nucleic acid analytes, such polymerizing means comprising a first set of primers, a second set of primers and a third set of primers, wherein the first set of primers are fixed or immobilized to a solid support, and wherein the third set comprises at least one production center; and b) contacting the library of nucleic acid analytes with the first set of primers to form more than one first bound entity; c) extending the bound first set of primers by means of template sequences provided by the nucleic acid an
  • Another process for detecting or quantifying more than one nucleic acid of interest in a library comprises the steps of a) providing (i) an array of fixed or immobilized nucleic acids identical in part or whole to sequences of the nucleic acids of interest; (ii) a library of nucleic acid analytes which may contain the nucleic acids of interest sought to be detected or quantified; and (iii) polymerizing means for synthesizing nucleic acid copies of the nucleic acid analytes, such polymerizing means comprising a first set of primers; b) contacting the nucleic acid analytes with the first set of primers to form a first bound entity; c) extending the bound set of first set of primers by means of template sequences provided by the nucleic acid analytes to form first nucleic acid copies of the analytes; d) separating the first nucleic acid copies from the analytes; e) repeating steps b), c) and d)
  • Another process for detecting or quantifying more than one nucleic acid of interest in a library comprises the steps of a) providing (i) an array of fixed or immobilized nucleic acids identical in part or whole to sequences of the nucleic acids of interest; (ii) a library of nucleic acid analytes which may contain the nucleic acids of interest sought to be detected or quantified; (iii) polymerizing means for synthesizing nucleic acid copies of the nucleic acid analytes, such polymerizing means comprising a first set of primers and a second set of primers; (iv) means for addition of sequences to the 3′ end of nucleic acids; b) contacting the nucleic acid analytes with the first set of primer to form a first bound entity; c) extending the bound set of first set of primers by means of template sequences provided by the nucleic acid analytes to form first nucleic acid copies of the analytes; d) extending the first nucleic acid
  • An illustrative example of this aspect of the present invention would be to bind a poly T primer to poly A mRNA and extend it by Tth DNA polymerase under conditions that allow it to be used as a Reverse Transcriptase. Thermal denaturation followed by binding of an unextended poly T primer would allow synthesis of another copy by Tth DNA Polymerase.
  • the amount of amplification would be proportional to a) the number of primer binding sites on an individual template molecule b) the efficiency of binding/extension and c) the number of cycles carried out.
  • the method of the present invention can produce 50 1 st cNA copies from a single analyte molecule.
  • primers are used to generate a library of nucleic acids with production centers capable of synthesizing multiple nucleic acid copies that comprise sequences that are either identical or complimentary to sequences in the original analytes.
  • the entire population or a subset of the population of nucleic acids analytes is used to synthesize 1 st strand nucleic acid copies as described previously for linear amplification.
  • the 1 st cNA strand is made available for further binding/extension events by the removal or destruction of the template strands. This can be carried out by a variety of physical, chemical and enzymatic means.
  • Examples of such methods can consist of but not be limited to denaturation, alkali or RNase treatments. Denaturation can be carried out by exposure to high heat or by the other methods described above for multiple cycles of linear amplification, thereby allowing them to participate in later steps.
  • primers are annealed to the 1 st cNA strand in order to synthesize the complementary strands, thereby generating double-stranded cNA copies of the original analyte population.
  • the primers used for 2 nd strand synthesis are designed such that their 5′ ends comprise sequences capable of acting as production centers. A description of such production centers is disclosed in Rabbani et al., U.S. patent application Ser. No. 08/574,443, filed on Dec.
  • RNA promoter segment An example of a production center that would be particularly useful in the present invention would comprise an RNA promoter segment.
  • random hexamer primers for 2 nd strand synthesis can have the structure:
  • the promoter is a phage promoter.
  • the sequences specific for their cognate polymerases are sufficiently short that their addition onto an oligounucleotide being used for priming allows synthesis to remain both efficient and inexpensive. At the same time, they are sufficiently long that they are unique compared to the genomic DNA they are being used with.
  • the phage RNA polymerases that recognize these promoters are usually single protein molecules that have no requirement for other subunits or cofactors.
  • phage promoter sequences that are recognized by the T3, T7 and SP6 RNA polymerases. These enzymes are well characterized and are commercially available from a number of sources.
  • the promoters cited as examples above should be in double-stranded form. This may be carried out in several different ways. A potential sequence of events for one such method is graphically depicted in FIG. 4. If the polymerase used for extension has strand displacement activity, the primer binding closest to the 3′ end of the 1 st strand (Primer A in FIG. 4) remains bound to the template, but the other extended primers (Primer B and Primer C) are released from the template in single stranded form.
  • a given individual template molecule may give rise to a plurality of complementary copies by multiple priming/extension events with two groups of products: essentially double-stranded molecules that comprise the 1 st cNA strands bound to their complements and single-stranded molecules derived from the displaced strands.
  • the displaced strands are in single-stranded form
  • the continued presence of other primers from either 1 st or 2 nd strand synthesis could allow further binding/extension events that convert the displaced single strands into double-stranded form.
  • Such double-ended constructs may not transcribe efficiently or may produce nucleic acids that hybridize with each other rather than the target elements of the array.
  • the same primers that were used to initiate synthesis of the 1 st cNA strand can be added to the mixture with the displaced 2 nd cNA strands as well as whatever reagents may also be necessary to convert the displaced single-stranded DNA molecules into double-stranded products.
  • random primers without promoters may be used for priming the displaced 2 nd cNA strands.
  • the synthesis of a complementary copy for the displaced single strands also converts the promoter segment in the 5′end of these molecules into double-stranded form.
  • the promoter in the extended primer that remains bound to the original 1 st cNA strand template needs different processes to render it into a functionally efficient form.
  • the single-stranded 3′ tail of the 1 st cNA strand could be digested by the 3′ to 5′ Exonuclease activity of T4 DNA polymerase.
  • the enzyme Upon reaching the double stranded portion, the enzyme could then use its polymerase activity to extend the shortened 3′ end by using the promoter segment of primer A as a template thereby generating a double-stranded promoter.
  • oligonucleotides can be provided that are complementary to the single-stranded promoter sequences (FIG. 5 a ) or the primers used for 2 nd strand cNA synthesis can be designed such that they are self-complementary and form stem loop structures that generate double-stranded functional promoters (FIG. 5 b ).
  • the 2 nd cNA strands bound to the template can be denatured and the same processes described above for converting the displaced 2 nd cNA strands can be used to convert them into double-stranded form.
  • RNA transcripts or cDNA copies of the RNA transcripts created from the processes described above can either be labeled or unlabeled.
  • the polynucleotides When the polynucleotides are unlabeled, they can use UDTs for signal generation.
  • the original anlytes may have inherent UDT sequences that may serve this function or the analytes may be modified by the incorporation of non-inherent UDT sequences.
  • the synthetic steps that are carried out in the series of reactions above provide the opportunity to incorporate non-inherent UDTs during either 1 st strand or 2 nd strand synthesis by primers with appropriate designs.
  • a primer design for 2 nd strand synthesis can have the following structure:
  • transcripts After binding the primer above to a 1 st cNA strand followed by extension, the transcripts could be generated with the structure:
  • transcript shown above has a UDT at its 5′ end
  • other designs allow the transcripts to be synthesized with UDTs in their 3′ ends. For instance, this can take place by either the sequence of the primer binding site used for the initial 1 st strand synthesis being capable of acting as a UDT or by incorporation of a UDT into the primer that is to be used for 1 st strand synthesis.
  • a transcription unit can be synthesized from poly A RNA by priming of the 1 st cNA strand with an oligonucleotide primer with the structure:
  • RNA molecules that have the following structure:
  • the product above can bind a UDE either through the an inherent UDT (the Poly A sequence) or through the artificially incorporated UDT.
  • UDTs for signal generation can be coupled with incorporation of labeled nucleotides if desired.
  • this aspect of the present invention provides for the synthesis of a library of detectable products that will reflect the initial levels of the various nucleic acid analytes of a library.
  • the present invention is in contrast to previously cited art that did not use primers for 2 nd strand synthesis. These methods of previous art depended upon the presence of RNaseH to create a second strand or else required self-priming events by a foldback mechanism and subsequent treatment with S1 nuclease or its equivalent. In the absence of such a nuclease treatment, transcripts made from hairpin derived constructs would be self-complementary and thus incapable of appreciable hybridization to arrays. In contrast to this prior art, the present invention discloses various methods where exogenous primers are used to synthesize the 2 nd strand.
  • the methods used to synthesize the 2 nd strand include means that selectively retain information from the 5′ ends of analytes.
  • the present invention describes the potential for the synthesis of multiple transcription units from a single 1 st strand cNA template thereby providing an additional level of amplification.
  • the 1 st cNA strands can be actively prevented from creating 2 nd cNA strands through a fold-back mechanism by blocking the extendability of a 1 st cNA strand.
  • One method of carrying this out is by the addition of a dideoxynucleotide to the 3′ terminus of a 1 st cNA copy by terminal transferase. Although this method would prevent a 1 st cNA strand from participating in self-priming reactions, a blocked 1 st can strand would retain its capability of being used as a template.
  • either the primer used for 1 st strand cNA synthesis or 2 nd strand cNA synthesis can comprise an RNA promoter or other replication center.
  • Another aspect of the present invention discloses the addition or incorporation of artificial primer binding sites to carry out the novel processes described above.
  • the translation of mRNA into a cDNA copy also frequently includes the terminal addition of a few non-template directed nucleotides into the 3′ end of the 1 st cNA strand by Reverse Transcriptase.
  • these added bases have been used as primer binding sites for cloning of full length cDNA molecules.
  • Primers that bind to interior poly C sequence and initiate extensions are as competent as bindings to poly C's at the end of cDNA (Matz et al., 1999) to synthesize 2 nd cDNA strands, thereby creating functional double stranded phage promoters.
  • this particular aspect of the present invention provides a promoter in the primer used for the 2 nd strand synthesis.
  • a primer for 2 nd strand synthesis that comprises oligo dG sequences at their 3′ end for binding to the termini of 1 st cNA strands.
  • priming events that derive from the terminal bindings and extensions will lead to double stranded promoters in molecules.
  • Step (D) in FIG. 6 a primer with a T7 promoter can bind to the terminus of the 1 st cNA strand.
  • Step (E) of FIG. 6 shows the binding of a primer with a T7 promoter to an internal segment of the cNA with.
  • the 3′ end of the cNA is unable to use the primer as a template, thus leaving the promoter in a non-functional single-stranded form.
  • Terminal Transferase can be added to increase control over the reaction and improve efficiency.
  • Terminal transferase use dGTP or dCTP.
  • Primers for 2 nd strand synthesis can then be designed whose sequences comprise a promoter and a 3′ segment complementary to the sequences added by the Terminal Transferase addition step. The steps of this process are shown in FIG.
  • the primers used for 2 nd strand synthesis can have longer corresponding homopolymeric segments thereby allowing higher temperatures for binding and extension. This heightened stringency should decrease the frequency of priming events with internal sequences in the 1 st cNA template strand and provide higher representation of sequences from the 5′ end of the original analytes. Therefore, when terminal transferase is used to generate a primer binding site for 2 nd strand synthesis, the promoter can be in either the 1 st strand or the 2 nd strand.
  • the step of terminal transferase addition to the 1 st cNA can be carried out while it is still bound to its template as described above, or it can be carried out after destruction of the template or separation of the template from the 1 st cNA strand.
  • This method should continue to enjoy 2 nd strand synthesis that is preferentially initiated by primers binding and being extended from the 3′ termini of 1 st cNA strands.
  • UDTs, as well as labeled or unlabeled nucleotides can all be utilized in carrying out this aspect of the present invention. Also, it is contemplated that higher yields of end products can be achieved by repetitions of one or more steps of the various process that are disclosed herein.
  • a cDNA copy that is a complete copy of its RNA template is a substrate for blunt end ligation by T4 DNA ligase with a double-stranded oligonucleotide.
  • the sequence of the oligonucleotide ligated to the 3′ end of the 1 st cNA strand can be chosen by the user and can function as a primer binding site for making a 2 nd cNA strand.
  • a 3′ single-stranded tail in the 1 st cNA strand is a substrate for ligation of a single-stranded DNA oligonucleotide by T4 RNA ligase (Edwards et al., 1991 Nucleic Acids Research 19; 5227-5232; incorporated herein by reference).
  • a double-stranded oligonucleotide with a 3′ single-stranded tail can be joined to a 1 st strand cNA through “sticky end” ligation by T4 DNA ligase when the 1 st cNA and oligonucleotide tails are complementary.
  • these cNA tails can be derived from non-template additions by Reverse Transcriptase or by Terminal transferase. Illustrative examples of these processes are given in FIG. 8. Since all of these processes are dependent upon preferential binding of primers to the 3′ ends 1 st strand can molecules, the promoter can be in either the 1 st or 2 nd cDNA strand.
  • a 1 st strand cNA strand is fragmented by physical, chemical or enzymatic means.
  • enzymatic means can include but not be limited to restriction enzymes such as Hha I, Hin P1 I and Mnl I, DNases such as DNase I and nucleases such as S1 nuclease and Mung Bean Nuclease. These fragments can be used as templates for synthesis of a 2 nd strand by any of the methods described previously. For example, hybridization and extension of random primers with T7 promoters can be used with the cNA strand fragments as templates in processes similar to those shown in FIGS. 4 and 5.
  • FIG. 8 is an illustration of this process using the homopolymeric method. Breaking down the 1 st strand copy into smaller segments followed by incorporation of a primer during 2 nd strand synthesis would provide smaller transcription units. This may be advantageous when using modified nucleotides for signal generation. For instance, when there are long stretches in the template strand that are complementary to the labeled nucleotide, the modification to the nucleotide may cause a blockage in downstream transcription or loss of processivity and result in under-representation of those sequences. In this particular aspect of the present invention, the partition of copies of analyte sequences into smaller individual transcription units allows each of the units to direct RNA synthesis independently thereby creating a more complete representation of the library of various nucleic acid sequences.
  • the novel methods disclosed for synthesis of a library are combined with capture methods to provide more efficient synthesis as well as flexibility in changing salts, buffers, enzymes and other components during multistep processes.
  • the present invention discloses the use of a 1 st strand primer that is bound to a solid matrix such as a bead followed by the processes described above.
  • a solid matrix such as a bead
  • the 3′ end of Oligo T sequences bound to a solid matrix can be extended using polyA mRNA as a template.
  • this 1 st cNA strand is thereupon used as a template for the 2 nd cNA strand.
  • a replicative center such as an RNA promoter sequence can be introduced into either the 1 st or 2 nd strand depending upon the particular method used. For instance, random primers with promoters in their 5′ ends can bind to the extended 1 st cDNA strands to create 2 nd strands that have a promoter incorporated into them. This process is depicted in FIG. 10.
  • the single-stranded promoter on the 5′ ends of the 2 nd cDNA strands can be converted into double-stranded form by any of the methods described previously.
  • the primer/template complex that remains bound to the bead in FIG. 10 can be treated with T4 DNA polymerase, hybridized with an oligonucleotide complementary to the promoter segment or the primer can be designed with self complementary regions. The latter two methods were previously discussed with reference to FIG. 5.
  • the presence of unextended oligo-T tails on the matrix material can provide further binding/extension events since the displaced strands carry poly A sequences on their 3′ ends.
  • oligo-T can be added whether associated with beads or free in solution. Extension of the oligo-T should ultimately result in conversion of the single-stranded promoters of the displaced 2 nd cDNA strands into functional double-stranded forms.
  • Another method that can be used in the present invention is to repeat one or more of the steps that have been described in the present invention. For instance, after using a library of analytes to synthesize 1 st can copies attached to a matrix, the anlytes can be separated from the 1 st cNA copies and used to create another pool of 1 st cNA copies. Similarly, after synthesis of 2 nd can strands, the library of 2 nd cNA strands can be separated from the 1 st can strands fixed to the matrix. All 2 nd cNA strands that have copied the 5′ ends of the 1 st cNA strands will have regenerated the sites that were initially used to bind to the primers linked to the beads.
  • the 2 nd strands can be rebound to the same beads. Since there are likely to be an enormous number of poly T primers on the beads compared to the number of templates used for 1 st cNA synthesis, the majority of primers on the matrix remain unextended and can be used for new priming events. Thus, complete copying of these rebound 2 nd can strands should allow generation of double-strand promoters at the ends of these molecules without a necessity for the use of T4 to do “trimming”. If desired the 1 st cNA strands that are attached to the matrix can be used to generate another pool of 2 nd cNA strands. The pool or pools of 2 nd can strands can then be added to fresh beads with primers complementary to their 3 ′ ends.
  • the extension of the primers attached to the matrix will convert all of the 2 nd can strands into double-stranded form including the promoter sequences that were at their 5′ ends.
  • the reaction products can be removed and the nucleic acid on the matrix can be used for more transcription reactions thereby accumulating more transcription products.
  • thee primers can also be prepared with one or more discrete bases at their 3′ ends. As described previously, these primers can be used as a group that represents all the possible variations or they can be used individually depending upon whether general amplification or separation into subclasses was desired.
  • the poly A sequence used above is understood to only be an illustrative example. As described previously, the sequences in analytes used for binding of 1 st strand primers can be derived from inherent sequences or they may be noninherent sequences in analytes that have been artificially introduced by any of the means that have been described previously. This particular embodiment of the present invention can utilize any of these primer binding sites by appropriate design of the primer sequence bound to the matrix.
  • the primer sequences for 1 st strand synthesis can be either directly or indirectly attached to a matrix.
  • Methods for direct attachment of oligonucleotides to matrixes are well known in the art.
  • beads with covalently attached extendable poly T segments are commercially available from a number of sources.
  • Methods for indirect attachment are also well known in the art.
  • FIG. 11 depicts a sandwich method where a primer has two segments, one of which is complementary to a capture segment attached to the matrix and the other is complementary to the poly A segment of the target RNA.
  • the two segments of the primer may form a continuous nucleotide sequence or there may be a disjunction between the two segments.
  • Hybridization of the two segments of the primer and the complementary sequences on the matrix and the binding site of the analyte can take place simultaneously or they can be carried out in a step-wise fashion. For instance, hybridization of target RNA to the capture element can be carried out in solution followed by capure to the matrix. It is preferred that the segment that is bound to the matrix be rendered incapable of extension.
  • binding and extension events can take place as described previously for FIG. 10 to synthesize 1 st and 2 nd cDNA copies of the original poly A mRNA. Conversion of the promoter sequences into double-stranded form can also take place as described above. Transcription can take place either while the transcription units are attached to the matrix or if desired separation from the matrix can take place in a step subsequent to the transcription.
  • RNA promoter during 1 st strand synthesis results in transcripts that comprise sequences that are complementary to sequences in the original analytes. Incorporation of an RNA promoter into the 2 nd strand synthesis results in the production of transcripts that comprise sequences that are identical to sequences in the original analytes. As described previously, these can easily be converted into complementary cDNA copies if desired.
  • transcription units can be synthesized without incorporating a promoter sequence into either the 1 st cNA (as described by Eberwine et al., op. cit.) or the 2 nd cNA strand (as described in previous embodiments of the present invention).
  • a promoter sequence As shown in step D of FIG. 12, when using extended 1 st cNA strands as templates for synthesis of the 2 nd cNA strands, a duplicate of the original primer binding sequence is synthesized.
  • a polyA segment is created at the 5′ ends for both displaced 2 nd cNA strands and for 2 nd cNA strands that remain bound to the beads.
  • oligonucleotide primers comprising an RNA promoter and oligo-T sequences can be hybridized to the 2 nd cNA strands.
  • the primers may be attached to a matrix or they may be free in solution. Provision of DNA Polymerase, nucleotides and appropriate cofactors can allow extension of both the 3′ ends of the promoter/primers as well as the 3′ ends of the cDNA copies thereby creating functional transcriptional units as shown in step F of FIG. 12.
  • oligo-T that is attached to a matrix such as cellulose or beads
  • a release step prior to synthesis of a library.
  • a special oligo T primer joined to a T7 promoter was extended using RNA as template to create a library (Eberwine op.cit.).
  • this system put the promoter in close proximity to the capture bead, potentially decreasing its ability to be converted into double-stranded form and/or for it to function as a promoter.
  • synthesis of the 2 nd strand by random priming does not prevent hairpin self-priming.
  • transcription units would direct synthesis of self-complementary RNAs from hairpin template sequences that would be incapable of hybridizing to target arrays. use of the templates for this non-productive synthesis may cause an inefficiency in the amount of effective labeled transcripts
  • a particular benefit of the use of promoters in primers used for 2 nd cNA synthesi present invention is that although 1 st cNA strands can be synthesized under conditions that have the potential for self-priming events i.e. creating 2 nd cDNA strands by a fold-back mechanism, the absence of a promoter in 1 st cDNA; strand would prevent these constructs from being transcriptionally active. Thus, only 2 nd cDNA strands that are derived from priming events by oligonucleotides with promoter sequences are functional for transcription. This in contrast to the system previously described by Eberwine (op. cit.).
  • This particular aspect takes advantage of competitive binding by an unlabeled population of RNA. Synthesis of this material can take place by any of the means described in the foregoing work.
  • the particular sequences can be homologous to sequences that are present on the arrays or they may be homologous to sequences that are present in the labeled material.
  • relative levels of increased or decreased mRNA synthesis can be established relative to the competitor, ie. differential competition.
  • Adjustments can be made in the relative amounts of unlabeled material being used or the housekeeping genes that are present as controls can allow for normalization values. This method provides the advantage that multiple sequential or parallel hybridizations can be carried out and compared with a single common labeled control population of RNA.
  • the various steps of the present invention can be carried out sequentially by adding various reagents and incubation steps as required.
  • the series of steps can be segregated by introducing additional steps that either remove or inactivate components of the reaction or where a desired product is separated from a reaction mixture.
  • An example of the former can be heat inactivation of Reverse Transcriptase.
  • An example of the latter can be isolation of RNA/DNA hybrids by selective matrices.
  • a production center is able to operate by other means as well.
  • various means of introducing UDTs that serve as primer binding sites have been previously described in the context of synthesis of 2 nd copy strands followed by RNA transcription. These primer binding sites can in themselves serve as production centers for multiple copies of various nucleic acids under isothermal conditions.
  • UDTs can be added to the various nucleic acids of a library to carry out the amplification disclosed in Rabbani et al., U.S. patent application Ser. No. 09/104,067, cited supra and incorporated herein by reference.
  • FIG. 13 is a depiction of a series of reactions that could be used to carry this out.
  • a UDT can be ligated to a library of poly A mRNA where the UDT comprises two segments (termed X and Y in this Figure).
  • a primer (Primer 1) that comprises two segments, a poly T sequence at the 3′ end and a segment termed Z at the 5′ end is hybridized to the poly A sequences at the 3′ end of the mRNA and extended by reverse transcription to make a 1 st cNA copy (Steps C and D of FIG. 13) that contains the sequnces X′ and Y′ at the 3′ end. Removal of the original template makes the X′ segment at the 3′ end of the 1 st cNA copy available for hybridization.
  • a second primer (Primer 2) that has two segments, segment X at the 3′ end and segment Y′ at the 5 ′ end can be annealed and extended to make a 2 nd copy (Steps D and E) of FIG. 12.
  • the presence of Primer 2 should also allow a further extension of the 1 st cNA copy such that a double stranded segment is formed where the Y and Y′ segments are capable of self-hybridizing and thereby creating a stem-loop structure with the X and X′ segments in the loop portions as described in Rabbani et al., U.S. patent application Ser. No. 09/104,067, cited supra and incorporated herein by reference.
  • a stem loop at the other end can be carried out by annealing a third primer (Primer 3) which comprises two segments, segment Z at the 3′ end and a Poly A segment at the 5′ end using a 2 nd cNA copy as a template.
  • Primary 3 a third primer
  • the availablity of 2 nd cNA copies as templates can be derived from multiple priming events by Primer 2 at the other end (as described in Rabbani et al., U.S. patent application Ser. No. 09/104,067, cited supra and incorporated herein by reference, or by denaturation of the 1 st and 2 nd strands from each other.
  • Extension of Primer 3 creates a structure that has the Poly T and Poly A segments forming a stem and the Z and Z′ segments forming the loops. Further binding and extension reactions under isothermal conditions can proceed as described previously for unique targets. It should be noted that the particular sequences used for X, Y and Z are arbitrary and can be chosen by the user. For instance, if the Z segment of Primer 1 used in step C of FIG. 13 was designed with X and Y sequences at the 5′ end, the unit length amplicon would have X′ and Y segments at the 3′ end of each strand. As such, amplification could be carried out using only Primer 2.
  • FIG. 14 Another example of the use of non-inherent UDTs being used as primer binding sites for isothermal amplification is shown in FIG. 14 for use with the Strand Displacement Amplification system described by Walker et al., in U.S. Pat. No. 5,270,184 herein incorporated by reference.
  • Incorporation of segment X takes place by two different methods.
  • segment X is introduced by ligation to an analyte of the library.
  • step C segment X is attached to a poly T primer and becomes incorporated by strand extension. The presence of the X segment at the 5′ end of each end of the amplicon unit allows primer binding by a single Strand Displacement primer.
  • FIGS. 13 and 14 show addition of an isothermal binding site directly to an analyte and also show incorporation of an isothermal binding site during synthesis of a first copy.
  • FIG. 15 shows a similar situation, but in this example segment X is incorporated during 1 st cNA synthesis, segment Q is added after first strand synthesis and segment Z is added during 2 nd cNA strand synthesis. As described previously, one or more of these segment can comprise primer binding sites for isothermal synthesis. It should also be pointed out that in FIGS. 13 through 15 both inherent and non-inherent UDTs were used as part of the examples.
  • each locus on an array comprises two sets of primers.
  • the first set of a locus comprises Selective Primer Elements (SPE's) that are specific for a particular analyte.
  • the second set of a locus comprises Universal Primer Elements (UPE's) that are identical or complementary to sequences in UDT elements.
  • SPE Selective Primer Elements
  • UDTs can be derived from naturally occurring sequences or they may be artificially incorporated.
  • the SPE”s at a locus would be able to bind to the complementary sequences in the nucleic acids of a library, thereby binding discrete species of nucleic acids to that particular locus of the array.
  • the use of appropriate conditions, reagents and enzymes would allow an extension of an SPE using the bound nucleic acid as a template.
  • FIG. 16 depicts an array with three different loci termed Locus P, Locus Q and Locus R.
  • Locus P there is a set of SPE's bound to the array that are complementary to a particular sequence in cDNA copies made from one of three species of poly A mRNA termed P, Q and R respectively.
  • each locus of the array in FIG. 16 has a set of UPE's that comprises poly T sequences. Synthesis of a cDNA copy of each of the mRNA templates by Poly T priming of their polyA tails creates cDNA P, cDNA Q and cDNA R respectively.
  • Binding of the 1 st cDNA strand of an analyte to an SPE should be selective for each species at a particular locus. On the other hand, there should be little or no binding of the cDNA copies to the universal Poly T sequences in the UPE's of the array of FIG. 16.
  • the addition of enzymes and reagents for extension should generate 2 nd cDNA copies of P, Q and R at the LP, LQ and LR sites on the array by extension of SPE's using the bound cDNA as templates. Each of these 2 nd cDNA copies would comprise unique sequences complementary to the 1 st cDNA strand templates.
  • the 2 nd strand copies would include a common poly A sequence at their 3′ ends.
  • the product at this stage is an array that has extended and un-extended SPE's at each locus where the number of extended SPE's should be in proportion to the amount of the original corresponding analytes.
  • the extended SPE's can now serve as templates when an unextended poly T UPE is in sufficient proximity.
  • the design and placement of pairs of unique primers for solid phase amplification has been previously described in detail in U.S. Pat. No.
  • compositions and processes for solid phase amplification are one that comprises an array of solid surfaces comprising discrete areas, wherein at least two of the discrete areas each comprises a first set of nucleic acid primers; and a second set of nucleic acid primers; wherein the nucleotide sequences in the first set of nucleic acid primers are different from the nucleotide sequences in the second set of nucleic acid primers; wherein the nucleotide sequences of a first set of nucleic acid primers of a first discrete area and the nucleotide sequences of a first set of nucleic acid primers of a second discrete area differ from each other by at least one base; and wherein the nucleotide sequences of the second set of nucleic acid primers of a first discrete area and the nucleotide sequences of the second set of nucleic acid primers of a second discrete area are substantially the same or identical.
  • a related composition of this invention is one comprising an array of solid surfaces comprising a plurality of discrete areas; wherein at least two of the discrete areas each comprises a first set of nucleic acid primers; and a second set of nucleic acid primers; wherein the nucleotide sequences in the first set of nucleic acid primers are different from the nucleotide sequences in the second set of nucleic acid primers; wherein the nucleotide sequences of a first set of nucleic acid primers of a first discrete area and the nucleotide sequences of a first set of nucleic acid primers of a second discrete area differ substantially from each other; and wherein the nucleotide sequences of the second set of nucleic acid primers of a first discrete area and the nucleotide sequences of the second set of nucleic acid primers of a second discrete area are substantially the same or identical. See this disclosure above and below for a description of any of the elements in this process
  • compositions for producing two or more copies of nucleic acids of interest in a library comprising the steps of a) providing (i) an array of solid surfaces comprising a plurality of discrete areas; wherein at least two of the discrete areas each comprises: (1) a first set of nucleic acid primers; and (2) a second set of nucleic acid primers; wherein the nucleotide sequences in the first set of nucleic acid primers are different from the nucleotide sequences in the second set of nucleic acid primers; wherein the nucleotide sequences of a first set of nucleic acid primers of a first discrete area and the nucleotide sequences of a first set of nucleic acid primers of a second discrete area differ from each other by at least one base; and wherein the nucleotide sequences of the second set of nucleic acid primers of a first discrete area and the nucleotide sequences of the second set
  • Another related process useful for detecting or quantifying more than one nucleic acid of interest in a library comprises the steps of a) providing (i) an array of solid surfaces comprising a plurality of discrete areas; wherein at least two of such discrete areas each comprises: (1) a first set of nucleic acid primers; and (2) a second set of nucleic acid primers; wherein the nucleotide sequences in the first set of nucleic acid primers are different from the nucleotide sequences in the second set of nucleic acid primers; wherein the nucleotide sequences of a first set of nucleic acid primers of a first discrete area and the nucleotide sequences of a first set of nucleic acid primers of a second discrete area differ from each other by at least one base; and wherein the nucleotide sequences of the second set of nucleic acid primers of a first discrete area and the nucleotide sequences of the second set of nucleic acid primers of
  • the UPE's will be present on the array during hybridization of the analyte to complementary SPE's. However, there may be circumstances where the presence of UPE's in this step may be deleterious. For example, binding of the diverse nucleic acids of a library should preferably take place only through the action of the SPE's on the array. In contrast to the example given above, there may be cases where due either to the nature of the library or the choice of UPE sequences, hybridization can take place between the library and the UPE's of an array. This event could result in a loss of efficiency in the reaction by binding of target nucleic acids to inappropriate areas of the array.
  • the SPE's at a particular locus would be unable to use complementary nucleic acid targets as a template if these targets are inappropriately bound to another physical location through binding of UPE's,.
  • UPE's would be rendered non-functional by being extended and synthesizing nucleic acid copies that lack complementary to the SPE's at that particular locus.
  • UPE's may be either non-functional or absent during the initial hybridization of a library to the SPE's in the array.
  • advantage is taken of the universal nature of the UPE's.
  • each particular species of SPE is relegated to a specific area of the array, the UPE's are intended to be present in multiple areas of the array.
  • an array can be synthesized where each locus comprises a set of SPE's and a set of chemically activated sites that are compatible with reactive groups on UPE's.
  • the UPE's with appropriate groups can be added universally to the array by a simultaneous attachment to all of the active sites on the array.
  • An example of compatible modifications that could be used in this aspect of the present invention could be arrays that have maleimide groups at each locus and UPE's that have amine groups attached to their 5′ ends.
  • UPE's that have been modified such that they are temporarily unable to function.
  • the UPE's could be synthesized with 3′ PO 4 groups thereby blocking any potential extension reactions.
  • the nucleic acids used as templates could be removed from the reaction.
  • the 3′ end of the UPE's could be rendered functional by removal of the 3′ PO 4 groups by treatment with reagents such as bacteriophage polynucleotide kinase or alkaline phosphatase. Thereafter, successive reactions can take place as described previously.
  • Tm of hybridization between nucleic acids is a function of their length and base composition. Therefore, the SPE's and UPE's can be designed with Tm's that are sufficiently different that salt or temperature conditions can be used that selectively allow hybridization of the nucleic acids in the sample to SPE's. The salt and temperature conditions can be altered later to allow hybridization to the UPE's on the array and carry out the appropriate series of reactions.
  • the poly A RNA in the example shown in FIGS. 16 - 19 made use of an inherent UDE in eucaryotic mRNA.
  • UDEs can also be added artificially either by polymerization or ligation. For instance, a selected arbitrary sequence can be added to the 5′ ends of a library of RNA analytes by the action of T4 RNA ligase. An array could then be used that has SPE's for unique RNA sequences and UPE's with the same sequences as the ligated segment.
  • RNA template After localization of the various species of RNA to their appropriate location on an array, an enzyme appropriate for reverse transcription can be added as well as the appropriate buffers and reagents to extend the SPE's thereby synthesizing 1 st strand cDNA copies linked to the array. Removal of the RNA template would then allow the complement of the UPE in the cDNA copy to bind to a nearby UPE on the array followed by a set of reactions as described previously. Since the choice of sequences for artificially added UPE's is of arbitrary nature, this aspect of the present invention can be applied to a simultaneous assay of different pools of analytes by adding different discrete UPE sequences to each library.
  • FIG. 20 An illustration of an array that could be used for this purpose is given in FIG. 20 where two libraries are being compared. One library has been prepared by joining sequences for UPE 1 to the nucleic acids and a second library has been prepared that has sequences for UPE 2 joined to the nucleic acids. It should be noted that in FIG. 20, Locus 1 of the array has the same SPE's as Locus 9 but they differ in the identity of the UPE where UPE 1 is at Locus 1 and UPE 2 is at locus 9 . This is also true for Locus 2 compared to Locus 10 and so on. Thus, binding of the same sequence can take place at either Locus 1 or Locus 9 , but the extent of amplification that will take place at each locus will be dependent upon the amount of bound material that contains the appropriate UPE sequence.
  • DNA may also be the initial analyte.
  • DNA can be digested with a restriction enzyme to create a library of fragments.
  • a double-stranded UDE can then be ligated to these fragments by the action of T4 DNA ligase.
  • the ligated products can then be denatured and hybridized to an array of SPE's.
  • sets of SPE's can be designed that differ by a single nucleotide at their 3′ ends.
  • nucleic acids that are being analyzed can be treated such that sequences that are complementary to UPE's are removed.
  • nucleic acids can be treated with a 3′ to 5′ double-stranded Exonuclease. This should selectively remove sequences complementary to the UPE's while retaining sequences that are identical to sequences in the UPE's. Regeneration of the sequence complementary to the UPE should then take place only after extension of an SPE.
  • the use of artificial addition of UPE sequences allows the simultaneous analysis of different pools by a selective choice of different UPE sequences for each pool.
  • a general array can be made that offers complete representation of all possible sequences.
  • a library of SPE's that are 4 bases in length with permutations of all 4 variable bases would comprise 4 ⁇ 4 ⁇ 4 ⁇ 4 distinct sequences, i.e. a total of 256 permutations.
  • a complexity of all potential octamer oligonucleotides with the four variable bases there would be a total of 256 ⁇ 256 for a total of 65,536 permutations.
  • an array covering all the possible amplification products would require two unique primers for each individual amplification.
  • the present invention overcomes this limitation by virtue of the use of UPE's. Accordingly, only the SPE's need to encompass all the possible octamer sequences which results in a requirement for a total of 65,536 different sequences, a number that is easily within the ability of current technology. The number of different nucleic acid that will be amplified at each locus will depend upon the complexity of the library of nucleic acids applied as templates as well as the conditions used for carrying out amplification.
  • the degree of complexity of the array can also be altered by increasing or decreasing the number of nucleotides comprising the SPE's. Conversely, it has previously been pointed out that a degree of differentiation can be achieved by adding one or more discrete bases to the UPE. For example, the use of a single variable nucleotide at the end of a polyT UPE would decrease the complexity of the analytes in a library that could be amplified since on average, only one out of three of the various diverse nucleic acid analytes bound to SPE's would be able to carry out strand extension.
  • octomers that have Tm's that are much higher or lower than the average Tm of a random population may be not be desired to be present.
  • octamers that have self-complementary 3′ and 5′ ends may exhibit poor binding ability.
  • this aspect can be carried out with amplification carried out simultaneously with each UPE. More preferably, reactions are carried out in parallel with a given UPE on an array for each set of reactions.
  • a mixed phase amplification is carried out where SPE's at fixed locations on an array are used for 1 st strand synthesis. but the primers used for synthesis of 2 nd strands are not attached to the matrix of the array.
  • a pool of primers for 2 nd strands in solution can make use of normal nucleic acid kinetics to find 1 st strand templates fixed to distinct loci on an array for 2 nd strand priming events.
  • FIGS. 22 - 25 show an example of a series of binding and extension reactions with only the SPE's fixed to an array.
  • SPE-P1 is a primer fixed to Locus P that is complementary to the (+) strand of target P and P2 is a primer that is free in solution and is complementary to the ( ⁇ ) strand of target P.
  • SPE-Q1 is a primer fixed to Locus Q that is complementary to the (+) strand of target Q and Q2 is a primer that is free in solution and is complementary to the ( ⁇ ) strand of target Q.
  • the primers for synthesis of 2 nd strands could also be a carried out by a mixture of UPE's or they can even comprise a pool of or random primers.
  • This particular aspect of the present invention also finds use with general arrays that represent multitudes of variations of sequences. For instance, an array that is created by in situ synthesis as described by Affymatrix can be synthesized with some or all of the 65,536 permutations of an octamer array and then used in conjunction with UPE's in solution.
  • chimeric compositions are disclosed that are comprised of two segments, a nucleic acid portion and a non-nucleic portion.
  • the nucleic acid portion is used to achieve a practical and more accessible method for attaching the non-nucleic acid portion to a solid support.
  • the nucleic acid portion is directly bound to the surface of the array where it serves as a linker between the array surface and the non-nucleic acid portions of the chimeric compositions.
  • each chimeric composition at a locus should exhibit repulsive forces that should minimize interactions between the chimeric compositions.
  • nucleic acid portion of the chimeric composition comprises discrete sequences that allow binding of the chimeric composition to the array through hybridization to complementary sequences that are immobilized on the support.
  • the nucleic acid portion of a chimeric composition can be comprised of deoxynucleotides, ribonucleotides, modified nucleotides, nucleic acid analogues such as peptide nucleic acids (PNAs), or any combination thereof.
  • the sequence of the nucleic acid portion is of completely arbitrary nature and may be chosen by the user.
  • advantage is taken of the intrinsic properties of nucleic acid hybridization for the attachment of the non-nucleic acid portion to the solid surface used for the array.
  • the present invention allows the high specificity, tight binding and favorable kinetics that are characteristic of nucleic acid interactions to be conveyed to a non-nucleic acid portion that does not enjoy these properties.
  • the non-nucleic acid portion of the chimeric composition of the present invention can be comprised of peptides, proteins, ligands or any other compounds capable of binding or interacting with a corresponding binding partner.
  • Peptides and proteins can be comprised of amino acid sequences ranging in length from small peptides to large proteins. This peptides and proteins can also comprise modified amino acids or analogues of amino acids.
  • the amino acids or analogues can comprise any desirable sequence.
  • the amino acid sequences can be derived from enzymes, antibodies, antigens, epitopes of antigens, receptors and glycoproteins.
  • the sequences of the nucleic acid portion are of arbitrary nature and have no correspondence to the amino acid sequences of the peptides or proteins.
  • Other molecules besides peptides and proteins may also find use in the present invention.
  • Examples of other constituents that could be used for the non-nucleic acid portion can comprise but not be limited to ligands of MW of 2000 or less, substrates, hormones, drugs and any possible protein binding entity.
  • the particular sequence of the nucleic acid is determined by the user.
  • each individual species that is used as the non-nucleic acid portion can be covalently joined to a unique nucleic acid sequence.
  • Hybridization of a the nucleic acid portion of the chimeric composition to a complementary sequence at a particular locus on an array thereby determines the identity of the particular species of the non-nucleic acid portion that is now bound to that locus.
  • one hundred different chimeric compositions can be synthesized that each comprises a unique peptide and a unique nucleic acid sequence.
  • Hybridization can then be carried out with an array that has one hundred different loci, where each locus has nucleic acids complementary to one of the unique nucleic acid sequences. Hybridization thereby results in the localization of each unique peptide to one particular locus on the array, transforming a nucleic acid array into a peptide array.
  • a useful method for selection of sequences that could be used for the nucleic acid portion has been described by Hirschhorn et al., (op.cit.) hereby incorporated by reference.
  • a different set of one hundred chimeric compositions can be designed that have different species used for the non-nucleic acid portion but use the same set of one hundred sequences for the nucleic acid portion.
  • a generic nucleic acid array can be used to create different peptide arrays by changing the identities of the chimeric compositions.
  • non-nucleic acid protein binding substances can be attached to oligonucleotides which all comprise the same sequence.
  • chimeric compositions with various non-nucleic portions could be synthesized where the nucleic acid portion of each chimeric compositions comprised a common poly T sequence.
  • the matrix can be prepared so that the oligonucleotides at each site consist of complementary Poly A sequences.
  • the chimeric compositions can then be applied to the matrix using an addressable arraying system that has been described by Heller et al. in U.S. Pat. No. 5,605,662 (herein incorporated by reference). By these means, each particular chimeric composition can be applied individually to the matrix using an electronically controlled system and immobilized through hybridization to the appropriate site.
  • oligonucleotide sequence can be attached to several different species of non-nucleic acid portions. For example, a series of one hundred peptides can be placed on the array in only four different sites by making Pool 1 with twenty-five peptides conjugated to oligonucleotide 1, Pool 2 with twenty-five peptides conjugated to oligonucleotide 2, Pool 3 with twenty-five peptides conjugated to oligonucleotide 3 and Pool 4 with twenty-five peptides conjugated to oligonucleotide 4.
  • Attachment of the various pools of chimeric compositions to each locus can be carried out by having oligounucleotide 1, 2, 3 and 4 comprising unique sequences complementary to different oligonucleotides at each site or as described above, an addressable arraying system can be used to localize each pool using nucleic acid portions with identical sequences.
  • the chimeric compositions comprised of nucleic acid and non-nucleic acid portions can be synthesized using any method known to those skilled in the art. Methods that may find use with the present invention are described in a review by Tung, C.-H.;(2000 Bioconjugate Chemistry 11, 5, 605-618) and Engelhardt et al., U.S. Pat. No. 5,241,060, issued Aug.
  • the chimeric composition can be prepared by the stepwise addition of amino acids and nucleotides on the same solid support, (de la Torre et al., (1994) Tetrahedron Lett 35; 2733-2736,. Bergmann and Bannwarth (1995) Tetrahedron Lett. 36; 1839-1842, Robles et al., (1999) Tetrahedron 55; 13,251-13,264, Antopolsky et al., (1999) Helv. Chim Acta 82; 2130-2140).
  • the peptide was synthesized first followed by the addition of bases to synthesize the oligonucleotide portion.
  • the solid support can be any material used for arrays including, but not limited to nylon or cellulose membranes, glass, synthetic, plastic, metal.
  • the materials can be opaque, reflective, transparent or translucent. They can be porous or they can be non-porous. Nucleic acids that are either part of chimeric compositions or meant to be complementary to chimeric compositions can be affixed to the solid support by any previously known methods used to prepare DNA arrays.
  • Binding of analytes to appropriate binding partners can be carried out in either a mixed phase or a liquid phase format.
  • the present invention has disclosed the direct fixation of binding substances to the array by the use of rigid arm linkers and chimeric compositions.
  • the binding substance on the array (the solid phase) can be exposed to a solution (the liquid phase) that contains the analytes of interest. Interactions between the binding substance on the array and analytes in solution can then later be quantified.
  • Examples of the interactions that may find use in the present invention can comprise but not be limited to peptide-protein, antigen-antibody, ligand-receptor or enzyme-substrates.
  • an array can be prepared with a series of peptides to determine their ability to bind to a particular antibody.
  • the array is incubated in a solution containing the antibody followed by washing away the unbound material.
  • Detection of the antibody bound to various components on the array can then be carried out by any of a number of conventional techniques.
  • the antibody that is applied to the array can be labeled with biotin for indirect detection, or a fluorescent compound for direct detection.
  • the antibody analyte is unlabeled and a secondary antibody can be utilized which either has a fluorescent label for direct detection or indirect label such as biotin.
  • the antibody-antigen interaction occurs with the antigen bound to the solid matrix.
  • the present invention has also disclosed the use of chimeric compositions that are indirectly bound to the array through hybridization of the nucleic acid portions of the chimeric compositions to complementary nucleic acids fixed or immobilized to the array. These can be used in the in the same mixed phase format that has been described above by hybridization of the chimeric compositions to the array followed by binding of analytes. However, the use of hybridization to immobilize the chimeric compositions to specific loci on the array allows the use of a completely liquid phase format for binding of analytes to the chimeric compositions.
  • the chimeric compositions can be combined with the target molecules in solution under optimal conditions for interactions between the analyte and the non-nucleic acid portions of the chimeric compositions.
  • the resultant solution, containing the chimeric compositions free in solution as well as the chimeric compositions that are bound into complexes with the analytes, can then be applied to the matrix and the various chimeric compositions will be localized to various locations on the array through hybridization to the nucleic acid portion to complementary sequences on the array. An illustration of this process is given in FIG. 28.
  • the hybridization can be carried out under mild conditions, which will not interfere with the ligand-receptor or protein-protein complex.
  • Protein-protein interactions are generally characterized by low Km's, in the order of magnitude of 10 ⁇ 5 to 10 ⁇ 9 .
  • the protein interactions can occur in solution rather than on a solid surfaces which will allow superior kinetics of binding and will also allow a wider variety of conditions for protein binding than can be obtained in the mixed format.
  • chimeric compositions and analytes together in solution direct interaction or interference with the matrix is avoided, thereby decreasing the background. Therefore, to use the example cited before, the solution containing the antibody target is combined with a solution containing the chimeric composition.
  • the proteins will remain in solution throughout the process preventing any problems associated with dehydrating the protein bound to the solid matrix.
  • the method of the present invention can be used to study many systems that involve interactions between compound. These can include but not be limited to antigen-antibody relationships, protein-protein interactions, enzyme-substrate receptor-ligand interactions, ligand-receptor, hormone-receptor, carbohydrate-lectins, drug screening, and patterns of expression of proteins in a cell or tissue.
  • Another method of use of the present invention is that instead of using unique nucleic acid portions for each individual non-nucleic acid portion, one specific binding substance can be combined with various nucleic acid sources to form a group of chimeric compositions with a common non-nucleic acid portion and a unique nucleic acid portion.
  • Each particular chimeric composition can be combined with an analyte from a different source and applied to the array by hybridizing the nucleic acid portions to their complementary sequences on the array.
  • the proteins bound to the array can then be detected following standard procedures.
  • a set of twenty different compositions can be synthesized where each member of the set will have a different nucleic acid portion but the same peptide. Another set can be made with a different peptide that is linked to twenty other nucleic acid portions. More sets can be made on the same basis. Protein extracts can then be made from twenty different tissues and each extract can be combined with a different member of the set of chimeric compositions.
  • the nucleic acid portion serves as a marker for not only the peptide but also for the particular tissue that was used as the source.
  • a group of sets can be made with peptides that have affinities for different receptors.
  • the mixtures After incubation of the mixtures with the chimeric compounds, the mixtures are applied to the array and detected. In this way, each particular receptor that is being studied can be quantified and compared simultaneously between various tissues.
  • the same nucleic acid sequence can be used in common for each source by using the addressable system described previously, and carrying out hybridization to each locus after addition of each individual reaction mixture.
  • the same method can be applied to tissues or cell cultures that are from the same source but are treated differently.
  • nine different drugs can be added to individual cell cultures to determine the effect on specific proteins.
  • Chimeric compositions are designed and synthesized with peptides that are known to react with each of proteins that is to be monitored.
  • a specific nucleic acid sequence will serve as a marker for each peptide and each particular treatment.
  • the proteins are extracted from each of the ten cell cultures (nine drug treated plus an untreated control) and incubated with the chimeric compositions.
  • the mixtures are applied to the array and the amount of analyte bound to the corresponding peptides at each locus of the array is measured for the various drug conditions.
  • the present invention can also be used for the isolation of analytes. This can be carried out by either disrupting the interaction between the analyte and the non-nucleic acid portion of the chimeric compositions or by denaturing the nucleic acid portion from the complementary sequence fixed or immobilized to the array. It is also contemplated that removal of chimeric compositions from the array may also allow the reuse of the array in other experiments.
  • this invention provides novel chimeric compositions and processes using such chimeric compositions.
  • One such composition of matter comprises an array of solid surfaces comprising a plurality of discrete areas, wherein at least two of such discrete areas comprise: a chimeric composition comprising a nucleic acid portion; and a non-nucleic acid portion, wherein the nucleic acid portion of a first discrete area has the same sequence as the nucleic acid portion of a second discrete area, and wherein the non-nucleic acid portion has a binding affinity for analytes of interest.
  • composition of matter comprises an array of solid surfaces comprising a plurality of discrete areas; wherein at least two of the discrete areas comprise a chimeric composition hybridized to complementary sequences of nucleic acids fixed or immobilized to the discrete areas, wherein the chimeric composition comprises a nucleic acid portion, and a non-nucleic acid portion, the nucleic acid portion comprising at least one sequence, wherein the non-nucleic acid portion has a binding affinity for analytes of interest, and wherein when the non-nucleic acid portion is a peptide or protein, the nucleic acid portion does not comprises sequences which are either identical or complementary to sequences that code for such peptide or protein.
  • a process for detecting or quantifying analytes of interest comprising the steps of 1) providing a) an array of solid surfaces comprising a plurality of discrete areas, wherein at least two of such discrete areas comprise a chimeric composition comprising a nucleic acid portion, and a non-nucleic acid portion; wherein the nucleic acid portion of a first discrete area has the same sequence as the nucleic acid portion of a second discrete area; and wherein the non-nucleic acid portion has a binding affinity for analytes of interest; b) a sample containing or suspected of containing one or more of the analytes of interest; and c) signal generating means; 2) contacting the array a) with the sample b) under conditions permissive of binding the analytes to the non-nucleic acid portion; 3) contacting the bound analytes with the signal generating means; and 4) detecting or quantifying the presence of the analy
  • Another process for detecting or quantifying analytes of interest comprises the steps of 1) providing a) an array of solid surfaces comprising a plurality of discrete areas; wherein at least two of such discrete areas comprise a chimeric composition comprising a nucleic acid portion; and a non-nucleic acid portion; wherein the nucleic acid portion of a first discrete area has the same sequence as the nucleic acid portion of a second discrete area; and wherein the non-nucleic acid portion has a binding affinity for analytes of interest; b) a sample containing or suspected of containing one or more of the analytes of interest; and c) signal generating means; 2) labeling the analytes of interest with the signal generating means; 3) contacting the array a) with the labeled analytes under conditions permissive of binding the labeled analytes to the non-nucleic acid portion; and 4) detecting or quantifying the presence of the analytes.
  • Another process for detecting or quantifying analytes of interest comprises the steps of 1) providing a) an array of solid surfaces comprising a plurality of discrete areas; wherein at least two of such discrete areas comprise nucleic acids fixed or immobilized to such discrete areas, b) chimeric compositions comprising: i) a nucleic acid portion; and ii) a non-nucleic acid portion; the nucleic acid portion comprising at least one sequence, wherein the non-nucleic acid portion has a binding affinity for analytes of interest, and wherein when the non-nucleic acid portion is a peptide or protein, the nucleic acid portion does not comprise sequences which are either identical or complementary to sequences that code for the peptide or protein; c) a sample containing or suspected of containing the analytes of interest; and d) signal generating means; 2) contacting the array with the chimeric compositions to hybridize the nucleic acid portions of the chimeric compositions to
  • Another process for detecting or quantifying analytes of interest comprises the steps of 1) providing a) an array of solid surfaces comprising a plurality of discrete areas; wherein at least two of the discrete areas comprise nucleic acids fixed or immobilized to the discrete areas, b) chimeric compositions comprising i) a nucleic acid portion; and ii) a non-nucleic acid portion, the nucleic acid portion comprising at least one sequence, wherein the non-nucleic acid portion has a binding affinity for analytes of interest, and wherein when the non-nucleic acid portion is a peptide or protein, the nucleic acid portion does not comprise sequences which are either identical or complementary to sequences that code for the peptide or protein; c) a sample containing or suspected of containing the analytes of interest; and d) signal generating means; 2) contacting the chimeric compositions with the sample b) under conditions permissive of binding the analytes to the non
  • Another useful process comprises the steps of 1) providing a) an array of solid surfaces comprising a plurality of discrete areas; wherein at least two of the discrete areas comprise nucleic acids fixed or immobilized to the discrete areas, b) chimeric compositions comprising i) a nucleic acid portion; and ii) a non-nucleic acid portion; the nucleic acid portion comprising at least one sequence, wherein the non-nucleic acid portion has a binding affinity for analytes of interest, and wherein when the non-nucleic acid portion is a peptide or protein, the nucleic acid portion does not comprise sequences which are either identical or complementary to sequences that code for the peptide or protein; c) a sample containing or suspected of containing the analytes of interest; and d) signal generating means; 2) contacting the array with the chimeric compositions to hybridize the nucleic acid portions of the chimeric compositions to complementary nucleic acids fixed or immobilized to the
  • Another process for detecting or quantifying analytes of interest comprises the steps of 1) providing a) an array of solid surfaces comprising a plurality of discrete areas; wherein at least two of the discrete areas comprise nucleic acids fixed or immobilized to the discrete areas, b) chimeric compositions comprising: i) a nucleic acid portion; and ii) a non-nucleic acid portion; the nucleic acid portion comprising at least one sequence, wherein the non-nucleic acid portion has a binding affinity for analytes of interest, and wherein when the non-nucleic acid portion is a peptide or protein, such nucleic acid portion does not comprise sequences which are either identical or complementary to sequences that code for the peptide or protein; c) a sample containing or suspected of containing the analytes of interest; and d) signal generating means; 2) contacting the array with the chimeric compositions to hybridize the nucleic acid portions of the chimeric compositions to
  • TPR primers consist of a T7 promoter sequence at their 5′ ends and 9 nucleotides with random sequences at their 3′ ends. 400 pmoles of TPR primers and other appropriate reagents were added for a final reaction mix of 30 ul containing 86.6 mM Tris-HCl (pH 7.6), 32 mM KCl, 200 mM KOAc (??), 15.6 mM MgCl 2 , 3.3 mM DTT, 10 mM Dithioerythritol (DTE), 10 mM (NH 4 ) 2 SO 4 , 0.15 mM ⁇ NAD, 200 ug/ml nuclease-free BSA (Bayer, Kankakee, Ill.), Annealing was carried out by heating the mixture to 65° C.
  • Transcription was carried out by using the BioArray High Yield Transcription Kit (T7) (ENZO Diagnostics, Farmingdale, N.Y.) following the manufacturers instructions with a final volume of 40 ul.
  • the reaction mixes also contained 10 uCi of 3 H-ATP with a specific activity of 45 Ci/mMol (Amersham Pharmacia, Piscataway, N.J.).
  • Incorporation was measured by addition of 5 ul of the transcription reaction to 1 ml of 10% TCA, 50 ug/ml Poly A, 5 mM EDTA followed by incubation on ice for 30 minutes. Precipitates were collected on 25 mm glass fiber filters (Whatman, Lifton, N.J.) followed by three washes with 5% TCA and three washes with ethanol
  • RNA transcripts were obtained from a library of nucleic acids by the steps described above and that under the conditions used, the Exo ( ⁇ ) version of Klenow resulted in more product compared to the use of DNA polymerase 1.
  • RNA targets were prepared by diluting I ug of mouse poly A RNA (Sigma Chemical Co, St. Louis, Mo.) or 1 ug of wheat germ tRNA (Sigma Chemical Co, St. Louis, Mo.) into RNase-free H 2 O (Ambion, Austin, Tex.) for a final volume of 50 ul, and heating the RNA solution at 65° C. for 5 minutes.
  • the RNA solution was combined with the beads prepared in Step 1 and mixed for 15 minutes at room temperature with a Dynal Sample Mixer (Dynal Inc., Lake Success, N.Y.). Unbound material was removed by magnetic separation with a Dynal Magnetic Particle Concentrator (Dynal, Inc.
  • Wash Buffer B 10 mM Tris-HCl (pH 7.5), 150 mM LiCl, 1 mM EDTA) and three washes with 250 ul of First Strand Buffer (50 mM Tris-HCl (pH 8.3), 75 mM KCl, 3 mM MgCl 2 )
  • the beads from Step 2 were resuspended in 50 mM Tris-HCl (pH 8.3), 75 mM KCl, 3 mM MgCl 2 , 10 mM DTT, 500 uM dNTPs and 400 units of Super Script II RNase H ⁇ Reverse Transcriptase (Life Technologies, Rockville, Md.) and incubated for 90 minutes at 42° C.
  • RNA templates were removed by heating the First Strand Synthesis reaction mixture of step 3 at 90° C. for 5 minutes followed by removal of the supernatant after magnetic separation.
  • the beads were washed two times with 100 ul of Buffer C (70 mM Tris-HCl (ph 6.9) 90 mM KCl, 14.6 mM MgCl 2 , 10 mM DTE, 10 mM (NH 4 ) 2 SO4 and 200 ug/ml nuclease-free BSA) and resuspended in 50 ul of Random Priming Mix A (86.7 mM Tris-HCl (pH 7.6), 113.3 mM KCl, 17 mM MgCl 2 , 11.3 mM DTT, 11.3 mM (NH 4 ) 2 SO 4 , 227 ug/mi nuclease-free BSA) containing 360 pmoles of TPR primers.
  • Buffer C 70 mM Tris-HCl (ph 6.9) 90
  • Transcription reactions were carried out by resuspending the beads in reagents from the BioArray High Yield Transcription Kit (T7) (ENZO Diagnostics, Farmingdale, N.Y.) using the manufacturer's instructions with a final volume of 40 ul.
  • the reaction mixtures also contained 10 uCi of 3 H-ATP with a specific activity of 45 Ci/mMol (Amersham Pharmacia, Piscataway, N.J.). Extent of transcription was measured by using TCA precipitation as described previously.
  • transcripts were obtained from a library of nucleic acids by the steps described above. Addition of extra beads can increase the amount of synthesis. The reaction can be carried out without a T4 DNA polymerization step but the amount of synthesis can be increased by the addition of such a reagent.
  • RNA targets were prepared by diluting I ug of mouse poly A mRNA (Sigma Chemical Co, St. Louis, Mo.) into nuclease-free H 2 O (Ambion Inc., Auistin Tex.) for a final volume of 50 ul , and heating the RNA solution at 65° C. for 15 minutes. The RNA solution was combined with the beads prepared in Step 1 and mixed for 15 minutes at Room Temperature with a Dynal Sample Mixer (Dynal Inc., Lake Success, N.Y.). Unbound material was removed by magnetic separation followed by two washes with 200 ul of Wash Buffer B and two washes with 100 ul of First Strand Buffer.
  • a Dynal Sample Mixer Dynal Sample Mixer
  • RNA templates were removed by heating the First Strand Synthesis reaction mixture of step 3 at 90° C. for 4 minutes followed by removal of the supernatant after magnetic separation.
  • the beads were washed two times with 100 ul of Wash Buffer B and resuspended in 50 ul of Random Priming Mix A containing 360 pmoles of TPR primers. Primers were allowed to anneal on ice for 15 minutes. Unbound primers were removed by magnetic separation and the beads were washed twice with 100 ul of cold Buffer D (20 mM Tris-HCl (pH 6.9), 90 mM KCl, 4.6 mM MgCl 2 , 10 mM (NH 4 ) 2 SO 4 .
  • the beads were then suspended in 40 ul of Buffer C that also contained 1 mM dNTPs and 10 units of the Klenow fragment of DNA Polymerase I (New England Biolabs, Beverly, Mass.). Incubation was carried out for 5 minutes at 4° C., 30 minutes at 15° C., and 30 minutes at 37° C. The reaction was carried out further by the addition of 2 ul (6 units) of T4 DNA Polymerase (New England Biolabs, Beverly, Mass.) and 2 ul of a 10 mM stock of dNTPs, followed by incubation for 30 minutes at 37° C.
  • Buffer C that also contained 1 mM dNTPs and 10 units of the Klenow fragment of DNA Polymerase I (New England Biolabs, Beverly, Mass.). Incubation was carried out for 5 minutes at 4° C., 30 minutes at 15° C., and 30 minutes at 37° C. The reaction was carried out further by the addition of 2 ul (6 units) of T4 DNA Polymerase (New England Biolabs, Beverly
  • the beads were washed two times with 100 ul of Wash Buffer B and once with 100 ul of 10 mM Tris-HCl (pH 7.5).
  • the beads were resuspended in 10 ul of 10 mM Tris-HCl (pH 7.5) and mixed with reagents from a BioArray High Yield Transcription Kit (T7) (ENZO Diagnostics, Farmingdale, N.Y.) using the manufacturer's instructions.
  • T7 BioArray High Yield Transcription Kit
  • the volume of the reaction was 30 ul and the incubation was carried out for 2 hours at 37° C.
  • Steps 1, 2 and 3 for Preparation of beads, binding of mRNA and 1 st strand synthesis were carried out as described in steps 1 through 3 of Example 3.
  • the beads were washed two times with 100 ul of Wash Buffer B and resuspended in 50 ul of Random Priming Mix A containing 360 pmoles of TPR primers. Primers were allowed to anneal on ice for 15 minutes. Unbound primers were removed by magnetic separation and the beads were washed twice with 100 ul of cold Buffer D (20 mM Tris-HCl (pH 6.9), 90 mM KCl, 4.6 mM MgCl 2 , 10 mM DTT, 10 mM (NH 4 ) 2 SO4).
  • the beads were then suspended in 40 ul of Buffer C that also contained 1 mM dNTPs and 10 units of the Klenow fragment of DNA Polymerase I (New England Biolabs, Beverly, Mass.). Incubation was carried out for 5 minutes at 4° C., 30 minutes at 15° C., and 30 minutes at 37° C. The reaction was carried out further by the addition of 2 ul (6 units) of T4 DNA Polymerase (New England Biolabs, Beverly, Mass.) and 2 ul of a 10 mM stock of dNTPs, followed by incubation for 30 minutes at 37° C.
  • Buffer C that also contained 1 mM dNTPs and 10 units of the Klenow fragment of DNA Polymerase I (New England Biolabs, Beverly, Mass.). Incubation was carried out for 5 minutes at 4° C., 30 minutes at 15° C., and 30 minutes at 37° C. The reaction was carried out further by the addition of 2 ul (6 units) of T4 DNA Polymerase (New England Biolabs, Beverly
  • the beads were then washed two times with 100 ul of Wash Buffer B, resuspended in 50 ul of 10 mM Tris-HCl (pH 7.5) and heated at 90° C. for 5 minutes. The supernatant was removed after magnetic separation and store as supernatant No.1. The beads were then washed once with 100 ul of Detergent Wash No.2, two times with 100 ul of Wash Buffer B and resuspended in 50 ul of Random Priming Mix A containing 360 pmoles of TPR primers. Primer annealing and extension was carried out as described above.
  • the beads were then washed two times with 100 ul of Wash Buffer B, resuspended in 50 ul of 10 mM Tris-HCl (pH 7.5) and heated at 90° C. for 5 minutes. The supernatant was removed after magnetic separation and store as supernatant No.2. The series of washes, annealing and extension steps were carried out again using the steps described above. The beads were then washed two times with 100 ul of Wash Buffer B, resuspended in 50 ul of 10 mM Tris-HCl (pH 7.5) and heated at for 5 minutes. The supernatant was removed after magnetic separation and stored as supernatant No.3.
  • a pool was created by combining supernatant No.1, supernatant No.2 and supernatant No.3.
  • This pool comprises a library of 2 nd strands free in solution with T7 promoters at their 5 ′ ends and poly A segments at their 3′ ends.
  • Fresh magnetic beads with poly T tails were prepared and annealed to the pool of 2 nd strands by the same processes described in Steps 1 and 2 of Example 2.
  • Extension was then carried out by resuspension of beads in 50 ul of Buffer C that also contained 1 mM dNTPs and 10 units of the Klenow fragment of DNA Polymerase I (New England Biolabs, Beverly, Mass.). Incubation was carried out at 37° C. for 90 minutes. Transcription was then carried out as described in step 5 of Example 3 except the reaction volume was reduced to 20 ul.
  • transcripts were obtained from a library of polyA mRNA by the steps described above.
  • This example demonstrated that a library of 2 nd strands was obtained after multiple rounds of 2 nd strand synthesis, isolated free in solution and then used to create functionally active production centers
  • the library of transcription constructs described in Example 4 were used for a second round of transcription. After removal of transcription products for analysis in Example 4, the beads were resuspended in 100 ul of 10 mM Tris-HCl (pH 7.5) and left overnight at 4° C. The next day, the beads were washed with 100 ul of Detergent Wash No.2, resuspended in 100 ul of Detergent Wash No.1 and heated at 42° C. for 5 minutes followed by two washes with 100 ul of Detergent Buffer No.2, two washes with 100 ul of Wash Buffer B and two washes with 100 ul of 10 mM Tris-HCl (pH 7.5). A transcription reaction was set up as described previously with a 20 ul volume.
  • Results of the transcription reaction are shown in FIG. 29 and show that the nucleic acids synthesized in Example 4 were stable and could be used for additional transcription synthesis.
  • RNA targets were prepared by diluting 3 ul of 0.5 ug/ul mouse poly A RNA (Sigma Chemical Co, St. Louis, Mo.) with 32 ul of RNase-free H 2 O (Ambion, Austin, Tex.) and 40 ul of Binding Buffer, and heating the RNA solution at 65° C. for 5 minutes. The RNA solution was combined with the beads prepared in Step 1 and mixed for 30 minutes at room temperature.
  • Unbound material was removed by magnetic separation followed by two washes with 200 ul of Wash Buffer B and one wash with 100 ul of First Strand Buffer.
  • the beads were resuspended in a 50 ul mixture of 50 mM Tris-HCl (pH 7.5), 75 mM KCl, 3 mM MgCl 2 , 10 mM DTT, 500 uM dNTPs and 400 units of Super Script II RNase H ⁇ Reverse Transcriptase (Life Technologies, Rockville, Md.) and incubated for 90 minutes at 42° C.
  • the liquid phase was removed by magnetic separation and the beads resuspended in 100 ul of Detergent Wash No.1 and heated at 90° C. for 5 minutes. The supernatant was removed by magnetic separation and the beads were washed with 100 ul of Detergent Wash No.2, two times with 100 ul of Wash Buffer B and resuspended in 300 ul of 10 mM Tris-HCl (pH 7.5).
  • T7-C9 primers Two methods were used for carrying out second strand synthesis.
  • the first method was as described for the previous examples, I.e the use of TPR primers that have a T7 promoter on their 5′ ends and random sequences at their 3′ ends.
  • the second method was the use of T7-C9 primers that have a T7 promoter at their 5′ ends and a poly C segment at their 3′ ends.
  • the sequence of the T7-C9 primers is as follows:
  • the product of Step 3 was divided into two portions.
  • the first portion (Sample No.1) consisted of 100 ul and was set aside to be used for random priming.
  • the second portion (the remaining 200 ul) was processed further by magnetically separating the buffer from the beads and resuspending the beads in 100 ul and adding 100 ul of Poly A Mix (1.6 ug/ul Poly A, 10 mM Tris-HCL (pH 7.5), 0.5 M LiCl, 1 mM EDTA).
  • the Poly A was obtained from (Amersham Pharmacia, Piscataway, N.J.) and had an average length of 350 nucleotides.
  • the beads and Poly A were mixed together for 30 minutes at room temperature with a Dynal Sample Mixer (Dynal Inc., Lake Success, N.Y.). The beads were washed two times with Wash Buffer B and resuspended in 200 ul of 10 m Tris-HCl (pH 7.5 ). This was divided into two 100 ul portions, Sample No.2 and Sample No.3. Sample No.3 was processed further by magnetically separating the buffer from the beads and resuspending the beads in an 80 ul reaction mixture using reagents and directions from the 3′ Oligonucleotide Tailing System (ENZO Biochem, Farmingdale, N.Y. 11561) with 0.5 mM dGTP present.
  • a Dynal Sample Mixer Dynal Sample Mixer
  • the beads were washed two times with Wash Buffer B and resuspended in 200 ul of 10 m Tris-HCl (pH 7.5 ). This was divided into two 100 ul portions, Sample No.2 and Sample No.
  • Sample No.3 was incubated for one hour at 37° C. followed by removal of the reagents by magnetic separation. The beads were then resuspended in 100 ul of Detergent Buffer No.1 and heated at 90° C. for 3 minutes. The beads were then washed once with 100 ul of Detergent Wash No.2 and twice with 100 ul of Wash Buffer B. Sample No. 3 was resuspended in 100 ul of 10 mM Tris-HCl (pH 7.5).
  • Example No.1 Sample No.2 and Sample No.3 were washed once with 100 ul Wash Buffer E (100 mM Tris-HCl pH7.4) 20 mM KCl, 10 mM MgCl 2 , 300 mM (NH4)2S04) and then resuspended in 50 ul of Buffer E.
  • Primers for 2 nd strand synthesis were added to each sample: 4 ul of 100 pMole/ul of TPR primers to Sample No.1 and 4 ul of 10 pMole/ul of T7-C9 primers to Samples No.2 and No.3.
  • Example 6 The transcription products of Example 6 were analyzed by gel electrophoresis as shown in FIG. 30. To obtain numerical evaluation of the method described in that example, the libraries attached to the beads in Samples No.1, No.2 and No.3 were used in another transcription reaction using 3 H-incorporation. Transcription was carried out as described in Example 3.
  • Poly dG addition was carried out as described for sample No. 3 in Example 6.
  • Second strand synthesis was performed as described in Example 6 except that 80 pMoles of primers were used in 100 ul reactions.
  • the 2nd strand primers were the T7-C9 primers previously described.
  • the 2nd strand primers were C9 primers with the sequence: 5′-CCCCCCC-3′.
  • all samples were washed twice with 100 ul 10 mM Tris-HCl (pH 7.5).
  • Samples No.2, No.3 and No.4 were processed further by resuspension of the beads in 26 ul of 10 mM Tris-HCl (pH 7.5) and heating at 90° C. for 3 minutes.
  • the second strands released by this process were isolated apart from the beads by magnetic separation and mixed with 40 pMoles of 3 rd strand primers for a final volume of 30 ul.
  • the 3 rd strand primers were T7-T 25 primers with the sequence
  • Reactions were stopped by the addition of EDTA (pH 8.0) to a final concentration of 10 mM.
  • the DNA from Samples 2, No.3 and No.4 was then purified by adjusting the volumes to 150 ul by adding appropriate amounts of 10 mM Tris-HCl. Reactions were mixed with an equal volume of Phenol:chloroform:isoamyl alcohol (25:24:1) and transferred to 2 ml Phase Lock Gel Heavy tubes(Eppendorf, Westbury, N.Y.). Tubes were vorteed for 1-2 minutes and centrifuged for 10 minutes at 16,000 rpm in a microfuge. The aquaeous phase was then transferred to another tube and DNA precipitated with Ethanol and Ammonium Acetate.
  • This example demonstrated that a promoter can be introduced during 3 rd strand synthesis to create functional production centers.
  • a T3 promoter was also functional in the present method.
  • different production centers could be introduced into each end of a construct (Sample No.2) and both production centers were functional.
  • Sample No.1 consisted of 1 ⁇ Taq PCR Buffer (Epicentre, Madison, Wis.), 3 m M MgCl 2 , 1 ⁇ PCR Enhancer (Epicentre, Madison, Wis.), 0.4 mM dNTPs, 40 pMoles C9 primers and 5 units of Master AmpTM Taq DNA Polymerase (Epicentre, Madison, Wis.); Sample No.2 was the same as sample No.1 except 100 pMoles of C9 primers were used; Sample No.3 consisted of 1 ⁇ Tth PCR Buffer (Epicentre, Madison, Wis.), 3 mM MgCl 2 , 1 ⁇ PCR Enhancer (Epicentre, Madison, Wis.), 0.4 mM dNTPs, 40 pM
  • thermostable polymerases could be used for 2 nd strand synthesis in the methods described above.
  • This example also demonstrated that by increasing the amount of primers and the number of cycles the amount of RNA copies derived from the original library of nucleic acids was increased.
  • Second strand synthesis was carried out as described for Sample No.3 in Example 8. Separation and isolation of the 2 nd strand products was carried out as described in Example 8 and set aside as Sample No.1. Fresh reagents were then added to the beads and another round of 2 nd strand synthesis was carried out. The products of this second reaction were separated from the beads and designated Sample No.2. The beads were then used once more for a third round of synthesis. The products of this reaction were set aside as Sample No.3.
  • Samples No.1, No.2 and No.3 were used as templates for 3 rd strand synthesis in individual reactions with the reagents and condition previously described in Example 8.
  • the starting material in the present example was twice the amount used in example 8 and as such the amounts of all reagents were doubled for this reaction as well.
  • 80 pMoles of T7-T 25 primers were used. Purification of the products from each reaction was carried out as described in Example 8.
  • Transcription reactions were carried out as with the BioArray High Yield Transcription Kit (T7) (ENZO Diagnostics, N.Y.). The DNA was used in a 20 ul final reaction volume which was incubated for 2 hours at 37° C. Gel analysis was then used to evaluate the amount of synthesis that was a result of each round of 2 nd strand synthesis described above. For purposes of contrast, various amounts of the transcription reaction (4 ul and 10 ul) were analyzed and in addition equvalent amounts of the DNA template that were not used in transcription reactions were also included. The results of this are shown in FIG. 32.
  • FIG. 32 also shows the contrast between the amount of transcript and the original DNA templates used for this synthesis thereby demonstrating the high levels of synthesis from each template.

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CA2841397A CA2841397C (en) 2001-06-30 2002-06-10 Novel compositions and processes for improved analyte detection using hybridization assays
CA2714119A CA2714119C (en) 2001-06-30 2002-06-10 Novel compositions and processes for improved analyte detection using hybridization assays
CA2390141A CA2390141C (en) 2001-06-30 2002-06-10 Novel compositions and processes for improved analyte detection using hybridization assays
IL210626A IL210626A (en) 2001-06-30 2002-06-13 Processes for analyte detection
IL210621A IL210621A (en) 2001-06-30 2002-06-13 Compositions for analyte detection
IL210636A IL210636A (en) 2001-06-30 2002-06-13 Compositions and processes for analyte detection
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EP10182833.3A EP2361992B1 (en) 2001-06-30 2002-07-01 Processes for analyte detection; quantification and amplification
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EP02014087.7A EP1275737B1 (en) 2001-06-30 2002-07-01 Process for mRNA detection or quantification
JP2002192771A JP2003088390A (ja) 2001-06-30 2002-07-01 分析物の検出、定量及び増幅のための新規な組成物および方法
US10/693,481 US20060057583A1 (en) 2001-06-30 2003-10-24 Novel compositions and methods for controlling the extendability of various components used in copying or amplification steps
US10/900,452 US20050233343A1 (en) 2001-06-30 2004-07-27 Composition of matter comprising library of analytes hybridized to nucleic acid array for generating complex formation and signaling domains
US10/900,455 US9790621B2 (en) 2001-06-30 2004-07-27 Composition of matter comprising library of first nucleic acid analyte copies
US10/900,453 US9309563B2 (en) 2001-06-30 2004-07-27 Compositions and processes for analyte detection, quantification and amplification
US10/900,009 US20070196828A1 (en) 2001-06-30 2004-07-27 Process for detecting or quantifying more than one nucleic acid in library via terminal attachment of non-inherent universal detection targets to nucleic acid copies produced thereby
US10/900,454 US9234234B2 (en) 2001-06-30 2004-07-27 Detection and quantification process for more than one nucleic acid in library
US10/900,451 US8557522B2 (en) 2001-06-30 2004-07-27 Processes for detecting or quantifying more than one nucleic acid in library
US10/902,640 US9279147B2 (en) 2001-06-30 2004-07-29 Processes for detecting or quantifying analytes of interest
US10/902,567 US8597888B2 (en) 2001-06-30 2004-07-29 Processes for detecting or quantifying more than one nucleic acid in a library
US10/902,564 US9163280B2 (en) 2001-06-30 2004-07-29 Process for detecting or quantifying nucleic acids in a library
US10/902,587 US9057100B2 (en) 2001-06-30 2004-07-29 Composition comprising array of nucleic acid primer sets
US10/902,682 US9428797B2 (en) 2001-06-30 2004-07-29 Nucleic acid detecting or quantifying processes
US10/902,629 US7807352B2 (en) 2001-06-30 2004-07-29 Process for producing two or more copies of nucleic acids in a library, and process for detecting or quantifiying more than one nucleic acid in a library
US10/902,597 US9434984B2 (en) 2001-06-30 2004-07-29 Composition comprising an array which further comprises chimeric compositions
US10/902,641 US9234235B2 (en) 2001-06-30 2004-07-29 Processes for detecting or quantifying nucleic acids using an array of fixed or immobilized nucleic acids
US10/902,586 US9487821B2 (en) 2001-06-30 2004-07-29 Composition comprising library of double stranded nucleic acids
US11/403,117 US20060257906A1 (en) 2001-06-30 2006-04-12 Compositions comprising a library of analytes for detection, quantification and analyses
US11/444,151 US9777312B2 (en) 2001-06-30 2006-05-31 Dual polarity analysis of nucleic acids
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US14/812,449 US9777406B2 (en) 2001-06-30 2015-07-29 Process for detecting or quantifying nucleic acids in a library
US14/812,254 US9637778B2 (en) 2001-06-30 2015-07-29 Processes for detecting or quantifying nucleic acids using an array of fixed or immobilized nucleic acids
US14/812,388 US9745619B2 (en) 2001-06-30 2015-07-29 Process for detecting or quantifying nucleic acids in a library
US14/812,487 US9765387B2 (en) 2001-06-30 2015-07-29 Process for detecting or quantifying nucleic acids in a library
US14/812,332 US9650666B2 (en) 2001-06-30 2015-07-29 Processes for detecting or quantifying nucleic acids using an array of fixed or immobilized nucleic acids
US14/812,293 US9617584B2 (en) 2001-06-30 2015-07-29 Processes for detecting or quantifying nucleic acids using an array of fixed or immobilized nucleic acids
US14/849,993 US9873956B2 (en) 2001-06-30 2015-09-10 Compositions and processes for analyte detection, quantification and amplification
US15/075,495 US9611508B2 (en) 2001-06-30 2016-03-21 Processes for detecting or quantifying nucleic acids in a library
US15/076,063 US9617585B2 (en) 2001-06-30 2016-03-21 Processes for detecting or quantifying more than one nucleic acid in a library
US15/285,749 US9771667B2 (en) 2001-06-30 2016-10-05 Arrays comprising chimeric compositions
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US10/900,453 Division US9309563B2 (en) 2001-06-30 2004-07-27 Compositions and processes for analyte detection, quantification and amplification
US10/900,455 Division US9790621B2 (en) 2001-06-30 2004-07-27 Composition of matter comprising library of first nucleic acid analyte copies
US10/900,009 Division US20070196828A1 (en) 2001-06-30 2004-07-27 Process for detecting or quantifying more than one nucleic acid in library via terminal attachment of non-inherent universal detection targets to nucleic acid copies produced thereby
US10/900,454 Division US9234234B2 (en) 2001-06-30 2004-07-27 Detection and quantification process for more than one nucleic acid in library
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US10/902,597 Division US9434984B2 (en) 2001-06-30 2004-07-29 Composition comprising an array which further comprises chimeric compositions
US10/902,629 Division US7807352B2 (en) 2001-06-30 2004-07-29 Process for producing two or more copies of nucleic acids in a library, and process for detecting or quantifiying more than one nucleic acid in a library
US10/902,586 Division US9487821B2 (en) 2001-06-30 2004-07-29 Composition comprising library of double stranded nucleic acids
US10/902,587 Division US9057100B2 (en) 2001-06-30 2004-07-29 Composition comprising array of nucleic acid primer sets
US10/902,641 Division US9234235B2 (en) 2001-06-30 2004-07-29 Processes for detecting or quantifying nucleic acids using an array of fixed or immobilized nucleic acids
US10/902,564 Division US9163280B2 (en) 2001-06-30 2004-07-29 Process for detecting or quantifying nucleic acids in a library
US10/902,682 Division US9428797B2 (en) 2001-06-30 2004-07-29 Nucleic acid detecting or quantifying processes
US10/902,640 Division US9279147B2 (en) 2001-06-30 2004-07-29 Processes for detecting or quantifying analytes of interest
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US11/403,117 Continuation US20060257906A1 (en) 2001-06-30 2006-04-12 Compositions comprising a library of analytes for detection, quantification and analyses
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US09/896,897 Abandoned US20040161741A1 (en) 2001-06-30 2001-06-30 Novel compositions and processes for analyte detection, quantification and amplification
US10/693,481 Abandoned US20060057583A1 (en) 2001-06-30 2003-10-24 Novel compositions and methods for controlling the extendability of various components used in copying or amplification steps
US10/900,453 Active 2026-10-22 US9309563B2 (en) 2001-06-30 2004-07-27 Compositions and processes for analyte detection, quantification and amplification
US10/900,454 Expired - Lifetime US9234234B2 (en) 2001-06-30 2004-07-27 Detection and quantification process for more than one nucleic acid in library
US10/900,452 Abandoned US20050233343A1 (en) 2001-06-30 2004-07-27 Composition of matter comprising library of analytes hybridized to nucleic acid array for generating complex formation and signaling domains
US10/900,451 Expired - Lifetime US8557522B2 (en) 2001-06-30 2004-07-27 Processes for detecting or quantifying more than one nucleic acid in library
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US10/900,455 Expired - Lifetime US9790621B2 (en) 2001-06-30 2004-07-27 Composition of matter comprising library of first nucleic acid analyte copies
US10/902,567 Expired - Lifetime US8597888B2 (en) 2001-06-30 2004-07-29 Processes for detecting or quantifying more than one nucleic acid in a library
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US10/902,564 Active 2025-01-19 US9163280B2 (en) 2001-06-30 2004-07-29 Process for detecting or quantifying nucleic acids in a library
US10/902,586 Active 2025-01-22 US9487821B2 (en) 2001-06-30 2004-07-29 Composition comprising library of double stranded nucleic acids
US10/902,587 Expired - Fee Related US9057100B2 (en) 2001-06-30 2004-07-29 Composition comprising array of nucleic acid primer sets
US11/403,117 Abandoned US20060257906A1 (en) 2001-06-30 2006-04-12 Compositions comprising a library of analytes for detection, quantification and analyses
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US14/812,487 Expired - Lifetime US9765387B2 (en) 2001-06-30 2015-07-29 Process for detecting or quantifying nucleic acids in a library
US14/812,449 Expired - Lifetime US9777406B2 (en) 2001-06-30 2015-07-29 Process for detecting or quantifying nucleic acids in a library
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US14/812,388 Expired - Lifetime US9745619B2 (en) 2001-06-30 2015-07-29 Process for detecting or quantifying nucleic acids in a library
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US10/693,481 Abandoned US20060057583A1 (en) 2001-06-30 2003-10-24 Novel compositions and methods for controlling the extendability of various components used in copying or amplification steps
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US10/900,454 Expired - Lifetime US9234234B2 (en) 2001-06-30 2004-07-27 Detection and quantification process for more than one nucleic acid in library
US10/900,452 Abandoned US20050233343A1 (en) 2001-06-30 2004-07-27 Composition of matter comprising library of analytes hybridized to nucleic acid array for generating complex formation and signaling domains
US10/900,451 Expired - Lifetime US8557522B2 (en) 2001-06-30 2004-07-27 Processes for detecting or quantifying more than one nucleic acid in library
US10/900,009 Abandoned US20070196828A1 (en) 2001-06-30 2004-07-27 Process for detecting or quantifying more than one nucleic acid in library via terminal attachment of non-inherent universal detection targets to nucleic acid copies produced thereby
US10/900,455 Expired - Lifetime US9790621B2 (en) 2001-06-30 2004-07-27 Composition of matter comprising library of first nucleic acid analyte copies
US10/902,567 Expired - Lifetime US8597888B2 (en) 2001-06-30 2004-07-29 Processes for detecting or quantifying more than one nucleic acid in a library
US10/902,640 Expired - Lifetime US9279147B2 (en) 2001-06-30 2004-07-29 Processes for detecting or quantifying analytes of interest
US10/902,641 Active 2024-10-12 US9234235B2 (en) 2001-06-30 2004-07-29 Processes for detecting or quantifying nucleic acids using an array of fixed or immobilized nucleic acids
US10/902,597 Expired - Lifetime US9434984B2 (en) 2001-06-30 2004-07-29 Composition comprising an array which further comprises chimeric compositions
US10/902,629 Expired - Lifetime US7807352B2 (en) 2001-06-30 2004-07-29 Process for producing two or more copies of nucleic acids in a library, and process for detecting or quantifiying more than one nucleic acid in a library
US10/902,682 Expired - Lifetime US9428797B2 (en) 2001-06-30 2004-07-29 Nucleic acid detecting or quantifying processes
US10/902,564 Active 2025-01-19 US9163280B2 (en) 2001-06-30 2004-07-29 Process for detecting or quantifying nucleic acids in a library
US10/902,586 Active 2025-01-22 US9487821B2 (en) 2001-06-30 2004-07-29 Composition comprising library of double stranded nucleic acids
US10/902,587 Expired - Fee Related US9057100B2 (en) 2001-06-30 2004-07-29 Composition comprising array of nucleic acid primer sets
US11/403,117 Abandoned US20060257906A1 (en) 2001-06-30 2006-04-12 Compositions comprising a library of analytes for detection, quantification and analyses
US14/055,547 Expired - Lifetime US9528146B2 (en) 2001-06-30 2013-10-16 Processes for detecting or quantifying more than one nucleic acid in a library
US14/812,293 Expired - Lifetime US9617584B2 (en) 2001-06-30 2015-07-29 Processes for detecting or quantifying nucleic acids using an array of fixed or immobilized nucleic acids
US14/812,332 Expired - Lifetime US9650666B2 (en) 2001-06-30 2015-07-29 Processes for detecting or quantifying nucleic acids using an array of fixed or immobilized nucleic acids
US14/812,487 Expired - Lifetime US9765387B2 (en) 2001-06-30 2015-07-29 Process for detecting or quantifying nucleic acids in a library
US14/812,449 Expired - Lifetime US9777406B2 (en) 2001-06-30 2015-07-29 Process for detecting or quantifying nucleic acids in a library
US14/812,254 Expired - Lifetime US9637778B2 (en) 2001-06-30 2015-07-29 Processes for detecting or quantifying nucleic acids using an array of fixed or immobilized nucleic acids
US14/812,388 Expired - Lifetime US9745619B2 (en) 2001-06-30 2015-07-29 Process for detecting or quantifying nucleic acids in a library
US14/849,993 Expired - Lifetime US9873956B2 (en) 2001-06-30 2015-09-10 Compositions and processes for analyte detection, quantification and amplification
US15/076,063 Expired - Lifetime US9617585B2 (en) 2001-06-30 2016-03-21 Processes for detecting or quantifying more than one nucleic acid in a library
US15/075,495 Expired - Lifetime US9611508B2 (en) 2001-06-30 2016-03-21 Processes for detecting or quantifying nucleic acids in a library
US15/285,749 Expired - Lifetime US9771667B2 (en) 2001-06-30 2016-10-05 Arrays comprising chimeric compositions

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