CA2390309A1 - Method for synthesizing the nucleic acid - Google Patents

Method for synthesizing the nucleic acid Download PDF

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Publication number
CA2390309A1
CA2390309A1 CA002390309A CA2390309A CA2390309A1 CA 2390309 A1 CA2390309 A1 CA 2390309A1 CA 002390309 A CA002390309 A CA 002390309A CA 2390309 A CA2390309 A CA 2390309A CA 2390309 A1 CA2390309 A1 CA 2390309A1
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region
complementary
oligonucleotide
synthesis
nucleic acid
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CA2390309C (en
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Tsugunori Notomi
Tetsu Hase
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Eiken Chemical Co Ltd
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Priority claimed from PCT/JP1999/006213 external-priority patent/WO2000028082A1/en
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    • CCHEMISTRY; METALLURGY
    • C12BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12QMEASURING OR TESTING PROCESSES INVOLVING ENZYMES, NUCLEIC ACIDS OR MICROORGANISMS; COMPOSITIONS OR TEST PAPERS THEREFOR; PROCESSES OF PREPARING SUCH COMPOSITIONS; CONDITION-RESPONSIVE CONTROL IN MICROBIOLOGICAL OR ENZYMOLOGICAL PROCESSES
    • C12Q1/00Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions
    • C12Q1/68Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions involving nucleic acids
    • C12Q1/6844Nucleic acid amplification reactions
    • CCHEMISTRY; METALLURGY
    • C12BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12NMICROORGANISMS OR ENZYMES; COMPOSITIONS THEREOF; PROPAGATING, PRESERVING, OR MAINTAINING MICROORGANISMS; MUTATION OR GENETIC ENGINEERING; CULTURE MEDIA
    • C12N15/00Mutation or genetic engineering; DNA or RNA concerning genetic engineering, vectors, e.g. plasmids, or their isolation, preparation or purification; Use of hosts therefor
    • C12N15/09Recombinant DNA-technology
    • C12N15/10Processes for the isolation, preparation or purification of DNA or RNA
    • CCHEMISTRY; METALLURGY
    • C12BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12QMEASURING OR TESTING PROCESSES INVOLVING ENZYMES, NUCLEIC ACIDS OR MICROORGANISMS; COMPOSITIONS OR TEST PAPERS THEREFOR; PROCESSES OF PREPARING SUCH COMPOSITIONS; CONDITION-RESPONSIVE CONTROL IN MICROBIOLOGICAL OR ENZYMOLOGICAL PROCESSES
    • C12Q1/00Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions
    • C12Q1/68Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions involving nucleic acids
    • C12Q1/6813Hybridisation assays
    • C12Q1/6827Hybridisation assays for detection of mutation or polymorphism
    • CCHEMISTRY; METALLURGY
    • C12BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12QMEASURING OR TESTING PROCESSES INVOLVING ENZYMES, NUCLEIC ACIDS OR MICROORGANISMS; COMPOSITIONS OR TEST PAPERS THEREFOR; PROCESSES OF PREPARING SUCH COMPOSITIONS; CONDITION-RESPONSIVE CONTROL IN MICROBIOLOGICAL OR ENZYMOLOGICAL PROCESSES
    • C12Q1/00Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions
    • C12Q1/68Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions involving nucleic acids
    • C12Q1/6844Nucleic acid amplification reactions
    • C12Q1/6858Allele-specific amplification

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  • Life Sciences & Earth Sciences (AREA)
  • Organic Chemistry (AREA)
  • Engineering & Computer Science (AREA)
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  • Wood Science & Technology (AREA)
  • Genetics & Genomics (AREA)
  • Bioinformatics & Cheminformatics (AREA)
  • Biotechnology (AREA)
  • General Engineering & Computer Science (AREA)
  • Proteomics, Peptides & Aminoacids (AREA)
  • General Health & Medical Sciences (AREA)
  • Molecular Biology (AREA)
  • Microbiology (AREA)
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  • Biochemistry (AREA)
  • Biomedical Technology (AREA)
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  • Crystallography & Structural Chemistry (AREA)
  • Measuring Or Testing Involving Enzymes Or Micro-Organisms (AREA)
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Abstract

An oligonucleotide having a novel structure and a method for synthesizing a nucleic acid by using the same as a primer. In the 5'-side of the primer, th is oligonucleotide is provided with a base sequence which is substantially identical with the region to be synthesized by using this primer as a starti ng point of the synthesis. Thus, a nucleic acid can be synthesized on the basis of an isothermal reaction with the use of a simple reagent constitution. Als o, provision is made of a method for synthesizing a nucleic acid having a high specificity based on the above method for synthesizing a nucleic acid.</SDOA B>

Claims (24)

1. A method of synthesizing nucleic acid having complementary nucleotide sequences linked alternately in a single-stranded chain, comprising:
a) the step of giving nucleic acid which is provided at the 3'-terminal thereof with a region F1 capable of annealing to a part F1c in the same chain and which upon annealing of the region F1 to F1c, is capable of forming a loop containing a region F2c capable of base pairing, b) the step of performing synthesis of a complementary chain wherein the 3' -terminal of F1 having annealed to F1c serves as the origin of synthesis, c) the step of annealing, to a region F2c, of an oligonucleotide provided with the 3'-terminal thereof with F2 consisting of a sequence complementary to the region F2c, followed by synthesis, with said oligonucleotide as the origin of synthesis, of a complementary chain by a polymerase catalyzing the strand displacement reaction of synthesizing a complementary chain to displace the complementary chain synthesized in step b), and d) the step of annealing, to the complementary chain displaced in step c) to be ready for base pairing, of a polynucleotide provided at the 3'-terminal thereof with a sequence complementary to an arbitrary region in said chain synthesized in step c), followed by synthesis, with said 3'-terminal as the origin of synthesis, of a complementary chain by a polymerase catalyzing the strand displacement reaction of synthesizing a complementary chain to displace the complementary chain synthesized in step c).
2. The method according to claim 1, wherein in step d), the origin of synthesis is a region R1 present at the 3'-terminal in the same chain and capable of annealing to a region R1c, and a loop containing the region R2c capable of base pairing is formed by annealing R1 to R1c.
3. An oligonucleotide composed of at least two regions X2 and X1c below, and X1c is linked to the 5'-side of X2, X2: a region having a nucleotide sequence complementary to an arbitrary region X2c in nucleic acid having a specific nucleotide sequence, and X1c: a region having substantially the same nucleotide sequence as in a region X1c located at the 5'-side of the region X2c in nucleic acid having a specific nucleotide sequence.
4. The method according to claim 1, wherein the nucleic acid in step a) is second nucleic acid provided by the following steps i) the step of annealing, to a region F2c in nucleic acid serving as a template, of a region F2 in the oligonucleotide described in claim 3 wherein the region X2 is a region F2 and the region X1c is a region F1c, ii) the step of synthesizing first nucleic acid having a nucleotide sequence complementary to the template wherein F2 in the oligonucleotide serves as the origin of synthesis, iii) the step of rendering an arbitrary region in the first nucleic acid synthesized in step ii) ready for base pairing, and iv) the step of annealing an oligonucleotide having a nucleotide sequence complementary to the region made ready for base pairing in the first nucleic acid in step iii), followed by synthesizing second nucleic acid with said oligonucleotide as the origin of synthesis and rendering F1 at the 3'-terminal thereof ready for base pairing.
5. The method according to claim 4, wherein the region enabling base pairing in step iii) is R2c, and the oligonucleotide in step iv) is the oligonucleotide described in claim 3 wherein the region X2c is a region R2c and the region X1c is a region R1c.
6. The method according to claim 4 or 5, wherein the step of rendering base pairing ready in steps iii) and iv) is conducted by the strand displacement synthesis of complementary chain by a polymerase catalyzing the strand displacement reaction of synthesizing complementary chain wherein an outer primer annealing to the 3'-side of F2c in the template and an outer primer annealing to the 3'-side of the region used as the origin of synthesis in step iv) for the first nucleic acid serve as the origin of synthesis.
7. The method according to claim 6, wherein the melting temperature of each oligonucleotide and its complementary region in the template used in the reaction is in the following relationship under the same stringency:
(outer primer/region at the 3'-side in the template) <= (F2c/F2 and R2c/R2) <= (F1c/F1 and R1c/R1).
8. The method according to any one of claims 4 to 7, wherein the nucleic acid serving as the template is RNA, and the synthesis of complementary chain in step ii) is conducted by an enzyme having a reverse transcriptase activity.
9. A method of amplifying nucleic acid having complementary nucleotide sequences linked alternately in a single-stranded chain by repeatedly conducting the following steps:
A) the step of providing a template which is provided at the 3'- and 5'-terminals thereof with a region consisting of a nucleotide sequence complementary to each terminal region in the same chain and which upon annealing of these mutually complementary nucleotide sequences, forms a loop capable of base pairing therebetween, B) the step of performing the synthesis of complementary chain wherein the 3'-terminal of said template annealed to the same chain serves as the origin of synthesis, C) the step of annealing, to the loop portion, of an oligonucleotide provided at the 3'-terminal thereof with a complementary nucleotide sequence to a loop which among said loops, is located at the 3'-terminal site, followed by synthesis, with the oligonucleotide as the origin of synthesis, of a complementary chain by a polymerase catalyzing the strand displacement reaction of synthesizing a complementary chain to displace the complementary chain synthesized in step B) to make the 3'-terminal thereof ready for base pairing, and D) the step wherein the chain with the 3'-terminal made ready for base pairing in step C) serves as a new template.
10. The method according to claim 9, wherein the oligonucleotide in step C) is provided at the 5'-terminal thereof with a nucleotide sequence complementary to the 3'-terminal serving as the origin of synthesis in step B).
11. The method according to claim 10, further comprising the step where a complementary chain synthesized with the oligonucleotide in step C) as the origin of synthesis is used as a template in step A).
12. The method according to claim 9, wherein the template in step A) is synthesized by the method described in claim 5.
13. The method according to claim 1 or 9, wherein the strand displacement reaction of synthesizing complementary chain is carried out in the presence of a melting temperature regulator.
14. The method according to claim 13, wherein the melting temperature regulator is betaine.
15. The method according to claim 14, wherein 0.2 to 3.0 M betaine is allowed to be present in the reaction solution.
16. A method of detecting a target nucleotide sequence in a sample, which comprises performing an amplification method described in any one of claims 9 to 15 and observing whether an amplification reaction product is generated or not.
17. The method according to claim 16, wherein a probe containing a nucleotide sequence complementary to the loop is added to the amplification reaction product and hybridization therebetween is observed.
18. The method according to claim 17, wherein the probe is labeled on particles and aggregation reaction occurring upon hybridization is observed.
19. The method according to claim 16, wherein an amplification method described in any one of claims 9 to 15 is conducted in the presence of a detector for nucleic acid, and whether an amplification reaction product is generated or not is observed on the basis of a change in the signal of the detector.
20. A method of detecting a mutation in a target nucleotide sequence by the detection method described in claim 16, wherein a mutation in a nucleotide sequence as the subject of amplification prevents synthesis of any one of complementary chains constituting the amplification method.
21. A kit for synthesis of nucleic acid having complementary chains alternately linked in a single-stranded chain, comprising the following elements:
i) the oligonucleotide described in claim 3 wherein the region F2c in nucleic acid as a template is X2c, and F1c located at the 5'-side of F2c is X1c;
ii) an oligonucleotide containing a nucleotide sequence complementary to an arbitrary region in a complementary chain synthesized with the oligonucleotide in (i) as a primer;
iii) an oligonucleotide having a nucleotide sequence complementary to a region F3c located at the 3'-side of the region F2c in the nucleic acid serving as a template;
iv) a DNA polymerase catalyzing the strand displacement-type reaction of synthesizing complementary chain; and v) a nucleotide serving as a substrate for the element iv).
22. The kit according to claim 21, wherein the oligonucleotide in ii) is the oligonucleotide described in claim 3 wherein an arbitrary region R2c in a complementary chain synthesized with the oligonucleotide in i) as the origin of synthesis is X2c, and R1c located at the 5' of R2c is X1c.
23. The kit according to claim 22, further comprising:
vi) an oligonucleotide having a nucleotide sequence complementary to a region R3c located at the 3'-side of the arbitrary R2c in a complementary chain synthesized with the oligonucleotide in i) as the origin of synthesis.
24. A kit for detection of a target nucleotide sequence, comprising a detector for detection of a product of nucleic acid synthetic reaction additionally in a kit described in any one of claims 21 to 23.
CA2390309A 1999-11-08 2000-03-28 Method for synthesizing the nucleic acid Expired - Lifetime CA2390309C (en)

Applications Claiming Priority (3)

Application Number Priority Date Filing Date Title
PCT/JP1999/006213 WO2000028082A1 (en) 1998-11-09 1999-11-08 Process for synthesizing nucleic acid
JPPCT/JP99/06213 1999-11-08
PCT/JP2000/001919 WO2001034790A1 (en) 1999-11-08 2000-03-28 Method for synthesizing nucleic acid

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CA2390309A1 true CA2390309A1 (en) 2001-05-17
CA2390309C CA2390309C (en) 2012-09-25

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KR (1) KR100612551B1 (en)
CN (2) CN100393875C (en)
BR (1) BR0015382B1 (en)
CA (1) CA2390309C (en)
IL (1) IL149446A0 (en)
NO (1) NO331732B1 (en)
RU (1) RU2252964C2 (en)
WO (1) WO2001034790A1 (en)
ZA (1) ZA200203293B (en)

Cited By (3)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
US7713691B2 (en) 1998-06-24 2010-05-11 Enzo Life Sciences, Inc. Modified nucleic acid polymers and methods for their production
US10745745B2 (en) 2013-03-15 2020-08-18 Labrador Diagnostics Llc Nucleic acid amplification
US11254960B2 (en) 2013-03-15 2022-02-22 Labrador Diagnostics Llc Nucleic acid amplification

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US8445664B2 (en) 1998-06-24 2013-05-21 Enzo Diagnostics, Inc. Kits for amplifying and detecting nucleic acid sequences
US8017357B2 (en) 2000-04-07 2011-09-13 Eiken Kagaku Kabushiki Kaisha Method of amplifying nucleic acid by using double-stranded nucleic acid as template
DE60139331D1 (en) 2000-09-19 2009-09-03 Eiken Chemical PROCESS FOR POLYNUCLEOTIDE SYNTHESIS
KR100806680B1 (en) * 2003-11-21 2008-02-26 한국표준과학연구원 Multiplex PCR mixtures for Testing the Performance of Thermocyclers
WO2010108325A1 (en) * 2009-03-26 2010-09-30 厦门艾德生物医药科技有限公司 Loop-shaped primer employed in nucleic acid amplification and the use thereof
CN101671674B (en) * 2009-03-27 2010-09-22 郑立谋 Annular primer for amplification of nucleic acid and application thereof
US9074251B2 (en) 2011-02-10 2015-07-07 Illumina, Inc. Linking sequence reads using paired code tags
WO2012106546A2 (en) 2011-02-02 2012-08-09 University Of Washington Through Its Center For Commercialization Massively parallel continguity mapping
TWI600766B (en) * 2012-08-09 2017-10-01 財團法人工業技術研究院 Kit for detecting a mutation and/or polymorphism of a specific region in a target nucleotide sequence
US10557133B2 (en) 2013-03-13 2020-02-11 Illumina, Inc. Methods and compositions for nucleic acid sequencing
KR102324117B1 (en) * 2013-11-22 2021-11-10 오리온 디아그노스티카 오와이 Detection of nucleic acids by strand invasion based amplification
WO2016011280A1 (en) 2014-07-16 2016-01-21 Tangen Biosciences, Inc. Isothermal methods for amplifying nucleic acid samples
WO2016061517A2 (en) 2014-10-17 2016-04-21 Illumina Cambridge Limited Contiguity preserving transposition
EP3215260B1 (en) 2014-11-03 2020-01-15 Tangen Biosciences Inc. Apparatus and method for cell, spore, or virus capture and disruption
CA2971006C (en) 2014-12-15 2024-05-21 Cepheid Exponential base-greater-than-2 nucleic acid amplification
WO2018132939A1 (en) * 2017-01-17 2018-07-26 中国科学院过程工程研究所 Method for synthesizing nucleic acid under constant temperature
EP3808843A1 (en) * 2017-09-14 2021-04-21 Zhongke Xinray (Suzhou) Biological Science Technologies Co., Ltd. Method and kit for synthesizing nucleic acid under constant temperature conditions
EP3874064A1 (en) 2018-10-29 2021-09-08 Cepheid Exponential base-3 nucleic acid amplification with reduced amplification time using nested overlapping primers
CN113302314A (en) 2019-01-15 2021-08-24 3M创新有限公司 Loop-mediated isothermal amplification primers for Shiga toxin-producing Escherichia coli (STEC) detection
EP4107292A1 (en) 2020-02-17 2022-12-28 3M Innovative Properties Company Loop-mediated isothermal amplification primers for vibrio parahaemolyticus detection and uses thereof
AU2021287968A1 (en) 2020-06-12 2023-02-09 Sherlock Biosciences, Inc. CRISPR-based SARS-CoV-2 detection
EP4193363A1 (en) 2020-08-07 2023-06-14 Oxford Nanopore Technologies plc Methods of identifying nucleic acid barcodes
CN113201583B (en) * 2021-04-29 2022-02-08 国科宁波生命与健康产业研究院 Method for synthesizing nucleic acid under constant temperature condition, kit and application
WO2022226870A1 (en) * 2021-04-29 2022-11-03 中国科学院大学宁波生命与健康产业研究院 Method for synthesizing nucleic acid under constant temperature conditions, kit, and application
KR20240072313A (en) 2022-11-10 2024-05-24 (주)레보스케치 Composition for RT-LAMP for diagnosing Staphylococcus aureus infection and use thereof

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ES2112302T3 (en) * 1991-10-11 1998-04-01 Behringwerke Ag METHOD FOR PRODUCING A POLYNUCLEOTIDE FOR USE IN AMPLIFICATION WITH A SINGLE PRIMER AND OLIGONUCLEOTIDES CONTAINING PHOSPHOROTIOATE AS PRIMERS FOR AMPLIFICATION OF NUCLEIC ACIDS.
WO1993017127A1 (en) * 1992-02-20 1993-09-02 The State Of Oregon Acting By And Through The Oregon State Board Of Higher Education On Behalf Of Oregon State University Boomerand dna amplification
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Cited By (7)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
US7713691B2 (en) 1998-06-24 2010-05-11 Enzo Life Sciences, Inc. Modified nucleic acid polymers and methods for their production
US8133989B2 (en) 1998-06-24 2012-03-13 Enzo Diagnostics, Inc. Nucleic acid primer/construct compositions
US8288092B2 (en) 1998-06-24 2012-10-16 Enzo Life Sciences, Inc. Modified nucleic acid polymers and methods for their production
US10745745B2 (en) 2013-03-15 2020-08-18 Labrador Diagnostics Llc Nucleic acid amplification
US11254960B2 (en) 2013-03-15 2022-02-22 Labrador Diagnostics Llc Nucleic acid amplification
US11603558B2 (en) 2013-03-15 2023-03-14 Labrador Diagnostics Llc Nucleic acid amplification
US11649487B2 (en) 2013-03-15 2023-05-16 Labrador Diagnostics Llc Nucleic acid amplification

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Publication number Publication date
BR0015382A (en) 2002-07-02
RU2002115268A (en) 2004-01-27
ZA200203293B (en) 2003-03-26
CN100393875C (en) 2008-06-11
IL149446A0 (en) 2002-11-10
NO20022171L (en) 2002-07-04
BR0015382B1 (en) 2014-04-29
CN1876843A (en) 2006-12-13
RU2252964C2 (en) 2005-05-27
CN1876843B (en) 2012-09-05
KR100612551B1 (en) 2006-08-11
WO2001034790A1 (en) 2001-05-17
KR20020064896A (en) 2002-08-10
NO20022171D0 (en) 2002-05-07
NO331732B1 (en) 2012-03-12
CA2390309C (en) 2012-09-25
CN1420928A (en) 2003-05-28

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