WO2003014398A3 - Methods and compositions for mutation detection by liquid chromatography - Google Patents

Methods and compositions for mutation detection by liquid chromatography Download PDF

Info

Publication number
WO2003014398A3
WO2003014398A3 PCT/US2001/045676 US0145676W WO03014398A3 WO 2003014398 A3 WO2003014398 A3 WO 2003014398A3 US 0145676 W US0145676 W US 0145676W WO 03014398 A3 WO03014398 A3 WO 03014398A3
Authority
WO
WIPO (PCT)
Prior art keywords
methods
dna
hybridization
mutation detection
compositions
Prior art date
Application number
PCT/US2001/045676
Other languages
French (fr)
Other versions
WO2003014398A2 (en
Inventor
Paul D Taylor
Original Assignee
Transgenomic Inc
Priority date (The priority date is an assumption and is not a legal conclusion. Google has not performed a legal analysis and makes no representation as to the accuracy of the date listed.)
Filing date
Publication date
Application filed by Transgenomic Inc filed Critical Transgenomic Inc
Publication of WO2003014398A2 publication Critical patent/WO2003014398A2/en
Publication of WO2003014398A3 publication Critical patent/WO2003014398A3/en

Links

Classifications

    • C—CHEMISTRY; METALLURGY
    • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12Q—MEASURING 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
    • C12Q1/00—Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions
    • C12Q1/68—Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions involving nucleic acids
    • C12Q1/6813—Hybridisation assays
    • C12Q1/6832—Enhancement of hybridisation reaction
    • C—CHEMISTRY; METALLURGY
    • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12Q—MEASURING 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
    • C12Q1/00—Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions
    • C12Q1/68—Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions involving nucleic acids
    • C12Q1/6813—Hybridisation assays
    • C12Q1/6827—Hybridisation assays for detection of mutation or polymorphism

Landscapes

  • Chemical & Material Sciences (AREA)
  • Life Sciences & Earth Sciences (AREA)
  • Organic Chemistry (AREA)
  • Engineering & Computer Science (AREA)
  • Zoology (AREA)
  • Wood Science & Technology (AREA)
  • Proteomics, Peptides & Aminoacids (AREA)
  • Health & Medical Sciences (AREA)
  • Biophysics (AREA)
  • General Engineering & Computer Science (AREA)
  • Immunology (AREA)
  • Microbiology (AREA)
  • Molecular Biology (AREA)
  • Analytical Chemistry (AREA)
  • Physics & Mathematics (AREA)
  • Genetics & Genomics (AREA)
  • Biochemistry (AREA)
  • Bioinformatics & Cheminformatics (AREA)
  • Biotechnology (AREA)
  • General Health & Medical Sciences (AREA)
  • Chemical Kinetics & Catalysis (AREA)
  • Measuring Or Testing Involving Enzymes Or Micro-Organisms (AREA)

Abstract

The present invention relates to improvements in methods of DNA mutation detection using chromatographic methods such as DHPLC. In particular, the invention relates to methods for increasing the level of heteroduplex during a hybridization process between a DNA fragment and a corresponding wild type DNA fragment by including during the hybridization process nitrogen-containing organic compounds such as betaine, trimethylamine N-oxide, and dimethylglycine. In another aspect the inventino provides improved PCR primers for amplifying the DNA to be used in the hybridization. The invention also provides for DNA hybridization kits containing these compounds and primers.
PCT/US2001/045676 2001-01-03 2001-10-31 Methods and compositions for mutation detection by liquid chromatography WO2003014398A2 (en)

Applications Claiming Priority (2)

Application Number Priority Date Filing Date Title
US25984701P 2001-01-03 2001-01-03
US60/259,847 2001-01-03

Publications (2)

Publication Number Publication Date
WO2003014398A2 WO2003014398A2 (en) 2003-02-20
WO2003014398A3 true WO2003014398A3 (en) 2003-07-10

Family

ID=22986670

Family Applications (1)

Application Number Title Priority Date Filing Date
PCT/US2001/045676 WO2003014398A2 (en) 2001-01-03 2001-10-31 Methods and compositions for mutation detection by liquid chromatography

Country Status (1)

Country Link
WO (1) WO2003014398A2 (en)

Families Citing this family (7)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
GB0428255D0 (en) 2004-12-23 2005-01-26 Health Prot Agency Detection of nucleic acid mutations
EP2285979B2 (en) 2008-05-27 2020-02-19 Dako Denmark A/S Hybridization compositions and methods
US9388456B2 (en) 2009-02-26 2016-07-12 Dako Denmark A/S Compositions and methods for performing a stringent wash step in hybridization applications
WO2013046033A1 (en) 2011-09-30 2013-04-04 Dako Denmark A/S Hybridization compositions and methods using formamide
WO2013057310A2 (en) 2011-10-21 2013-04-25 Dako Denmark A/S Hybridization compositions and methods
US20150050649A1 (en) 2012-03-22 2015-02-19 Wako Pure Chemical Industries, Ltd. Method for detecting dna having microsatellite region
EP2840137B1 (en) 2012-03-22 2018-07-25 FUJIFILM Wako Pure Chemical Corporation Method for identification and detection of mutant gene using intercalator

Citations (5)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
DE4411588C1 (en) * 1994-03-30 1995-09-28 Deutsches Rheuma Forschungszen Buffer, contg. betaine, for RNA- and DNA-polymerase reactions
WO1997043450A1 (en) * 1996-05-16 1997-11-20 Affymetrix, Inc. Hybridization assays on oligonucleotide arrays
US5795976A (en) * 1995-08-08 1998-08-18 The Board Of Trustees Of The Leland Stanford Junior University Detection of nucleic acid heteroduplex molecules by denaturing high-performance liquid chromatography and methods for comparative sequencing
WO1999009217A1 (en) * 1997-08-15 1999-02-25 Hyseq, Inc. Methods and compositions for detection or quantification of nucleic acid species
EP0952228A2 (en) * 1996-09-24 1999-10-27 Rapigene, Inc. Compositions and methods for enhancing hybridization specificity

Patent Citations (5)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
DE4411588C1 (en) * 1994-03-30 1995-09-28 Deutsches Rheuma Forschungszen Buffer, contg. betaine, for RNA- and DNA-polymerase reactions
US5795976A (en) * 1995-08-08 1998-08-18 The Board Of Trustees Of The Leland Stanford Junior University Detection of nucleic acid heteroduplex molecules by denaturing high-performance liquid chromatography and methods for comparative sequencing
WO1997043450A1 (en) * 1996-05-16 1997-11-20 Affymetrix, Inc. Hybridization assays on oligonucleotide arrays
EP0952228A2 (en) * 1996-09-24 1999-10-27 Rapigene, Inc. Compositions and methods for enhancing hybridization specificity
WO1999009217A1 (en) * 1997-08-15 1999-02-25 Hyseq, Inc. Methods and compositions for detection or quantification of nucleic acid species

Non-Patent Citations (15)

* Cited by examiner, † Cited by third party
Title
CHAKRABARTI R ET AL: "The enhancement of PCR amplification by low molecular weight amides.", NUCLEIC ACIDS RESEARCH. ENGLAND 1 JUN 2001, vol. 29, no. 11, 1 June 2001 (2001-06-01), pages 2377 - 2381, XP002227234, ISSN: 1362-4962 *
CHAKRABARTI R ET AL: "The enhancement of PCR amplification by low molecular-weight sulfones.", GENE. NETHERLANDS 22 AUG 2001, vol. 274, no. 1-2, 22 August 2001 (2001-08-22), pages 293 - 298, XP002227233, ISSN: 0378-1119 *
DE SILVA D ET AL: "Monitoring hybridization during polymerase chain reaction.", JOURNAL OF CHROMATOGRAPHY. B, BIOMEDICAL SCIENCES AND APPLICATIONS. NETHERLANDS 28 APR 2000, vol. 741, no. 1, 28 April 2000 (2000-04-28), pages 3 - 13, XP002227231, ISSN: 1387-2273 *
HENGEN P N: "Optimizing multiplex and LA-PCR with betaine", TIBS TRENDS IN BIOCHEMICAL SCIENCES, ELSEVIER PUBLICATION, CAMBRIDGE, EN, vol. 22, no. 6, 1 June 1997 (1997-06-01), pages 225 - 226, XP004074684, ISSN: 0968-0004 *
HENKE W ET AL: "Recently, betaine has been introduced as an additive in different PCR strategies.", NUCLEIC ACIDS RESEARCH. ENGLAND 15 JAN 1998, vol. 26, no. 2, 15 January 1998 (1998-01-15), pages 687, XP001097595, ISSN: 0305-1048 *
LIU W ET AL: "DENATURING HIGH PERFORMANCE LIQUID CHROMATOGRAPHY (DHPLC) USED IN THE DETECTION OF GERMLINE AND SOMATIC MUTATIONS", NUCLEIC ACIDS RESEARCH, OXFORD UNIVERSITY PRESS, SURREY, GB, vol. 26, no. 6, 1998, pages 1396 - 1400, XP002911657, ISSN: 0305-1048 *
MELCHIOR W B JR ET AL: "Alteration of the relative stability of dA-dT and dG-dC base pairs in DNA.", PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA. UNITED STATES FEB 1973, vol. 70, no. 2, February 1973 (1973-02-01), pages 298 - 302, XP002027509, ISSN: 0027-8424 *
MYERS R M ET AL: "MODIFICATION OF THE MELTING PROPERTIES OF DUPLEX DNA BY ATTACHMENT OF A GC-RICH DNA SEQUENCE AS DETERMINED BY DENATURING GRADIENT GEL ELECTROPHORESIS", NUCLEIC ACIDS RESEARCH, OXFORD UNIVERSITY PRESS, SURREY, GB, vol. 13, no. 9, 1985, pages 3111 - 3129, XP002911668, ISSN: 0305-1048 *
MYERS R M ET AL: "Nearly all single base substitutions in DNA fragments joined to a GC-clamp can be detected by denaturing gradient gel electrophoresis.", NUCLEIC ACIDS RESEARCH. ENGLAND 10 MAY 1985, vol. 13, no. 9, 10 May 1985 (1985-05-10), pages 3131 - 3145, XP009004065, ISSN: 0305-1048 *
NARAYANASWAMI G ET AL: "Improved efficiency of mutation detection by denaturing high-performance liquid chromatography using modified primers and hybridization procedure.", GENETIC TESTING. UNITED STATES 2001 SPRING, vol. 5, no. 1, April 2001 (2001-04-01), pages 9 - 16, XP009003995, ISSN: 1090-6576 *
OEFNER P J: "Allelic discrimination by denaturing high-performance liquid chromatography", JOURNAL OF CHROMATOGRAPHY. BIOMEDICAL APPLICATIONS, ELSEVIER, AMSTERDAM, NL, vol. 739, no. 2, March 2000 (2000-03-01), pages 345 - 355, XP004202696, ISSN: 0378-4347 *
REES W A ET AL: "BETAINE CAN ELIMINATE THE BASE PAIR COMPOSITION DEPENDENCE OF DNA MELTING", BIOCHEMISTRY, AMERICAN CHEMICAL SOCIETY. EASTON, PA, US, vol. 32, no. 1, 1 December 1993 (1993-12-01), pages 137 - 144, XP000602183, ISSN: 0006-2960 *
SKOPEK T R ET AL: "Analysis of sequence alterations in a defined DNA region: comparison of temperature-modulated heteroduplex analysis and denaturing gradient gel electrophoresis.", MUTATION RESEARCH. NETHERLANDS 29 NOV 1999, vol. 430, no. 1, 29 November 1999 (1999-11-29), pages 13 - 21, XP002227232, ISSN: 0027-5107 *
WOOD W I ET AL: "BASE COMPOSITION-INDEPENDENT HYBRIDIZATION IN TETRAMETHYLAMMONIUM CHLORIDE: A METHOD FOR OLIGONUCLEOTIDE SCREENING OF HIGHLY COMPLEX GENE LIBRARIES", PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF USA, NATIONAL ACADEMY OF SCIENCE. WASHINGTON, US, vol. 82, no. 3, 1 March 1985 (1985-03-01), pages 1585 - 1588, XP002027508, ISSN: 0027-8424 *
WU Y ET AL: "Improvement of fragment and primer selection for mutation detection by denaturing gradient gel electrophoresis.", NUCLEIC ACIDS RESEARCH. ENGLAND 1 DEC 1998, vol. 26, no. 23, 1 December 1998 (1998-12-01), pages 5432 - 5440, XP002227230, ISSN: 0305-1048 *

Also Published As

Publication number Publication date
WO2003014398A2 (en) 2003-02-20

Similar Documents

Publication Publication Date Title
WO2005044836A3 (en) Macromolecular nucleotide compounds and methods for using the same
WO2006003439A3 (en) Method for stabilising reagents which are useful for nucleic acid amplification
WO2005087951A3 (en) Reagents, methods and kits for use in deactivating nucleic acids
WO2007070381A3 (en) Nucleic acid purification with a binding matrix
WO2006023880A3 (en) Compounds and methods for the characterization of oligonucleotides
WO2005059097A3 (en) Methods for high fidelity production of long nucleic acid molecules
WO2007065918A3 (en) Method for purifying fsh or a fsh mutant
WO2007070359A3 (en) Quinolone based compounds exhibiting prolyl hydroxylase inhibitory activity, and compositions, and uses thereof
TW200636075A (en) Detection of nucleic acid variation by cleavage-amplification method
WO2004067779A3 (en) Genetic polymorphisms associated with rheumatoid arthritis, methods of detection and uses thereof
WO2007103485A3 (en) Small rna purification
WO2006066924A3 (en) Azole derivatives with antimuscarinic activity
WO2006101745A3 (en) Alpha7 neuronal nicotinic receptor ligand and antipsychotic compositions
WO2005083127A3 (en) Genetic polymorphisms associated with stroke, methods of detection and uses thereof
WO2007038058A3 (en) Amino-aza-adamantane derivatives and methods of use
WO2003033732A3 (en) Real-time detection of dna amplification products
WO2003031580A3 (en) Methods and compositions for mutation analysis by liquid chromatography
WO2005095652A3 (en) Pnmt as a novel marker for progenitor cells
WO2004003220A3 (en) Methods and composition for analyzing compromised samples using snps
WO2003014398A3 (en) Methods and compositions for mutation detection by liquid chromatography
WO2002034883A3 (en) A one-well assay for high throughput detection of single nucleotide polymorphisms
WO2005054270A3 (en) Identification and design of sirna molecules
WO2005024068A3 (en) Allele-specific sequence variation analysis
WO2004077038A3 (en) Stationary phase for use in capillary electrophoresis, capillary electrochromatography, microfluidics, and related methods
WO2005031004A3 (en) Method for the specific rapid detection of beverage-spoiling micro-organisms

Legal Events

Date Code Title Description
AK Designated states

Kind code of ref document: A2

Designated state(s): AE AG AL AM AT AU AZ BA BB BG BR BY BZ CA CH CN CR CU CZ DE DK DM DZ EE ES FI GB GD GE GH GM HR HU ID IL IN IS JP KE KG KP KR KZ LC LK LR LS LT LU LV MA MD MG MK MN MW MX MZ NO NZ PL PT RO RU SD SE SG SI SK SL TJ TM TR TT TZ UA UG UZ VN YU ZA ZW

Kind code of ref document: A2

Designated state(s): AE AG AL AM AT AU AZ BA BB BG BY BZ CA CH CN CR CU CZ DE DK DZ EE ES FI GB GD GE GH GM HR ID IL IN IS JP KE KG KP KR KZ LC LR LS LT LU LV MA MD MG MK MN MX MZ NO NZ PL PT RO RU SD SE SG SK SL TJ TM TR TT TZ UA UG UZ VN ZA

AL Designated countries for regional patents

Kind code of ref document: A2

Designated state(s): GH GM KE LS MW MZ SD SL SZ TZ UG ZW AM AZ BY KG KZ MD RU TJ TM AT BE CH CY DE DK ES FI FR GB GR IE IT LU MC NL PT SE TR BF BJ CF CG CI CM GA GN GQ GW ML MR NE SN TD TG

Kind code of ref document: A2

Designated state(s): GH GM KE LS MW MZ SD SL SZ UG ZW AM AZ BY KG KZ MD TJ TM AT BE CH CY DE DK ES FR GB GR IE IT LU MC NL PT SE TR BF BJ CF CG CI CM GA GN GQ GW MR NE SN TD TG

121 Ep: the epo has been informed by wipo that ep was designated in this application
DFPE Request for preliminary examination filed prior to expiration of 19th month from priority date (pct application filed before 20040101)
REG Reference to national code

Ref country code: DE

Ref legal event code: 8642

122 Ep: pct application non-entry in european phase
NENP Non-entry into the national phase

Ref country code: JP