WO2005090599A3 - Methods and adaptors for analyzing specific nucleic acid populations - Google Patents

Methods and adaptors for analyzing specific nucleic acid populations Download PDF

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Publication number
WO2005090599A3
WO2005090599A3 PCT/GB2005/000989 GB2005000989W WO2005090599A3 WO 2005090599 A3 WO2005090599 A3 WO 2005090599A3 GB 2005000989 W GB2005000989 W GB 2005000989W WO 2005090599 A3 WO2005090599 A3 WO 2005090599A3
Authority
WO
WIPO (PCT)
Prior art keywords
nucleic acid
adaptor
tester
driver
acid complexes
Prior art date
Application number
PCT/GB2005/000989
Other languages
French (fr)
Other versions
WO2005090599A2 (en
Inventor
Guoliang Fu
Original Assignee
Plant Bioscience Ltd
Guoliang Fu
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 Plant Bioscience Ltd, Guoliang Fu filed Critical Plant Bioscience Ltd
Publication of WO2005090599A2 publication Critical patent/WO2005090599A2/en
Publication of WO2005090599A3 publication Critical patent/WO2005090599A3/en

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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
    • C12Q1/6827—Hybridisation assays for detection of mutation or polymorphism
    • C—CHEMISTRY; METALLURGY
    • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12N—MICROORGANISMS OR ENZYMES; COMPOSITIONS THEREOF; PROPAGATING, PRESERVING, OR MAINTAINING MICROORGANISMS; MUTATION OR GENETIC ENGINEERING; CULTURE MEDIA
    • C12N15/00—Mutation or genetic engineering; DNA or RNA concerning genetic engineering, vectors, e.g. plasmids, or their isolation, preparation or purification; Use of hosts therefor
    • C12N15/09—Recombinant DNA-technology
    • C12N15/10—Processes for the isolation, preparation or purification of DNA or RNA
    • C12N15/1034—Isolating an individual clone by screening libraries
    • C—CHEMISTRY; METALLURGY
    • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12N—MICROORGANISMS OR ENZYMES; COMPOSITIONS THEREOF; PROPAGATING, PRESERVING, OR MAINTAINING MICROORGANISMS; MUTATION OR GENETIC ENGINEERING; CULTURE MEDIA
    • C12N15/00—Mutation or genetic engineering; DNA or RNA concerning genetic engineering, vectors, e.g. plasmids, or their isolation, preparation or purification; Use of hosts therefor
    • C12N15/09—Recombinant DNA-technology
    • C12N15/10—Processes for the isolation, preparation or purification of DNA or RNA
    • C12N15/1096—Processes for the isolation, preparation or purification of DNA or RNA cDNA Synthesis; Subtracted cDNA library construction, e.g. RT, RT-PCR
    • 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
    • C12Q1/6811—Selection methods for production or design of target specific oligonucleotides or binding molecules
    • 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
    • C12Q1/6844—Nucleic acid amplification reactions
    • C12Q1/6853—Nucleic acid amplification reactions using modified primers or templates
    • C12Q1/6855—Ligating adaptors

Abstract

The invention provides a method of comparing a tester and a driver sample of nucleic, which tester sample is believed to contain a target nucleic acid not present in a driver sample, the method comprising: (a) providing tester and driver nucleic acid samples; (b) covalently attaching a first adaptor to said tester nucleic acid such as to form adaptor : tester nucleic acid complexes; (c) covalently attachning a second, different, adaptor to said driver nucleic acid such as to form adaptor: driver nucleic acid complexes; (d) combining said adaptor: tester nucleic acid complexes and said adaptor: driver nucleic acid complexes to form a combined sample; (e) subjecting said combined sample to denaturing and annealing conditions such that hybrid double-stranded adaptor: tester/adaptor: driver nucleic acid complexes are formed; (f) adding one ore more restriction enzymes capable of preferentially digesting hybrid non-target nucleic acid complexes, and incubating under restriction digestion conditions, (g) optionally repeating steps (e) and (f), (h) optionally amplifying one or more double-stranded nucleic acid complexes from step (g) using primers specific to the adaptors present in the or each complex. Also provided are related methods, and adaptors and kits for use in performing them.
PCT/GB2005/000989 2004-03-16 2005-03-15 Methods and adaptors for analyzing specific nucleic acid populations WO2005090599A2 (en)

Applications Claiming Priority (2)

Application Number Priority Date Filing Date Title
GB0405878A GB2412170A (en) 2004-03-16 2004-03-16 A method for enriching for target nucleic acids in a sample
GB0405878.0 2004-03-16

Publications (2)

Publication Number Publication Date
WO2005090599A2 WO2005090599A2 (en) 2005-09-29
WO2005090599A3 true WO2005090599A3 (en) 2006-06-01

Family

ID=32117779

Family Applications (1)

Application Number Title Priority Date Filing Date
PCT/GB2005/000989 WO2005090599A2 (en) 2004-03-16 2005-03-15 Methods and adaptors for analyzing specific nucleic acid populations

Country Status (2)

Country Link
GB (1) GB2412170A (en)
WO (1) WO2005090599A2 (en)

Cited By (2)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
US9404150B2 (en) 2007-08-29 2016-08-02 Sequenom, Inc. Methods and compositions for universal size-specific PCR
US9512478B2 (en) 2007-02-02 2016-12-06 Illumina Cambridge Limited Methods for indexing samples and sequencing multiple polynucleotide templates

Families Citing this family (13)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
GB0514910D0 (en) 2005-07-20 2005-08-24 Solexa Ltd Method for sequencing a polynucleotide template
GB0514935D0 (en) 2005-07-20 2005-08-24 Solexa Ltd Methods for sequencing a polynucleotide template
GB0522310D0 (en) 2005-11-01 2005-12-07 Solexa Ltd Methods of preparing libraries of template polynucleotides
GB0524069D0 (en) 2005-11-25 2006-01-04 Solexa Ltd Preparation of templates for solid phase amplification
DK1987159T4 (en) 2006-02-08 2020-11-16 Illumina Cambridge Ltd PROCEDURE FOR SEQUENCE OF A POLYNUCLEOTID TEMPLATE
WO2008015396A2 (en) * 2006-07-31 2008-02-07 Solexa Limited Method of library preparation avoiding the formation of adaptor dimers
US8932994B2 (en) 2006-08-24 2015-01-13 Illumina, Inc. Method for retaining even coverage of short insert libraries
US7754429B2 (en) 2006-10-06 2010-07-13 Illumina Cambridge Limited Method for pair-wise sequencing a plurity of target polynucleotides
US7902345B2 (en) 2006-12-05 2011-03-08 Sequenom, Inc. Detection and quantification of biomolecules using mass spectrometry
WO2008096146A1 (en) 2007-02-07 2008-08-14 Solexa Limited Preparation of templates for methylation analysis
WO2011025477A1 (en) 2009-08-25 2011-03-03 Illumina, Inc. Methods for selecting and amplifying polynucleotides
EP2408936A4 (en) * 2009-03-18 2013-01-30 Sequenom Inc Use of thermostable endonucleases for generating reporter molecules
EP4055188A4 (en) * 2019-11-05 2023-11-22 Ultima Genomics, Inc. Methods for preparing a library of polynucleotide molecules

Citations (4)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
US6060245A (en) * 1996-12-13 2000-05-09 Stratagene Methods and adaptors for generating specific nucleic acid populations
US6090548A (en) * 1996-05-14 2000-07-18 Roche Diagnostics Gmbh Method for identifying and/or quantifying expression of nucleic acid molecules in a sample
US6316192B1 (en) * 1999-03-11 2001-11-13 Jianhua Luo Method for enrichment of unique DNA fragments through cyclical removal of PCR adapter attached to DNA fragments whose sequences are shared between two DNA pools
US6372434B1 (en) * 1998-09-18 2002-04-16 Molecular Staging, Inc. Methods for reducing the complexity of DNA sequences

Family Cites Families (5)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
US5436142A (en) * 1992-11-12 1995-07-25 Cold Spring Harbor Laboratory Methods for producing probes capable of distingushing variant genomic sequences
US5804382A (en) * 1996-05-10 1998-09-08 Beth Israel Deaconess Medical Center, Inc. Methods for identifying differentially expressed genes and differences between genomic nucleic acid sequences
US5935788A (en) * 1996-06-25 1999-08-10 Lifespan Biosciences, Inc. Subtractive hybridization techniques for identifying differentially expressed and commonly expressed nucleic acid
US6455255B1 (en) * 2000-08-02 2002-09-24 Abbott Laboratories Method of performing subtractive hybridization using RDA
WO2002103007A1 (en) * 2001-06-19 2002-12-27 Eisai C0. Ltd. Method of uniformizing dna fragment contents and subtraction method

Patent Citations (4)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
US6090548A (en) * 1996-05-14 2000-07-18 Roche Diagnostics Gmbh Method for identifying and/or quantifying expression of nucleic acid molecules in a sample
US6060245A (en) * 1996-12-13 2000-05-09 Stratagene Methods and adaptors for generating specific nucleic acid populations
US6372434B1 (en) * 1998-09-18 2002-04-16 Molecular Staging, Inc. Methods for reducing the complexity of DNA sequences
US6316192B1 (en) * 1999-03-11 2001-11-13 Jianhua Luo Method for enrichment of unique DNA fragments through cyclical removal of PCR adapter attached to DNA fragments whose sequences are shared between two DNA pools

Cited By (2)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
US9512478B2 (en) 2007-02-02 2016-12-06 Illumina Cambridge Limited Methods for indexing samples and sequencing multiple polynucleotide templates
US9404150B2 (en) 2007-08-29 2016-08-02 Sequenom, Inc. Methods and compositions for universal size-specific PCR

Also Published As

Publication number Publication date
GB0405878D0 (en) 2004-04-21
GB2412170A (en) 2005-09-21
WO2005090599A2 (en) 2005-09-29

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