WO2001012856A3 - Analysis of sequence tags with hairpin primers - Google Patents

Analysis of sequence tags with hairpin primers Download PDF

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Publication number
WO2001012856A3
WO2001012856A3 PCT/US2000/022246 US0022246W WO0112856A3 WO 2001012856 A3 WO2001012856 A3 WO 2001012856A3 US 0022246 W US0022246 W US 0022246W WO 0112856 A3 WO0112856 A3 WO 0112856A3
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WO
WIPO (PCT)
Prior art keywords
fragments
sequence
nucleic acid
detection
coupling
Prior art date
Application number
PCT/US2000/022246
Other languages
French (fr)
Other versions
WO2001012856A2 (en
Inventor
Paul M Lizardi
Darin R Latimer
Original Assignee
Univ Yale
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
Priority claimed from US09/544,713 external-priority patent/US6261782B1/en
Application filed by Univ Yale filed Critical Univ Yale
Priority to AU67708/00A priority Critical patent/AU6770800A/en
Publication of WO2001012856A2 publication Critical patent/WO2001012856A2/en
Publication of WO2001012856A3 publication Critical patent/WO2001012856A3/en

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    • 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
    • C—CHEMISTRY; METALLURGY
    • C07—ORGANIC CHEMISTRY
    • C07K—PEPTIDES
    • C07K14/00—Peptides having more than 20 amino acids; Gastrins; Somatostatins; Melanotropins; Derivatives thereof
    • C07K14/435—Peptides having more than 20 amino acids; Gastrins; Somatostatins; Melanotropins; Derivatives thereof from animals; from humans
    • C07K14/705—Receptors; Cell surface antigens; Cell surface determinants
    • C07K14/70578—NGF-receptor/TNF-receptor superfamily, e.g. CD27, CD30, CD40, CD95
    • 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
    • C12Q1/6809—Methods for determination or identification of nucleic acids involving differential detection
    • 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
    • C12Q1/6834—Enzymatic or biochemical coupling of nucleic acids to a solid phase
    • C12Q1/6837—Enzymatic or biochemical coupling of nucleic acids to a solid phase using probe arrays or probe chips
    • A—HUMAN NECESSITIES
    • A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
    • A61K—PREPARATIONS FOR MEDICAL, DENTAL OR TOILETRY PURPOSES
    • A61K38/00—Medicinal preparations containing peptides
    • Y—GENERAL TAGGING OF NEW TECHNOLOGICAL DEVELOPMENTS; GENERAL TAGGING OF CROSS-SECTIONAL TECHNOLOGIES SPANNING OVER SEVERAL SECTIONS OF THE IPC; TECHNICAL SUBJECTS COVERED BY FORMER USPC CROSS-REFERENCE ART COLLECTIONS [XRACs] AND DIGESTS
    • Y10—TECHNICAL SUBJECTS COVERED BY FORMER USPC
    • Y10T—TECHNICAL SUBJECTS COVERED BY FORMER US CLASSIFICATION
    • Y10T436/00—Chemistry: analytical and immunological testing
    • Y10T436/14—Heterocyclic carbon compound [i.e., O, S, N, Se, Te, as only ring hetero atom]
    • Y10T436/142222—Hetero-O [e.g., ascorbic acid, etc.]
    • Y10T436/143333—Saccharide [e.g., DNA, etc.]

Abstract

Disclosed is a method for the comprehensive analysis of nucleic acid samples and a detector composition for use in the method. The method involves amplifying nucleic acid fragments of interest using a primer that can form a hairpin structure; sequence-based coupling of the amplified fragments to detector probes; and detection of the coupled fragments. The amplified fragments are coupled by hybridization and coupling, preferably by ligation, to detector probes. A hairpin structure formed at the end of the amplified fragments facilitates coupling of the fragments to the probes. The method allows detection of the fragments where detection provides some sequence information for the fragments. The method allows a complex sample of nucleic acid to be quickly and easily cataloged in a reproducible and sequence-specific manner. The method can also be used to detect amplified fragments having a known sequence.
PCT/US2000/022246 1999-08-13 2000-08-11 Analysis of sequence tags with hairpin primers WO2001012856A2 (en)

Priority Applications (1)

Application Number Priority Date Filing Date Title
AU67708/00A AU6770800A (en) 1999-08-13 2000-08-11 Analysis of sequence tags with hairpin primers

Applications Claiming Priority (4)

Application Number Priority Date Filing Date Title
US14887099P 1999-08-13 1999-08-13
US60/148,870 1999-08-13
US09/544,713 US6261782B1 (en) 1999-04-06 2000-04-06 Fixed address analysis of sequence tags
US09/544,713 2000-04-06

Publications (2)

Publication Number Publication Date
WO2001012856A2 WO2001012856A2 (en) 2001-02-22
WO2001012856A3 true WO2001012856A3 (en) 2002-01-24

Family

ID=26846245

Family Applications (2)

Application Number Title Priority Date Filing Date
PCT/US2000/022164 WO2001012855A2 (en) 1999-08-13 2000-08-11 Binary encoded sequence tags
PCT/US2000/022246 WO2001012856A2 (en) 1999-08-13 2000-08-11 Analysis of sequence tags with hairpin primers

Family Applications Before (1)

Application Number Title Priority Date Filing Date
PCT/US2000/022164 WO2001012855A2 (en) 1999-08-13 2000-08-11 Binary encoded sequence tags

Country Status (8)

Country Link
US (4) US6403319B1 (en)
EP (1) EP1206577B1 (en)
JP (1) JP2003527087A (en)
AT (1) ATE318932T1 (en)
AU (2) AU6638000A (en)
CA (1) CA2383264A1 (en)
DE (1) DE60026321D1 (en)
WO (2) WO2001012855A2 (en)

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