WO2002029003A3 - Massive parallel method for decoding dna and rna - Google Patents

Massive parallel method for decoding dna and rna Download PDF

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Publication number
WO2002029003A3
WO2002029003A3 PCT/US2001/031243 US0131243W WO0229003A3 WO 2002029003 A3 WO2002029003 A3 WO 2002029003A3 US 0131243 W US0131243 W US 0131243W WO 0229003 A3 WO0229003 A3 WO 0229003A3
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WIPO (PCT)
Prior art keywords
rna
parallel method
massive parallel
nucleotide analogue
dna
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PCT/US2001/031243
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French (fr)
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WO2002029003A2 (en
Inventor
Trustees Of Columbia Unive The
Jingyue Ju
Zengmin Li
John Robert Edwards
Yasuhiro Itagaki
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Trustees Of Columbia Unive The
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Application filed by Trustees Of Columbia Unive The filed Critical Trustees Of Columbia Unive The
Priority to EP01977533A priority Critical patent/EP1337541B1/en
Priority to EP15195765.1A priority patent/EP3034627B1/en
Priority to CA2425112A priority patent/CA2425112C/en
Priority to JP2002532574A priority patent/JP2004510433A/en
Priority to AU2001296645A priority patent/AU2001296645A1/en
Priority to DE60127162T priority patent/DE60127162T2/en
Publication of WO2002029003A2 publication Critical patent/WO2002029003A2/en
Publication of WO2002029003A3 publication Critical patent/WO2002029003A3/en

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    • C—CHEMISTRY; METALLURGY
    • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
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    • 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
    • C12Q1/6869—Methods for sequencing
    • C—CHEMISTRY; METALLURGY
    • C07—ORGANIC CHEMISTRY
    • C07H—SUGARS; DERIVATIVES THEREOF; NUCLEOSIDES; NUCLEOTIDES; NUCLEIC ACIDS
    • C07H19/00—Compounds containing a hetero ring sharing one ring hetero atom with a saccharide radical; Nucleosides; Mononucleotides; Anhydro-derivatives thereof
    • C07H19/02—Compounds containing a hetero ring sharing one ring hetero atom with a saccharide radical; Nucleosides; Mononucleotides; Anhydro-derivatives thereof sharing nitrogen
    • C07H19/04—Heterocyclic radicals containing only nitrogen atoms as ring hetero atom
    • C07H19/06—Pyrimidine radicals
    • C07H19/10—Pyrimidine radicals with the saccharide radical esterified by phosphoric or polyphosphoric acids
    • C—CHEMISTRY; METALLURGY
    • C07—ORGANIC CHEMISTRY
    • C07H—SUGARS; DERIVATIVES THEREOF; NUCLEOSIDES; NUCLEOTIDES; NUCLEIC ACIDS
    • C07H19/00—Compounds containing a hetero ring sharing one ring hetero atom with a saccharide radical; Nucleosides; Mononucleotides; Anhydro-derivatives thereof
    • C07H19/02—Compounds containing a hetero ring sharing one ring hetero atom with a saccharide radical; Nucleosides; Mononucleotides; Anhydro-derivatives thereof sharing nitrogen
    • C07H19/04—Heterocyclic radicals containing only nitrogen atoms as ring hetero atom
    • C07H19/14—Pyrrolo-pyrimidine radicals
    • C—CHEMISTRY; METALLURGY
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    • C07H—SUGARS; DERIVATIVES THEREOF; NUCLEOSIDES; NUCLEOTIDES; NUCLEIC ACIDS
    • C07H21/00—Compounds containing two or more mononucleotide units having separate phosphate or polyphosphate groups linked by saccharide radicals of nucleoside groups, e.g. nucleic acids
    • C—CHEMISTRY; METALLURGY
    • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
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    • 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
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    • 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
    • C12Q1/686—Polymerase chain reaction [PCR]
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    • 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
    • C12Q1/6869—Methods for sequencing
    • C12Q1/6872—Methods for sequencing involving mass spectrometry
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    • 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
    • C12Q1/6869—Methods for sequencing
    • C12Q1/6874—Methods for sequencing involving nucleic acid arrays, e.g. sequencing by hybridisation
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    • C12Q1/68—Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions involving nucleic acids
    • C12Q1/6876—Nucleic acid products used in the analysis of nucleic acids, e.g. primers or probes
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    • C07—ORGANIC CHEMISTRY
    • C07B—GENERAL METHODS OF ORGANIC CHEMISTRY; APPARATUS THEREFOR
    • C07B2200/00—Indexing scheme relating to specific properties of organic compounds
    • C07B2200/11—Compounds covalently bound to a solid support
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    • C12Q2525/00—Reactions involving modified oligonucleotides, nucleic acids, or nucleotides
    • C12Q2525/10—Modifications characterised by
    • C12Q2525/117—Modifications characterised by incorporating modified base
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    • C12Q2525/00—Reactions involving modified oligonucleotides, nucleic acids, or nucleotides
    • C12Q2525/10—Modifications characterised by
    • C12Q2525/186—Modifications characterised by incorporating a non-extendable or blocking moiety
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    • C12Q2535/00—Reactions characterised by the assay type for determining the identity of a nucleotide base or a sequence of oligonucleotides
    • C12Q2535/101—Sanger sequencing method, i.e. oligonucleotide sequencing using primer elongation and dideoxynucleotides as chain terminators
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    • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
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    • C12Q2535/00—Reactions characterised by the assay type for determining the identity of a nucleotide base or a sequence of oligonucleotides
    • C12Q2535/122—Massive parallel sequencing
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    • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
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    • C12Q2563/00—Nucleic acid detection characterized by the use of physical, structural and functional properties
    • C12Q2563/107—Nucleic acid detection characterized by the use of physical, structural and functional properties fluorescence
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    • C12Q2565/00—Nucleic acid analysis characterised by mode or means of detection
    • C12Q2565/50—Detection characterised by immobilisation to a surface
    • C12Q2565/501—Detection characterised by immobilisation to a surface being an array of oligonucleotides
    • C—CHEMISTRY; METALLURGY
    • C40—COMBINATORIAL TECHNOLOGY
    • C40B—COMBINATORIAL CHEMISTRY; LIBRARIES, e.g. CHEMICAL LIBRARIES
    • C40B40/00—Libraries per se, e.g. arrays, mixtures

Abstract

This invention provides methods for attaching a nucleic acid to a solid surface and for sequencing nucleic acid by detecting the identity of each nucleotide analogue after the nucleotide analogue is incorporated into a growing strand of DNA in a polymerase reaction. The invention also provides nucleotide analogues which comprise unique labels attached to the nucleotide analogue through a cleavable linker, and a cleavable chemical group to cap the -OH group at the 3'-position of the deoxyribose.
PCT/US2001/031243 2000-10-06 2001-10-05 Massive parallel method for decoding dna and rna WO2002029003A2 (en)

Priority Applications (6)

Application Number Priority Date Filing Date Title
EP01977533A EP1337541B1 (en) 2000-10-06 2001-10-05 Massive parallel method for decoding DNA and RNA
EP15195765.1A EP3034627B1 (en) 2000-10-06 2001-10-05 Massive parallel method for decoding dna and rna
CA2425112A CA2425112C (en) 2000-10-06 2001-10-05 Massive parallel method for decoding dna and rna
JP2002532574A JP2004510433A (en) 2000-10-06 2001-10-05 Massively parallel methods for decoding DNA and RNA
AU2001296645A AU2001296645A1 (en) 2000-10-06 2001-10-05 Massive parallel method for decoding dna and rna
DE60127162T DE60127162T2 (en) 2000-10-06 2001-10-05 Massive parallel method for the decoding of DNA and RNA

Applications Claiming Priority (4)

Application Number Priority Date Filing Date Title
US68467000A 2000-10-06 2000-10-06
US09/684,670 2000-10-06
US30089401P 2001-06-26 2001-06-26
US60/300,894 2001-06-26

Publications (2)

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WO2002029003A2 WO2002029003A2 (en) 2002-04-11
WO2002029003A3 true WO2002029003A3 (en) 2002-07-18

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PCT/US2001/031243 WO2002029003A2 (en) 2000-10-06 2001-10-05 Massive parallel method for decoding dna and rna

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US (25) US6664079B2 (en)
EP (3) EP1790736A3 (en)
JP (1) JP2004510433A (en)
AT (1) ATE356222T1 (en)
AU (1) AU2001296645A1 (en)
CA (1) CA2425112C (en)
DE (2) DE20122767U1 (en)
HK (1) HK1227441A1 (en)
WO (1) WO2002029003A2 (en)

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