WO2009051807A1 - Design and synthesis of cleavable fluorescent nucleotides as reversible terminators for dna sequencing by synthesis - Google Patents

Design and synthesis of cleavable fluorescent nucleotides as reversible terminators for dna sequencing by synthesis Download PDF

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Publication number
WO2009051807A1
WO2009051807A1 PCT/US2008/011891 US2008011891W WO2009051807A1 WO 2009051807 A1 WO2009051807 A1 WO 2009051807A1 US 2008011891 W US2008011891 W US 2008011891W WO 2009051807 A1 WO2009051807 A1 WO 2009051807A1
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WO
WIPO (PCT)
Prior art keywords
nucleic acid
dntp
fluorophore
consecutive nucleotide
analogues
Prior art date
Application number
PCT/US2008/011891
Other languages
English (en)
French (fr)
Inventor
Jingyue Ju
Huanyan Cao
Zengmin Li
Qinglin Meng
Jia GUO
Shenglong Zhang
Lin Yu
Original Assignee
The Trustees Of Columbia University In The City Of New York
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 The Trustees Of Columbia University In The City Of New York filed Critical The Trustees Of Columbia University In The City Of New York
Priority to EP23212547.6A priority Critical patent/EP4310194A2/en
Priority to US12/734,227 priority patent/US20110014611A1/en
Priority to EP15165262.5A priority patent/EP2940029B1/en
Priority to EP20080839081 priority patent/EP2207900B1/en
Publication of WO2009051807A1 publication Critical patent/WO2009051807A1/en
Priority to US13/951,269 priority patent/US9175342B2/en
Priority to US14/859,853 priority patent/US9670539B2/en
Priority to US15/596,379 priority patent/US10144961B2/en
Priority to US16/208,379 priority patent/US11208691B2/en
Priority to US17/560,928 priority patent/US20220112552A1/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
    • C12Q1/6869—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
    • 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
    • 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
    • C07H19/16—Purine radicals
    • 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
    • C07H19/16—Purine radicals
    • C07H19/20—Purine radicals with the saccharide radical esterified by phosphoric or polyphosphoric acids
    • 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
    • C12Q2525/00—Reactions involving modified oligonucleotides, nucleic acids, or nucleotides
    • C12Q2525/30—Oligonucleotides characterised by their secondary structure
    • C12Q2525/301—Hairpin oligonucleotides
    • 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
    • C12Q2537/00—Reactions characterised by the reaction format or use of a specific feature
    • C12Q2537/10—Reactions characterised by the reaction format or use of a specific feature the purpose or use of
    • C12Q2537/157—A reaction step characterised by the number of molecules incorporated or released
PCT/US2008/011891 2007-10-19 2008-10-17 Design and synthesis of cleavable fluorescent nucleotides as reversible terminators for dna sequencing by synthesis WO2009051807A1 (en)

Priority Applications (9)

Application Number Priority Date Filing Date Title
EP23212547.6A EP4310194A2 (en) 2007-10-19 2008-10-17 Design and synthesis of cleavable fluorescent nucleotides as reversible terminators for dna sequencing by synthesis
US12/734,227 US20110014611A1 (en) 2007-10-19 2008-10-17 Design and synthesis of cleavable fluorescent nucleotides as reversible terminators for dna sequences by synthesis
EP15165262.5A EP2940029B1 (en) 2007-10-19 2008-10-17 Design and synthesis of cleavable fluorescent nucleotides as reversible terminators for dna sequencing by synthesis
EP20080839081 EP2207900B1 (en) 2007-10-19 2008-10-17 Design and synthesis of cleavable fluorescent nucleotides as reversible terminators for dna sequencing by synthesis
US13/951,269 US9175342B2 (en) 2007-10-19 2013-07-25 Synthesis of cleavable fluorescent nucleotides as reversible terminators for DNA sequencing by synthesis
US14/859,853 US9670539B2 (en) 2007-10-19 2015-09-21 Synthesis of cleavable fluorescent nucleotides as reversible terminators for DNA sequencing by synthesis
US15/596,379 US10144961B2 (en) 2007-10-19 2017-05-16 Synthesis of cleavable fluorescent nucleotides as reversible terminators for DNA sequencing by synthesis
US16/208,379 US11208691B2 (en) 2007-10-19 2018-12-03 Synthesis of cleavable fluorescent nucleotides as reversible terminators for DNA sequencing by synthesis
US17/560,928 US20220112552A1 (en) 2007-10-19 2021-12-23 Design and synthesis of cleavable fluorescent nucleotides as reversible terminators for dna sequencing by synthesis

Applications Claiming Priority (2)

Application Number Priority Date Filing Date Title
US99957607P 2007-10-19 2007-10-19
US60/999,576 2007-10-19

Related Child Applications (2)

Application Number Title Priority Date Filing Date
US12/734,227 A-371-Of-International US20110014611A1 (en) 2007-10-19 2008-10-17 Design and synthesis of cleavable fluorescent nucleotides as reversible terminators for dna sequences by synthesis
US13/951,269 Continuation US9175342B2 (en) 2007-10-19 2013-07-25 Synthesis of cleavable fluorescent nucleotides as reversible terminators for DNA sequencing by synthesis

Publications (1)

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WO2009051807A1 true WO2009051807A1 (en) 2009-04-23

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PCT/US2008/011891 WO2009051807A1 (en) 2007-10-19 2008-10-17 Design and synthesis of cleavable fluorescent nucleotides as reversible terminators for dna sequencing by synthesis

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US (6) US20110014611A1 (US20110014611A1-20110120-C00023.png)
EP (3) EP4310194A2 (US20110014611A1-20110120-C00023.png)
HK (1) HK1217106A1 (US20110014611A1-20110120-C00023.png)
WO (1) WO2009051807A1 (US20110014611A1-20110120-C00023.png)

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US8754244B1 (en) 2013-03-08 2014-06-17 Illumina Cambridge Limited Rhodamine compounds and their use as fluorescent labels
US8796432B2 (en) 2005-10-31 2014-08-05 The Trustees Of Columbia University In The City Of New York Chemically cleavable 3'-o-allyl-DNTP-allyl-fluorophore fluorescent nucleotide analogues and related methods
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CN104292117A (zh) * 2013-07-15 2015-01-21 上海交通大学 酸敏感连接单元的合成及其在dna测序中的用途
US8962242B2 (en) 2011-01-24 2015-02-24 Genia Technologies, Inc. System for detecting electrical properties of a molecular complex
US8986629B2 (en) 2012-02-27 2015-03-24 Genia Technologies, Inc. Sensor circuit for controlling, detecting, and measuring a molecular complex
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US9169510B2 (en) 2005-06-21 2015-10-27 The Trustees Of Columbia University In The City Of New York Pyrosequencing methods and related compositions
US9175342B2 (en) 2007-10-19 2015-11-03 The Trustees Of Columbia University In The City Of New York Synthesis of cleavable fluorescent nucleotides as reversible terminators for DNA sequencing by synthesis
US9255292B2 (en) 2005-10-31 2016-02-09 The Trustees Of Columbia University In The City Of New York Synthesis of four-color 3′-O-allyl modified photocleavable fluorescent nucleotides and related methods
WO2016020691A1 (en) * 2014-08-08 2016-02-11 Illumina Cambridge Limited Modified nucleotide linkers
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CN114634488A (zh) * 2020-12-15 2022-06-17 湖北华大基因研究院 琥珀酰亚胺酯及其制备、处理和检测方法
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