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WO2008037568A3 - Reversible terminators for efficient sequencing by synthesis - Google Patents

Reversible terminators for efficient sequencing by synthesis Download PDF

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Publication number
WO2008037568A3
WO2008037568A3 PCT/EP2007/059207 EP2007059207W WO2008037568A3 WO 2008037568 A3 WO2008037568 A3 WO 2008037568A3 EP 2007059207 W EP2007059207 W EP 2007059207W WO 2008037568 A3 WO2008037568 A3 WO 2008037568A3
Authority
WO
WIPO (PCT)
Prior art keywords
hydrogen
group
compounds
detectable group
detectable
Prior art date
Legal status (The legal status 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 status listed.)
Ceased
Application number
PCT/EP2007/059207
Other languages
French (fr)
Other versions
WO2008037568A2 (en
Inventor
Diana Katerina Knapp
Joachim W Engels
Angelica Keller
Yangzhou Li
Julius Gagilas
Saulius Serva
Alina Stura
Andras Foldesi
Nilsson Camilla Estmer
Marek Kwiatkowski
Current Assignee (The listed assignees may be inaccurate. Google has not performed a legal analysis and makes no representation or warranty as to the accuracy of the list.)
Quiatech AB
Original Assignee
Quiatech AB
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 Quiatech AB filed Critical Quiatech AB
Publication of WO2008037568A2 publication Critical patent/WO2008037568A2/en
Publication of WO2008037568A3 publication Critical patent/WO2008037568A3/en
Anticipated expiration legal-status Critical
Ceased legal-status Critical Current

Links

Classifications

    • 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
    • C07H19/16—Purine radicals
    • C07H19/20—Purine 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
    • 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

Landscapes

  • Chemical & Material Sciences (AREA)
  • Organic Chemistry (AREA)
  • Health & Medical Sciences (AREA)
  • Life Sciences & Earth Sciences (AREA)
  • Biochemistry (AREA)
  • Molecular Biology (AREA)
  • Engineering & Computer Science (AREA)
  • Biotechnology (AREA)
  • General Health & Medical Sciences (AREA)
  • Genetics & Genomics (AREA)
  • Saccharide Compounds (AREA)
  • Measuring Or Testing Involving Enzymes Or Micro-Organisms (AREA)

Abstract

The invention relates to compounds of general structure (I) or salts thereof, wherein B is a nucleobase, X and Y independently are oxygen or sulphur, Z is a chemical group characterized by strong electron withdrawing properties, R1 is hydrogen, hydroxyl or a protected hydroxyl, R2 and R3 are together or separately hydrogen or a hydrocarbyl, R4 is hydrogen or a chemical moiety consisting of a linker molecule L, linking a detectable group to the rest of the structure (I), R5 is hydrogen or an additional electron withdrawing group. R5 can be identical with Z or different. R6 is hydrogen or a chemical moiety consisting of a linker unit L, a cleavable group and a detectable group joined together in the following order R6 = -L-cleavable group-detectable group. The detectable group is placed either on R4 or R6 or is absent, thus either R4 is hydrogen and the detectable group is placed on R6, or R6 is hydrogen and the detectable group is placed on R4, or both R4 and R6 are hydrogen. Numbers m and n are independently 0 or 1. Compounds of formula (I) are useful as reversible chain extension terminators. The invention also relates to the use of the compounds (I) in nucleic acid sequencing as well as to a method of preparing compounds of Formula (I).
PCT/EP2007/059207 2006-09-04 2007-09-04 Reversible terminators for efficient sequencing by synthesis Ceased WO2008037568A2 (en)

Applications Claiming Priority (2)

Application Number Priority Date Filing Date Title
US82445306P 2006-09-04 2006-09-04
US60/824,453 2006-09-04

Publications (2)

Publication Number Publication Date
WO2008037568A2 WO2008037568A2 (en) 2008-04-03
WO2008037568A3 true WO2008037568A3 (en) 2008-10-02

Family

ID=39230564

Family Applications (1)

Application Number Title Priority Date Filing Date
PCT/EP2007/059207 Ceased WO2008037568A2 (en) 2006-09-04 2007-09-04 Reversible terminators for efficient sequencing by synthesis

Country Status (1)

Country Link
WO (1) WO2008037568A2 (en)

Cited By (4)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
US10738072B1 (en) 2018-10-25 2020-08-11 Singular Genomics Systems, Inc. Nucleotide analogues
US10822653B1 (en) 2019-01-08 2020-11-03 Singular Genomics Systems, Inc. Nucleotide cleavable linkers and uses thereof
US11591647B2 (en) 2017-03-06 2023-02-28 Singular Genomics Systems, Inc. Nucleic acid sequencing-by-synthesis (SBS) methods that combine SBS cycle steps
US12215124B2 (en) 2018-02-21 2025-02-04 Singular Genomics Systems, Inc. Fluorinated nucleotides and uses thereof

Families Citing this family (14)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
CA2725239C (en) 2008-05-27 2019-02-26 Trilink Biotechnologies Chemically modified nucleoside 5'-triphosphates for thermally initiated amplification of nucleic acid
US9150896B2 (en) 2012-09-06 2015-10-06 Illumina, Inc. Nucleotides and primers with removable blocking groups
US9146248B2 (en) 2013-03-14 2015-09-29 Intelligent Bio-Systems, Inc. Apparatus and methods for purging flow cells in nucleic acid sequencing instruments
US9591268B2 (en) 2013-03-15 2017-03-07 Qiagen Waltham, Inc. Flow cell alignment methods and systems
EP3209781B8 (en) 2014-10-20 2020-01-15 Molecular Assemblies Inc. Modified template-independent enzymes for polydeoxynucleotide synthesis
US9868947B2 (en) 2015-05-04 2018-01-16 Washington University Compositions and methods for the construction of a random allelic series
EP3356381A4 (en) 2015-09-28 2019-06-12 The Trustees of Columbia University in the City of New York NUCLEOTIDE DERIVATIVES AND METHODS OF USE
EP3463381A4 (en) 2016-05-23 2020-01-01 The Trustees of Columbia University in the City of New York NUCLEOTIDE DERIVATIVES AND METHOD FOR USE THEREOF
US12018325B2 (en) 2017-03-28 2024-06-25 The Trustees Of Columbia University In The City Of New York 3′-O-modified nucleotide analogues with different cleavable linkers for attaching fluorescent labels to the base for DNA sequencing by synthesis
US12188086B2 (en) 2018-03-15 2025-01-07 The Trustees Of Columbia University In The City Of New York Nucleotide analogues and use thereof for nucleic acid sequencing and analysis preliminary class
WO2020033681A2 (en) 2018-08-10 2020-02-13 Life Technologies Corporation Silicon-substituted rhodamine dyes and dye conjugates
EP4077344B1 (en) 2019-12-18 2025-07-23 F. Hoffmann-La Roche AG Methods of sequencing by synthesis using a consecutive labeling scheme
WO2022083686A1 (en) * 2020-10-21 2022-04-28 深圳华大生命科学研究院 Modified nucleoside or nucleotide
US12391970B2 (en) 2020-11-11 2025-08-19 Microsoft Technology Licensing, Llc Spatial control of polynucleotide synthesis by strand capping

Citations (4)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
US5302509A (en) * 1989-08-14 1994-04-12 Beckman Instruments, Inc. Method for sequencing polynucleotides
WO2001025247A1 (en) * 1999-10-05 2001-04-12 Quiatech Ab Compounds for protecting hydroxyls and methods for their use
WO2002029003A2 (en) * 2000-10-06 2002-04-11 The Trustees Of Columbia University In The City Of New York Massive parallel method for decoding dna and rna
WO2004018497A2 (en) * 2002-08-23 2004-03-04 Solexa Limited Modified nucleotides for polynucleotide sequencing

Patent Citations (4)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
US5302509A (en) * 1989-08-14 1994-04-12 Beckman Instruments, Inc. Method for sequencing polynucleotides
WO2001025247A1 (en) * 1999-10-05 2001-04-12 Quiatech Ab Compounds for protecting hydroxyls and methods for their use
WO2002029003A2 (en) * 2000-10-06 2002-04-11 The Trustees Of Columbia University In The City Of New York Massive parallel method for decoding dna and rna
WO2004018497A2 (en) * 2002-08-23 2004-03-04 Solexa Limited Modified nucleotides for polynucleotide sequencing

Non-Patent Citations (3)

* Cited by examiner, † Cited by third party
Title
OHGI T ET AL: "A New RNA Synthetic Method with a 2'-O-(2-Cyanoethoxymethyl) Protecting Group", ORGANIC LETTERS, AMERICAN CHEMICAL SOCIETY, COLUMBUS, OH; US, vol. 7, no. 16, 1 January 2005 (2005-01-01), pages 3477 - 3480, XP003009345, ISSN: 1523-7060 *
SANEYOSHI H ET AL: "A General Method for the Synthesis of 2'-O-Cyanoethylated Oligoribonucleotides Having Promising Hybridization Affinity for DNA and RNA and Enhanced Nuclease Resistance", JOURNAL OF ORGANIC CHEMISTRY, AMERICAN CHEMICAL SOCIETY. EASTON, vol. 70, no. 25, 1 January 2005 (2005-01-01), pages 10453 - 10460, XP003017305, ISSN: 0022-3263 *
UMEMOTO T ET AL: "Oligoribonucleotide synthesis by the use of 1-(2-cyanoethoxy)ethyl (CEE) as a 2'-hydroxy protecting group", TETRAHEDRON LETTERS, ELSEVIER, AMSTERDAM, vol. 45, no. 52, 20 December 2004 (2004-12-20), pages 9529 - 9531, XP004727393, ISSN: 0040-4039 *

Cited By (10)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
US11591647B2 (en) 2017-03-06 2023-02-28 Singular Genomics Systems, Inc. Nucleic acid sequencing-by-synthesis (SBS) methods that combine SBS cycle steps
US11773439B2 (en) 2017-03-06 2023-10-03 Singular Genomics Systems, Inc. Nucleic acid sequencing-by-synthesis (SBS) methods that combine SBS cycle steps
US12215124B2 (en) 2018-02-21 2025-02-04 Singular Genomics Systems, Inc. Fluorinated nucleotides and uses thereof
US10738072B1 (en) 2018-10-25 2020-08-11 Singular Genomics Systems, Inc. Nucleotide analogues
US11878993B2 (en) 2018-10-25 2024-01-23 Singular Genomics Systems, Inc. Nucleotide analogues
US11958877B2 (en) 2018-10-25 2024-04-16 Singular Genomics Systems, Inc. Nucleotide analogues
US12145960B2 (en) 2018-10-25 2024-11-19 Singular Genomics Systems, Inc. Nucleotide analogues
US12215122B2 (en) 2018-10-25 2025-02-04 Singular Genomics Systems, Inc. Nucleotide analogues
US10822653B1 (en) 2019-01-08 2020-11-03 Singular Genomics Systems, Inc. Nucleotide cleavable linkers and uses thereof
US11970735B2 (en) 2019-01-08 2024-04-30 Singular Genomics Systems, Inc. Nucleotide cleavable linkers and uses thereof

Also Published As

Publication number Publication date
WO2008037568A2 (en) 2008-04-03

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