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WO2000070095A3 - Homogeneous isothermal amplification and detection of nucleic acids using a template switch oligonucleotide - Google Patents

Homogeneous isothermal amplification and detection of nucleic acids using a template switch oligonucleotide Download PDF

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Publication number
WO2000070095A3
WO2000070095A3 PCT/US2000/013526 US0013526W WO0070095A3 WO 2000070095 A3 WO2000070095 A3 WO 2000070095A3 US 0013526 W US0013526 W US 0013526W WO 0070095 A3 WO0070095 A3 WO 0070095A3
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WIPO (PCT)
Prior art keywords
primer
target
amplification
detection
nucleic acid
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Ceased
Application number
PCT/US2000/013526
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French (fr)
Other versions
WO2000070095A2 (en
Inventor
Nurith Kurn
Yen Ping Liu
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Dade Behring Inc
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Dade Behring Inc
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Publication date
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Publication of WO2000070095A2 publication Critical patent/WO2000070095A2/en
Publication of WO2000070095A3 publication Critical patent/WO2000070095A3/en
Anticipated expiration legal-status Critical
Ceased legal-status Critical Current

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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
    • C12Q1/6813—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
    • 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
    • C12Q1/6816—Hybridisation assays characterised by the detection means
    • 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
    • C12Q1/6865—Promoter-based amplification, e.g. nucleic acid sequence amplification [NASBA], self-sustained sequence replication [3SR] or transcription-based amplification system [TAS]

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  • Chemical & Material Sciences (AREA)
  • Organic Chemistry (AREA)
  • Life Sciences & Earth Sciences (AREA)
  • Zoology (AREA)
  • Wood Science & Technology (AREA)
  • Proteomics, Peptides & Aminoacids (AREA)
  • Health & Medical Sciences (AREA)
  • Engineering & Computer Science (AREA)
  • Microbiology (AREA)
  • Biochemistry (AREA)
  • Physics & Mathematics (AREA)
  • Molecular Biology (AREA)
  • Biotechnology (AREA)
  • Biophysics (AREA)
  • Analytical Chemistry (AREA)
  • Immunology (AREA)
  • Bioinformatics & Cheminformatics (AREA)
  • General Engineering & Computer Science (AREA)
  • General Health & Medical Sciences (AREA)
  • Genetics & Genomics (AREA)
  • Chemical Kinetics & Catalysis (AREA)
  • Measuring Or Testing Involving Enzymes Or Micro-Organisms (AREA)

Abstract

An isothermal, transcription-based nucleic acid amplification method based on the formation of a target-dependent nucleic acid species by template switching. This product species can be amplified further to produce multiple copies of both double stranded DNA products and single stranded RNA product. The single stranded RNA amplification products are the same sense as the target sequence. Also provided is a branch migration inhibition based procedure for scanning nucleic acid sequences using the strand switch isothermal amplification. A template switch oligonucleotide used in the amplification includes a 3' region capable of hybridizing to a target sequence and a 5' region which does not hybridize to the target. The 5' region includes a promoter sequence of DNA dependent RNA polymerase. A first primer and a second primer may be used during amplification and detection. The first primer is capable of hybridizing to the target and the second primer is not target dependent. For detection, either the first primer or the second primer has a label.
PCT/US2000/013526 1999-05-17 2000-05-16 Homogeneous isothermal amplification and detection of nucleic acids using a template switch oligonucleotide Ceased WO2000070095A2 (en)

Applications Claiming Priority (2)

Application Number Priority Date Filing Date Title
US31324099A 1999-05-17 1999-05-17
US09/313,240 1999-05-17

Publications (2)

Publication Number Publication Date
WO2000070095A2 WO2000070095A2 (en) 2000-11-23
WO2000070095A3 true WO2000070095A3 (en) 2001-08-02

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PCT/US2000/013526 Ceased WO2000070095A2 (en) 1999-05-17 2000-05-16 Homogeneous isothermal amplification and detection of nucleic acids using a template switch oligonucleotide

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Cited By (11)

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US7351557B2 (en) 2001-03-09 2008-04-01 Nugen Technologies, Inc. Amplification of RNA sequences using composite RNA-DNA primers and strand displacement
US7402386B2 (en) 2003-04-14 2008-07-22 Nugen Technologies, Inc. Global amplification using random priming by a composite primer
US7501254B2 (en) 2006-07-20 2009-03-10 Ghc Technologies, Inc. Methods and compositions for amplification and capture of nucleic acid sequences
US7771946B2 (en) 2001-03-09 2010-08-10 Nugen Technologies, Inc. Methods, kits and compositions for single primer linear isothermal amplification of nucleic acid sequences
US7771934B2 (en) 2000-12-13 2010-08-10 Nugen Technologies, Inc. Methods and compositions for generation of multiple copies of nucleic acid sequences and methods of detection thereof
US7846733B2 (en) 2000-06-26 2010-12-07 Nugen Technologies, Inc. Methods and compositions for transcription-based nucleic acid amplification
US7846666B2 (en) 2008-03-21 2010-12-07 Nugen Technologies, Inc. Methods of RNA amplification in the presence of DNA
US7939258B2 (en) 2005-09-07 2011-05-10 Nugen Technologies, Inc. Nucleic acid amplification procedure using RNA and DNA composite primers
US8034568B2 (en) 2008-02-12 2011-10-11 Nugen Technologies, Inc. Isothermal nucleic acid amplification methods and compositions
US9074246B2 (en) 2010-01-25 2015-07-07 Rd Biosciences, Inc. Self-folding amplification of target nucleic acid
US9487823B2 (en) 2002-12-20 2016-11-08 Qiagen Gmbh Nucleic acid amplification

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US6692918B2 (en) 1999-09-13 2004-02-17 Nugen Technologies, Inc. Methods and compositions for linear isothermal amplification of polynucleotide sequences
DK1218542T3 (en) * 1999-09-13 2004-08-02 Nugen Technologies Inc Methods and compositions for linear isothermal amplification of polynucleotide sequences
MXPA02012735A (en) * 2000-06-26 2004-04-20 Nugen Tgechnologies Inc Methods and compositions for transcription-based nucleic acid amplification.
EP1762627A1 (en) 2005-09-09 2007-03-14 Qiagen GmbH Method for the activation of a nucleic acid for performing a polymerase reaction
DE102006020885A1 (en) * 2006-05-05 2007-11-08 Qiagen Gmbh Inserting a tag sequence into a nucleic acid comprises using an anchor oligonucleotide comprising a hybridizing anchor sequence and a nonhybridizing tag-template sequence
WO2010080691A1 (en) * 2009-01-06 2010-07-15 Qimin You Cross priming amplification of target nucleic acids
EP2847353B1 (en) 2012-05-10 2022-01-19 The General Hospital Corporation Methods for determining a nucleotide sequence
US10221442B2 (en) 2012-08-14 2019-03-05 10X Genomics, Inc. Compositions and methods for sample processing
US10752949B2 (en) 2012-08-14 2020-08-25 10X Genomics, Inc. Methods and systems for processing polynucleotides
US10273541B2 (en) 2012-08-14 2019-04-30 10X Genomics, Inc. Methods and systems for processing polynucleotides
WO2014028537A1 (en) 2012-08-14 2014-02-20 10X Technologies, Inc. Microcapsule compositions and methods
US11591637B2 (en) 2012-08-14 2023-02-28 10X Genomics, Inc. Compositions and methods for sample processing
US9701998B2 (en) 2012-12-14 2017-07-11 10X Genomics, Inc. Methods and systems for processing polynucleotides
US9951386B2 (en) 2014-06-26 2018-04-24 10X Genomics, Inc. Methods and systems for processing polynucleotides
US10323279B2 (en) 2012-08-14 2019-06-18 10X Genomics, Inc. Methods and systems for processing polynucleotides
US10400280B2 (en) 2012-08-14 2019-09-03 10X Genomics, Inc. Methods and systems for processing polynucleotides
CA2894694C (en) 2012-12-14 2023-04-25 10X Genomics, Inc. Methods and systems for processing polynucleotides
US10533221B2 (en) 2012-12-14 2020-01-14 10X Genomics, Inc. Methods and systems for processing polynucleotides
DK2954065T3 (en) 2013-02-08 2021-09-06 10X Genomics Inc Division and processing of analytes and other species
US10450597B2 (en) 2014-01-27 2019-10-22 The General Hospital Corporation Methods of preparing nucleic acids for sequencing
CA2943624A1 (en) 2014-04-10 2015-10-15 10X Genomics, Inc. Fluidic devices, systems, and methods for encapsulating and partitioning reagents, and applications of same
US12312640B2 (en) 2014-06-26 2025-05-27 10X Genomics, Inc. Analysis of nucleic acid sequences
CA2953374A1 (en) * 2014-06-26 2015-12-30 10X Genomics, Inc. Methods of analyzing nucleic acids from individual cells or cell populations
AU2015279617A1 (en) 2014-06-26 2017-01-12 10X Genomics, Inc. Analysis of nucleic acid sequences
EP4141128A1 (en) * 2014-10-20 2023-03-01 Envirologix Inc. Compositions and methods for detecting an rna virus
BR112017008877A2 (en) 2014-10-29 2018-07-03 10X Genomics Inc methods and compositions for targeting nucleic acid sequencing
US9975122B2 (en) 2014-11-05 2018-05-22 10X Genomics, Inc. Instrument systems for integrated sample processing
BR112017014902A2 (en) 2015-01-12 2018-03-13 10X Genomics, Inc processes and systems for the preparation of nucleic acid sequencing libraries and libraries prepared using them
WO2016137973A1 (en) 2015-02-24 2016-09-01 10X Genomics Inc Partition processing methods and systems
CN115651972A (en) 2015-02-24 2023-01-31 10X 基因组学有限公司 Methods for targeted nucleic acid sequence coverage
KR20240161696A (en) 2015-12-04 2024-11-12 10엑스 제노믹스, 인크. Methods and compositions for nucleic acid analysis
WO2017197343A2 (en) 2016-05-12 2017-11-16 10X Genomics, Inc. Microfluidic on-chip filters
WO2017197338A1 (en) 2016-05-13 2017-11-16 10X Genomics, Inc. Microfluidic systems and methods of use
CN109790535A (en) * 2016-07-29 2019-05-21 新英格兰生物实验室公司 Prevent the method and composition of concatemerization during template switch
JP6997773B2 (en) 2016-09-15 2022-01-18 アーチャーディーエックス， エルエルシー Method for preparing nucleic acid sample for analysis of cell-free DNA
WO2018053362A1 (en) 2016-09-15 2018-03-22 ArcherDX, Inc. Methods of nucleic acid sample preparation
US10011872B1 (en) 2016-12-22 2018-07-03 10X Genomics, Inc. Methods and systems for processing polynucleotides
US10815525B2 (en) 2016-12-22 2020-10-27 10X Genomics, Inc. Methods and systems for processing polynucleotides
US10550429B2 (en) 2016-12-22 2020-02-04 10X Genomics, Inc. Methods and systems for processing polynucleotides
US12264411B2 (en) 2017-01-30 2025-04-01 10X Genomics, Inc. Methods and systems for analysis
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US10844372B2 (en) 2017-05-26 2020-11-24 10X Genomics, Inc. Single cell analysis of transposase accessible chromatin
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Patent Citations (3)

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Cited By (17)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
US7846733B2 (en) 2000-06-26 2010-12-07 Nugen Technologies, Inc. Methods and compositions for transcription-based nucleic acid amplification
US7771934B2 (en) 2000-12-13 2010-08-10 Nugen Technologies, Inc. Methods and compositions for generation of multiple copies of nucleic acid sequences and methods of detection thereof
US8334116B2 (en) 2000-12-13 2012-12-18 Nugen Technologies, Inc. Methods and compositions for generation of multiple copies of nucleic acid sequences and methods of detection thereof
US7771946B2 (en) 2001-03-09 2010-08-10 Nugen Technologies, Inc. Methods, kits and compositions for single primer linear isothermal amplification of nucleic acid sequences
US9181582B2 (en) 2001-03-09 2015-11-10 Nugen Technologies, Inc. Compositions for amplification of RNA sequences using composite primers
US7351557B2 (en) 2001-03-09 2008-04-01 Nugen Technologies, Inc. Amplification of RNA sequences using composite RNA-DNA primers and strand displacement
US8071311B2 (en) 2001-03-09 2011-12-06 Nugen Technologies, Inc. Methods and compositions for amplification of RNA sequences
US9487823B2 (en) 2002-12-20 2016-11-08 Qiagen Gmbh Nucleic acid amplification
US8465950B2 (en) 2003-04-14 2013-06-18 Nugen Technologies, Inc. Global amplification using a randomly primed composite primer
US7402386B2 (en) 2003-04-14 2008-07-22 Nugen Technologies, Inc. Global amplification using random priming by a composite primer
US9175325B2 (en) 2003-04-14 2015-11-03 Nugen Technologies, Inc. Global amplification using a randomly primed composite primer
US8852867B2 (en) 2005-09-07 2014-10-07 Nugen Technologies, Inc. Nucleic acid amplification procedure using RNA and DNA composite primers
US7939258B2 (en) 2005-09-07 2011-05-10 Nugen Technologies, Inc. Nucleic acid amplification procedure using RNA and DNA composite primers
US7501254B2 (en) 2006-07-20 2009-03-10 Ghc Technologies, Inc. Methods and compositions for amplification and capture of nucleic acid sequences
US8034568B2 (en) 2008-02-12 2011-10-11 Nugen Technologies, Inc. Isothermal nucleic acid amplification methods and compositions
US7846666B2 (en) 2008-03-21 2010-12-07 Nugen Technologies, Inc. Methods of RNA amplification in the presence of DNA
US9074246B2 (en) 2010-01-25 2015-07-07 Rd Biosciences, Inc. Self-folding amplification of target nucleic acid

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Publication number Publication date
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