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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WO
WIPO (PCT)
Prior art keywords
primer
target
amplification
detection
nucleic acid
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Application number
PCT/US2000/013526
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French (fr)
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WO2000070095A2 (en
Inventor
Nurith Kurn
Yen Ping Liu
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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

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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]

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 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 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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WO (1) WO2000070095A2 (en)

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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
US7846666B2 (en) 2008-03-21 2010-12-07 Nugen Technologies, Inc. Methods of RNA amplification in the presence of DNA
US7846733B2 (en) 2000-06-26 2010-12-07 Nugen Technologies, Inc. Methods and compositions for transcription-based nucleic acid amplification
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
US8465950B2 (en) 2003-04-14 2013-06-18 Nugen Technologies, Inc. Global amplification using a randomly primed composite primer
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
ATE455186T1 (en) * 2000-06-26 2010-01-15 Nugen Technologies Inc METHODS AND COMPOSITIONS FOR TRANSCRIPTION-BASED DUPLICATION OF NUCLEIC ACIDS
JP2005508135A (en) * 2001-03-09 2005-03-31 ニューゲン テクノロジーズ， インコーポレイテッド Methods and compositions for amplification of RNA sequences
EP1762627A1 (en) 2005-09-09 2007-03-14 Qiagen GmbH Method for the activation of a nucleic acid for performing a polymerase reaction
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US7501254B2 (en) 2006-07-20 2009-03-10 Ghc Technologies, Inc. Methods and compositions for amplification and capture of nucleic acid sequences
EP2382330B1 (en) * 2009-01-06 2015-03-11 Ustar Biotechnologies Ltd Cross priming amplification of target nucleic acids
CN102725424B (en) 2010-01-25 2014-07-09 Rd生物科技公司 Self-folding amplification of target nucleic acid
EP2847353B1 (en) 2012-05-10 2022-01-19 The General Hospital Corporation Methods for determining a nucleotide sequence
US11591637B2 (en) 2012-08-14 2023-02-28 10X Genomics, Inc. Compositions and methods for sample processing
US10273541B2 (en) 2012-08-14 2019-04-30 10X Genomics, Inc. Methods and systems for processing polynucleotides
US9701998B2 (en) 2012-12-14 2017-07-11 10X Genomics, Inc. Methods and systems for processing polynucleotides
CN111748607A (en) 2012-08-14 2020-10-09 10X基因组学有限公司 Microcapsule compositions and methods
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
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
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US10533221B2 (en) 2012-12-14 2020-01-14 10X Genomics, Inc. Methods and systems for processing polynucleotides
CA2900543C (en) 2013-02-08 2023-01-31 10X Genomics, Inc. Partitioning and processing of analytes and other species
AU2015209079B2 (en) 2014-01-27 2021-07-15 Archerdx, Llc Methods of preparing nucleic acids for sequencing
MX2016013156A (en) 2014-04-10 2017-02-14 10X Genomics Inc Fluidic devices, systems, and methods for encapsulating and partitioning reagents, and applications of same.
KR102531677B1 (en) * 2014-06-26 2023-05-10 10엑스 제노믹스, 인크. Methods of analyzing nucleic acids from individual cells or cell populations
AU2015336086C1 (en) * 2014-10-20 2021-07-29 Envirologix Inc. Compositions and methods for detecting an RNA virus
EP3212807B1 (en) 2014-10-29 2020-09-02 10X Genomics, Inc. Methods and compositions for targeted nucleic acid sequencing
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MX367432B (en) 2015-01-12 2019-08-08 10X Genomics Inc Processes and systems for preparing nucleic acid sequencing libraries and libraries prepared using same.
WO2016137973A1 (en) 2015-02-24 2016-09-01 10X Genomics Inc Partition processing methods and systems
KR20170119710A (en) 2015-02-24 2017-10-27 10엑스 제노믹스, 인크. Targeted nucleic acid sequence coverage method
PT3882357T (en) 2015-12-04 2022-09-05 10X Genomics Inc Methods and compositions for nucleic acid analysis
WO2017197338A1 (en) 2016-05-13 2017-11-16 10X Genomics, Inc. Microfluidic systems and methods of use
EP3491128B1 (en) * 2016-07-29 2021-09-08 New England Biolabs, Inc. Methods and compositions for preventing concatemerization during template- switching
AU2017328953B2 (en) 2016-09-15 2023-09-14 Archerdx, Llc Methods of nucleic acid sample preparation for analysis of cell-free DNA
EP3933039A1 (en) 2016-09-15 2022-01-05 ArcherDX, LLC Methods of nucleic acid sample preparation
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US10815525B2 (en) 2016-12-22 2020-10-27 10X Genomics, Inc. Methods and systems for processing polynucleotides
US10011872B1 (en) 2016-12-22 2018-07-03 10X Genomics, Inc. Methods and systems for processing polynucleotides
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Cited By (13)

* 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
US8071311B2 (en) 2001-03-09 2011-12-06 Nugen Technologies, Inc. Methods and compositions for amplification of RNA 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
US9181582B2 (en) 2001-03-09 2015-11-10 Nugen Technologies, Inc. Compositions for amplification of RNA sequences using composite primers
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
US9175325B2 (en) 2003-04-14 2015-11-03 Nugen Technologies, Inc. Global amplification using a randomly primed composite primer
US7939258B2 (en) 2005-09-07 2011-05-10 Nugen Technologies, Inc. Nucleic acid amplification procedure using RNA and DNA composite primers
US8852867B2 (en) 2005-09-07 2014-10-07 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
US7846666B2 (en) 2008-03-21 2010-12-07 Nugen Technologies, Inc. Methods of RNA amplification in the presence of DNA

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