WO2013119784A1 - Procédés de séquençage d'acides nucléiques à l'aide de nanopores et correction d'épreuves cinétique active - Google Patents

Procédés de séquençage d'acides nucléiques à l'aide de nanopores et correction d'épreuves cinétique active Download PDF

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Publication number
WO2013119784A1
WO2013119784A1 PCT/US2013/025106 US2013025106W WO2013119784A1 WO 2013119784 A1 WO2013119784 A1 WO 2013119784A1 US 2013025106 W US2013025106 W US 2013025106W WO 2013119784 A1 WO2013119784 A1 WO 2013119784A1
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Prior art keywords
nanopore
ssdna
probes
probe
dna
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PCT/US2013/025106
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English (en)
Inventor
Xinsheng Sean Ling
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Brown University
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Publication of WO2013119784A1 publication Critical patent/WO2013119784A1/fr

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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

Definitions

  • Inchworm motors rely on the highly precise positioning properties of piezoelectric materials which undergo dimensional change when voltage is applied. Inchworm motors are available commercially, for example Burleigh Inchworm motors from EXFO Burleigh Products Group, Victor, New York, USA.
  • the SBH approach cannot be used for sequencing human DNA longer than approximately 1000 bases (Drmanac R. et al. 2002 Adv. Biochem. Eng. Biotechnol. 77:75-101).
  • the HANS approach is a method of solving the "repeat problem" in SBH using solid-state nanopores.
  • the major difference between the HANS approach and that of the direct nanopore sequencing of Church et al. (U.S. patent number 5,795,782) is that the HANS approach bypasses the harsh requirement of single-base spatial resolution (0.4nm). This advantage comes at the expense of a large number of samples needed to analyze DNA sequence.
  • the bead is impelled into, i.e., sucked up by a pressure difference and is in physical contact with the tip of the micropipette.
  • the diffusion of the bead is greatly suppressed as it is anchored onto the end of the micropipette which is significantly bulkier than the bead and has less Brownian motion.
  • kinetic proofreading is accomplished in DNSS by simply using a forward-reverse-forward-reverse-... translocation procedure.
  • the error rate in sequencing is reduced exponentially with the wait time i w , the time duration between binding of a probe detected in the forward translocation and again re-detected in the reverse translocation.
  • DNA is held on one end by a standard biotin-streptavidin linker to a micron-sized bead, which in turn is held by a micropipette.
  • the other end of the DNA is held inside a nanopore by an applied electric field.
  • the ssDNA is obtained by melting and flushing away the complementary strand by using high pH at the beginning of the experiment.
  • the ssDNA is held under tension inside the nanopore by the applied electric field, which prevents the ssDNA from self-hybridization.
  • a concentrated solution of oligonucleotides probes is introduced into the chamber having bead end of the ssDNA, the cis-chamber.
  • the pH of the buffer is re-adjusted to a lower value such that the hybridization condition is optimal for the probes.

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

Abstract

L'invention concerne une hybridation transitoire de di-nucléotides et/ou tri-nucléotides à une matrice d'ADN simple brin qui est mesurée par le passage du complexe à travers un nanopore, de telle sorte que des diminutions d'un courant ionique indiquent la présence et les emplacements du di-nucléotide ou du tri-nucléotide lié à l'ADN simple brin. Des analyses répétées avec tous les membres de chaque ensemble de di-nucléotides ou de tri-nucléotides génèrent une séquence de l'ADN.
PCT/US2013/025106 2012-02-08 2013-02-07 Procédés de séquençage d'acides nucléiques à l'aide de nanopores et correction d'épreuves cinétique active WO2013119784A1 (fr)

Applications Claiming Priority (2)

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US201261596491P 2012-02-08 2012-02-08
US61/596,491 2012-02-08

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WO2013119784A1 true WO2013119784A1 (fr) 2013-08-15

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Cited By (12)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
CN103940864A (zh) * 2014-03-25 2014-07-23 西北大学 双管式单分子微流装置
WO2016059375A1 (fr) * 2014-10-17 2016-04-21 Oxford Nanopore Technologies Limited Méthodes d'administration d'une substance à analyser à des pores transmembranaires
WO2016088486A1 (fr) * 2014-12-04 2016-06-09 株式会社日立ハイテクノロジーズ Système de mesure de biomolécules et procédé de mesure de biomolécules
CN108348819A (zh) * 2015-10-30 2018-07-31 环球测序技术公司 用于控制dna、rna和其他生物分子穿过纳米孔的方法和系统
US10047392B2 (en) 2014-02-21 2018-08-14 Northeastern University Fluorescence-based analysis of biopolymers using nanopores
CN110608843A (zh) * 2019-08-21 2019-12-24 岭澳核电有限公司 核电站开关设备灭弧室压力测量方法、装置、设备及介质
CN111088154A (zh) * 2019-12-25 2020-05-01 广东工业大学 一种石墨烯纳米孔测序仪及其测序方法
CN111455034A (zh) * 2020-04-09 2020-07-28 南京罗岛纳米科技有限公司 一种基于固态纳米孔机构的单分子检测方法和系统
US10774378B2 (en) 2014-04-04 2020-09-15 Oxford Nanopore Technologies Ltd. Method of target molecule characterisation using a molecular pore
CN112941160A (zh) * 2021-01-27 2021-06-11 中国科学院重庆绿色智能技术研究院 一种基于纳米操纵的纳米孔测序方法
US11041194B2 (en) 2011-05-27 2021-06-22 Oxford Nanopore Technologies Ltd. Coupling method
US11236385B2 (en) 2014-04-04 2022-02-01 Oxford Nanopore Technologies Ltd. Method for characterising a double stranded nucleic acid using a nano-pore and anchor molecules at both ends of said nucleic acid

Citations (4)

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US20020197618A1 (en) * 2001-01-20 2002-12-26 Sampson Jeffrey R. Synthesis and amplification of unstructured nucleic acids for rapid sequencing
US20070190542A1 (en) * 2005-10-03 2007-08-16 Ling Xinsheng S Hybridization assisted nanopore sequencing
US20100331194A1 (en) * 2009-04-10 2010-12-30 Pacific Biosciences Of California, Inc. Nanopore sequencing devices and methods
US20110236984A1 (en) * 2010-01-04 2011-09-29 Life Technologies Corporation Dna sequencing methods and detectors and systems for carrying out the same

Patent Citations (4)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
US20020197618A1 (en) * 2001-01-20 2002-12-26 Sampson Jeffrey R. Synthesis and amplification of unstructured nucleic acids for rapid sequencing
US20070190542A1 (en) * 2005-10-03 2007-08-16 Ling Xinsheng S Hybridization assisted nanopore sequencing
US20100331194A1 (en) * 2009-04-10 2010-12-30 Pacific Biosciences Of California, Inc. Nanopore sequencing devices and methods
US20110236984A1 (en) * 2010-01-04 2011-09-29 Life Technologies Corporation Dna sequencing methods and detectors and systems for carrying out the same

Non-Patent Citations (1)

* Cited by examiner, † Cited by third party
Title
GU ET AL.: "Single molecule sensing by nanopores and nanopore devices", ANALYST, vol. 135, no. 3, March 2010 (2010-03-01), pages 441 - 451, XP055080324 *

Cited By (31)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
US11959135B2 (en) 2011-05-27 2024-04-16 Oxford Nanopore Technologies Plc Coupling method
US11946102B2 (en) 2011-05-27 2024-04-02 Oxford Nanopore Technologies Plc Coupling method
US11136623B2 (en) 2011-05-27 2021-10-05 Oxford Nanopore Technologies Limited Coupling method
US11041194B2 (en) 2011-05-27 2021-06-22 Oxford Nanopore Technologies Ltd. Coupling method
US10047392B2 (en) 2014-02-21 2018-08-14 Northeastern University Fluorescence-based analysis of biopolymers using nanopores
CN103940864A (zh) * 2014-03-25 2014-07-23 西北大学 双管式单分子微流装置
US10774378B2 (en) 2014-04-04 2020-09-15 Oxford Nanopore Technologies Ltd. Method of target molecule characterisation using a molecular pore
US11649490B2 (en) 2014-04-04 2023-05-16 Oxford Nanopore Technologies Plc Method of target molecule characterisation using a molecular pore
US11236385B2 (en) 2014-04-04 2022-02-01 Oxford Nanopore Technologies Ltd. Method for characterising a double stranded nucleic acid using a nano-pore and anchor molecules at both ends of said nucleic acid
CN107002151A (zh) * 2014-10-17 2017-08-01 牛津纳米孔技术公司 向跨膜孔输送分析物的方法
WO2016059375A1 (fr) * 2014-10-17 2016-04-21 Oxford Nanopore Technologies Limited Méthodes d'administration d'une substance à analyser à des pores transmembranaires
US11613771B2 (en) 2014-10-17 2023-03-28 Oxford Nanopore Technologies Plc Methods for delivering an analyte to transmembrane pores
CN107002151B (zh) * 2014-10-17 2022-04-01 牛津纳米孔技术公司 向跨膜孔输送分析物的方法
CN114107457A (zh) * 2014-10-17 2022-03-01 牛津纳米孔技术公司 向跨膜孔输送分析物的方法
US10760114B2 (en) 2014-10-17 2020-09-01 Oxford Nanopore Technologies Ltd. Methods for delivering an analyte to transmembrane pores
JP2016106563A (ja) * 2014-12-04 2016-06-20 株式会社日立ハイテクノロジーズ 生体分子測定装置及び生体分子測定方法
US11169139B2 (en) 2014-12-04 2021-11-09 Hitachi High-Tech Corporation Biomolecule measurement system and biomolecule measurement method
WO2016088486A1 (fr) * 2014-12-04 2016-06-09 株式会社日立ハイテクノロジーズ Système de mesure de biomolécules et procédé de mesure de biomolécules
GB2549860B (en) * 2014-12-04 2020-11-25 Hitachi High Tech Corp Biomolecule measurement system and biomolecule measurement method
GB2549860A (en) * 2014-12-04 2017-11-01 Hitachi High Tech Corp Biomolecule measurement system and biomolecule measurement method
CN108348819B (zh) * 2015-10-30 2023-04-25 环球测序技术公司 用于控制dna、rna和其他生物分子穿过纳米孔的方法和系统
CN108348819A (zh) * 2015-10-30 2018-07-31 环球测序技术公司 用于控制dna、rna和其他生物分子穿过纳米孔的方法和系统
EP3368178A4 (fr) * 2015-10-30 2019-04-17 Universal Sequencing Technology Corporation Procédés et systèmes de régulation d'adn, d'arn et d'autres molécules biologiques traversant des nanopores
JP2018533729A (ja) * 2015-10-30 2018-11-15 ユニバーサル シークエンシング テクノロジー コーポレーション Ｄｎａ、ｒｎａおよび他の生体分子によるナノ細孔の通過を制御するための方法およびシステム
CN110608843A (zh) * 2019-08-21 2019-12-24 岭澳核电有限公司 核电站开关设备灭弧室压力测量方法、装置、设备及介质
CN110608843B (zh) * 2019-08-21 2021-02-09 岭澳核电有限公司 核电站开关设备灭弧室压力测量方法、装置、设备及介质
CN111088154A (zh) * 2019-12-25 2020-05-01 广东工业大学 一种石墨烯纳米孔测序仪及其测序方法
CN111455034A (zh) * 2020-04-09 2020-07-28 南京罗岛纳米科技有限公司 一种基于固态纳米孔机构的单分子检测方法和系统
CN111455034B (zh) * 2020-04-09 2024-04-09 苏州罗岛纳米科技有限公司 一种基于固态纳米孔机构的单分子检测方法和系统
CN112941160B (zh) * 2021-01-27 2023-07-07 中国科学院重庆绿色智能技术研究院 一种基于纳米操纵的纳米孔测序方法
CN112941160A (zh) * 2021-01-27 2021-06-11 中国科学院重庆绿色智能技术研究院 一种基于纳米操纵的纳米孔测序方法

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