AU2014218911B2 - Methods and compositions for nanostructure-based nucleic acid sequencing - Google Patents
Methods and compositions for nanostructure-based nucleic acid sequencing Download PDFInfo
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- AU2014218911B2 AU2014218911B2 AU2014218911A AU2014218911A AU2014218911B2 AU 2014218911 B2 AU2014218911 B2 AU 2014218911B2 AU 2014218911 A AU2014218911 A AU 2014218911A AU 2014218911 A AU2014218911 A AU 2014218911A AU 2014218911 B2 AU2014218911 B2 AU 2014218911B2
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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
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- General Health & Medical Sciences (AREA)
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- Measuring Or Testing Involving Enzymes Or Micro-Organisms (AREA)
- Apparatus Associated With Microorganisms And Enzymes (AREA)
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| AU2012264497B2 (en) | 2011-05-27 | 2017-06-15 | Oxford Nanopore Technologies Limited | Coupling method |
| CN111187811B (zh) | 2013-05-06 | 2024-03-08 | 加利福尼亚太平洋生物科学股份有限公司 | 实时电子测序 |
| GB201406155D0 (en) | 2014-04-04 | 2014-05-21 | Oxford Nanopore Tech Ltd | Method |
| EP3126515B1 (en) | 2014-04-04 | 2018-08-29 | Oxford Nanopore Technologies Limited | Method for characterising a double stranded nucleic acid using a nano-pore and anchor molecules at both ends of said nucleic acid |
| GB201418469D0 (en) | 2014-10-17 | 2014-12-03 | Oxford Nanopore Tech Ltd | Method |
| WO2017024049A1 (en) | 2015-08-06 | 2017-02-09 | Pacific Biosciences Of California, Inc. | Single-molecule nanofet sequencing systems and methods |
| CN105170209B (zh) * | 2015-10-15 | 2017-05-10 | 华中科技大学 | 一种表面图案化修饰的基片及其制备方法 |
| CN109071212A (zh) * | 2016-01-28 | 2018-12-21 | 罗斯韦尔生物技术股份有限公司 | 使用大规模分子电子传感器阵列测量分析物的方法和装置 |
| CN110168109B (zh) * | 2016-08-04 | 2022-09-20 | 致优制药株式会社 | 检测及鉴定结核菌和非结核菌感染的诊断方法及结核杆菌对利凡平耐药性的确认及其试剂组 |
| CN106244712B (zh) * | 2016-08-31 | 2019-11-19 | 北京大学 | Dna测序方法 |
| EP3571286A4 (en) * | 2017-01-19 | 2020-10-28 | Roswell Biotechnologies, Inc | SEMICONDUCTOR SEQUENCING DEVICES INCLUDING TWO-DIMENSIONAL LAYER MATERIALS |
| JP6559814B2 (ja) * | 2018-01-26 | 2019-08-14 | 株式会社日立ハイテクノロジーズ | 生体分子測定方法 |
| CA3104272A1 (en) * | 2019-06-18 | 2020-12-24 | Illumina, Inc. | Polymerase attachment to a conductive channel |
| CN110452817A (zh) * | 2019-07-08 | 2019-11-15 | 广东工业大学 | 一种dna测序装置及测序方法 |
| 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 |
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| WO2012033524A2 (en) * | 2010-09-07 | 2012-03-15 | The Regents Of The University Of California | Control of dna movement in a nanopore at one nucleotide precision by a processive enzyme |
| WO2012083249A2 (en) * | 2010-12-17 | 2012-06-21 | The Trustees Of Columbia University In The City Of New York | Dna sequencing by synthesis using modified nucleotides and nanopore detection |
Family Cites Families (25)
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|---|---|---|---|---|
| US5693489A (en) | 1984-03-30 | 1997-12-02 | Associated Universities, Inc. | Cloning and expression of the gene for bacteriophage T7 RNA polymerase |
| US5795782A (en) * | 1995-03-17 | 1998-08-18 | President & Fellows Of Harvard College | Characterization of individual polymer molecules based on monomer-interface interactions |
| US20020172953A1 (en) * | 1996-07-29 | 2002-11-21 | Mirkin Chad A. | Movement of biomolecule-coated nanoparticles in an electric field |
| US6232075B1 (en) | 1998-12-14 | 2001-05-15 | Li-Cor, Inc. | Heterogeneous assay for pyrophosphate detection |
| US6529240B2 (en) | 1999-11-18 | 2003-03-04 | Agilent Technologies, Inc. | Random access memory integrated with CMOS sensors |
| US7238477B2 (en) | 2001-09-24 | 2007-07-03 | Intel Corporation | Methods to increase nucleotide signals by Raman scattering |
| ATE432365T1 (de) * | 2003-02-21 | 2009-06-15 | Geneform Technologies Ltd | Verfahren, kits und reagenzien zur nukleinsäuresequenzierung |
| US20070077575A1 (en) | 2004-03-05 | 2007-04-05 | Mcallister William T | Use of rna polymerase as an information-dependent molecular motor |
| WO2006028508A2 (en) * | 2004-03-23 | 2006-03-16 | President And Fellows Of Harvard College | Methods and apparatus for characterizing polynucleotides |
| WO2007111924A2 (en) * | 2006-03-23 | 2007-10-04 | The Board Of Trustees Of The Leland Stanford Junior University | Motion resolved molecular sequencing |
| AU2008236694B2 (en) * | 2007-04-04 | 2014-01-23 | The Regents Of The University Of California | Compositions, devices, systems, and methods for using a nanopore |
| US9395352B2 (en) * | 2007-04-06 | 2016-07-19 | Arizona Board Of Regents On Behalf Of Arizona State University | Devices and methods for target molecule characterization |
| AU2008331824B2 (en) | 2007-12-04 | 2014-07-24 | Pacific Biosciences Of California, Inc. | Alternate labeling strategies for single molecule sequencing |
| US8815576B2 (en) | 2007-12-27 | 2014-08-26 | Lawrence Livermore National Security, Llc. | Chip-based sequencing nucleic acids |
| WO2009117522A2 (en) * | 2008-03-18 | 2009-09-24 | Reinhart, Kevin | Nanopore and carbon nanotube based dna sequencer and a serial recognition sequencer |
| US20100261185A1 (en) * | 2009-03-27 | 2010-10-14 | Life Technologies Corporation | Labeled enzyme compositions, methods and systems |
| US9017937B1 (en) * | 2009-04-10 | 2015-04-28 | Pacific Biosciences Of California, Inc. | Nanopore sequencing using ratiometric impedance |
| CA2790672C (en) * | 2010-02-23 | 2018-05-29 | University Of Washington | Artificial mycolic acid membranes |
| JP6018092B2 (ja) * | 2011-02-23 | 2016-11-02 | イブ バイオメディカル インコーポレイテッド | 回転依存転写配列決定システムおよび使用方法 |
| AU2012264497B2 (en) | 2011-05-27 | 2017-06-15 | Oxford Nanopore Technologies Limited | Coupling method |
| JP6298404B2 (ja) * | 2011-07-25 | 2018-03-20 | オックスフォード ナノポール テクノロジーズ リミテッド | 膜貫通ポアを用いる二重鎖ポリヌクレオチド配列決定のためのヘアピンループ方法 |
| US9164053B2 (en) * | 2011-09-26 | 2015-10-20 | The Regents Of The University Of California | Electronic device for monitoring single molecule dynamics |
| US9279154B2 (en) * | 2011-12-21 | 2016-03-08 | Illumina, Inc. | Apparatus and methods for kinetic analysis and determination of nucleic acid sequences |
| WO2013185137A1 (en) * | 2012-06-08 | 2013-12-12 | Pacific Biosciences Of California, Inc. | Modified base detection with nanopore sequencing |
| US20140147833A1 (en) * | 2012-11-28 | 2014-05-29 | International Business Machines Corporation | Base recognition based on the conformation change of a motor molecule |
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2014
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- 2014-02-20 RU RU2015139609A patent/RU2015139609A/ru not_active Application Discontinuation
- 2014-02-20 EP EP14754640.2A patent/EP2958927A4/en not_active Withdrawn
- 2014-02-20 JP JP2015558959A patent/JP2016507249A/ja active Pending
- 2014-02-20 CA CA2900921A patent/CA2900921A1/en not_active Abandoned
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Patent Citations (2)
| Publication number | Priority date | Publication date | Assignee | Title |
|---|---|---|---|---|
| WO2012033524A2 (en) * | 2010-09-07 | 2012-03-15 | The Regents Of The University Of California | Control of dna movement in a nanopore at one nucleotide precision by a processive enzyme |
| WO2012083249A2 (en) * | 2010-12-17 | 2012-06-21 | The Trustees Of Columbia University In The City Of New York | Dna sequencing by synthesis using modified nucleotides and nanopore detection |
Also Published As
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| CN105308062A (zh) | 2016-02-03 |
| RU2015139609A (ru) | 2017-03-24 |
| US9725763B2 (en) | 2017-08-08 |
| AU2014218911A1 (en) | 2015-08-27 |
| EP2958927A2 (en) | 2015-12-30 |
| JP2016507249A (ja) | 2016-03-10 |
| HK1221227A1 (zh) | 2017-05-26 |
| US20180010181A1 (en) | 2018-01-11 |
| WO2014130686A2 (en) | 2014-08-28 |
| EP2958927A4 (en) | 2016-09-14 |
| WO2014130686A3 (en) | 2014-10-09 |
| CA2900921A1 (en) | 2014-08-28 |
| KR20150119353A (ko) | 2015-10-23 |
| US20140235462A1 (en) | 2014-08-21 |
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