WO2007137060A3 - Systems, methods, and apparatus for single molecule sequencing - Google Patents

Systems, methods, and apparatus for single molecule sequencing Download PDF

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Publication number
WO2007137060A3
WO2007137060A3 PCT/US2007/069026 US2007069026W WO2007137060A3 WO 2007137060 A3 WO2007137060 A3 WO 2007137060A3 US 2007069026 W US2007069026 W US 2007069026W WO 2007137060 A3 WO2007137060 A3 WO 2007137060A3
Authority
WO
WIPO (PCT)
Prior art keywords
systems
methods
single molecule
molecule sequencing
transparent substrate
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/US2007/069026
Other languages
French (fr)
Other versions
WO2007137060A2 (en
Inventor
Richard T Reel
Mark F Oldham
Eric Nordman
Steven J Boege
Timothy Woudenburg
Steve Menchen
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.)
Applied Biosystems Inc
Original Assignee
Applied Biosystems Inc
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 Applied Biosystems Inc filed Critical Applied Biosystems Inc
Priority to EP07797499A priority Critical patent/EP2027442A2/en
Priority to JP2009511218A priority patent/JP2009537148A/en
Publication of WO2007137060A2 publication Critical patent/WO2007137060A2/en
Publication of WO2007137060A3 publication Critical patent/WO2007137060A3/en
Anticipated expiration legal-status Critical
Ceased legal-status Critical Current

Links

Classifications

    • G—PHYSICS
    • G01—MEASURING; TESTING
    • G01N—INVESTIGATING OR ANALYSING MATERIALS BY DETERMINING THEIR CHEMICAL OR PHYSICAL PROPERTIES
    • G01N21/00—Investigating or analysing materials by the use of optical means, i.e. using sub-millimetre waves, infrared, visible or ultraviolet light
    • G01N21/62—Systems in which the material investigated is excited whereby it emits light or causes a change in wavelength of the incident light
    • G01N21/63—Systems in which the material investigated is excited whereby it emits light or causes a change in wavelength of the incident light optically excited
    • G01N21/64—Fluorescence; Phosphorescence
    • G01N21/6428—Measuring fluorescence of fluorescent products of reactions or of fluorochrome labelled reactive substances, e.g. measuring quenching effects, using measuring "optrodes"
    • G—PHYSICS
    • G01—MEASURING; TESTING
    • G01N—INVESTIGATING OR ANALYSING MATERIALS BY DETERMINING THEIR CHEMICAL OR PHYSICAL PROPERTIES
    • G01N21/00—Investigating or analysing materials by the use of optical means, i.e. using sub-millimetre waves, infrared, visible or ultraviolet light
    • G01N21/62—Systems in which the material investigated is excited whereby it emits light or causes a change in wavelength of the incident light
    • G01N21/63—Systems in which the material investigated is excited whereby it emits light or causes a change in wavelength of the incident light optically excited
    • G01N21/64—Fluorescence; Phosphorescence
    • G01N21/645—Specially adapted constructive features of fluorimeters
    • G01N21/6452—Individual samples arranged in a regular 2D-array, e.g. multiwell plates
    • G—PHYSICS
    • G01—MEASURING; TESTING
    • G01N—INVESTIGATING OR ANALYSING MATERIALS BY DETERMINING THEIR CHEMICAL OR PHYSICAL PROPERTIES
    • G01N21/00—Investigating or analysing materials by the use of optical means, i.e. using sub-millimetre waves, infrared, visible or ultraviolet light
    • G01N21/62—Systems in which the material investigated is excited whereby it emits light or causes a change in wavelength of the incident light
    • G01N21/63—Systems in which the material investigated is excited whereby it emits light or causes a change in wavelength of the incident light optically excited
    • G01N21/64—Fluorescence; Phosphorescence
    • G01N21/645—Specially adapted constructive features of fluorimeters
    • G01N21/648—Specially adapted constructive features of fluorimeters using evanescent coupling or surface plasmon coupling for the excitation of fluorescence
    • G—PHYSICS
    • G01—MEASURING; TESTING
    • G01N—INVESTIGATING OR ANALYSING MATERIALS BY DETERMINING THEIR CHEMICAL OR PHYSICAL PROPERTIES
    • G01N21/00—Investigating or analysing materials by the use of optical means, i.e. using sub-millimetre waves, infrared, visible or ultraviolet light
    • G01N21/62—Systems in which the material investigated is excited whereby it emits light or causes a change in wavelength of the incident light
    • G01N21/63—Systems in which the material investigated is excited whereby it emits light or causes a change in wavelength of the incident light optically excited
    • G01N21/64—Fluorescence; Phosphorescence
    • G01N21/6428—Measuring fluorescence of fluorescent products of reactions or of fluorochrome labelled reactive substances, e.g. measuring quenching effects, using measuring "optrodes"
    • G01N2021/6432—Quenching

Landscapes

  • Health & Medical Sciences (AREA)
  • Immunology (AREA)
  • Chemical & Material Sciences (AREA)
  • Physics & Mathematics (AREA)
  • Analytical Chemistry (AREA)
  • Nuclear Medicine, Radiotherapy & Molecular Imaging (AREA)
  • Life Sciences & Earth Sciences (AREA)
  • Biochemistry (AREA)
  • General Health & Medical Sciences (AREA)
  • General Physics & Mathematics (AREA)
  • Pathology (AREA)
  • Optics & Photonics (AREA)
  • Chemical Kinetics & Catalysis (AREA)
  • Investigating, Analyzing Materials By Fluorescence Or Luminescence (AREA)
  • Investigating Or Analysing Materials By The Use Of Chemical Reactions (AREA)
  • Apparatus Associated With Microorganisms And Enzymes (AREA)

Abstract

An embodiment generally relates to a system for analysis of an analyte. The system can include a transparent substrate. The system also includes an excitation light source configured to induce an evanescent wave excitation of a fluorescently labeled molecule near the access to the transparent substrate and a detector for detecting the fluorescently labeled molecule.
PCT/US2007/069026 2006-05-16 2007-05-16 Systems, methods, and apparatus for single molecule sequencing Ceased WO2007137060A2 (en)

Priority Applications (2)

Application Number Priority Date Filing Date Title
EP07797499A EP2027442A2 (en) 2006-05-16 2007-05-16 Systems, methods, and apparatus for single molecule sequencing
JP2009511218A JP2009537148A (en) 2006-05-16 2007-05-16 System, method and apparatus for unimolecular alignment

Applications Claiming Priority (2)

Application Number Priority Date Filing Date Title
US80044006P 2006-05-16 2006-05-16
US60/800,440 2006-05-16

Publications (2)

Publication Number Publication Date
WO2007137060A2 WO2007137060A2 (en) 2007-11-29
WO2007137060A3 true WO2007137060A3 (en) 2008-04-03

Family

ID=38723981

Family Applications (1)

Application Number Title Priority Date Filing Date
PCT/US2007/069026 Ceased WO2007137060A2 (en) 2006-05-16 2007-05-16 Systems, methods, and apparatus for single molecule sequencing

Country Status (4)

Country Link
US (2) US7709808B2 (en)
EP (1) EP2027442A2 (en)
JP (1) JP2009537148A (en)
WO (1) WO2007137060A2 (en)

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AU2007289057C1 (en) * 2006-09-01 2014-01-16 Pacific Biosciences Of California, Inc. Substrates, systems and methods for analyzing materials
US8471230B2 (en) 2006-09-01 2013-06-25 Pacific Biosciences Of California, Inc. Waveguide substrates and optical systems and methods of use thereof
US8207509B2 (en) 2006-09-01 2012-06-26 Pacific Biosciences Of California, Inc. Substrates, systems and methods for analyzing materials
US20080241866A1 (en) * 2007-03-30 2008-10-02 Pacific Biosciences Of California, Inc. Systems and methods for enhancing fluorescent signals
JP5222599B2 (en) * 2007-07-20 2013-06-26 株式会社日立ハイテクノロジーズ Nucleic acid analysis device and nucleic acid analysis apparatus using the same
US8652781B2 (en) 2008-02-12 2014-02-18 Pacific Biosciences Of California, Inc. Cognate sampling kinetics
US8530164B2 (en) 2008-09-05 2013-09-10 Pacific Biosciences Of California, Inc. Method for sequencing using branching fraction of incorporatable nucleotides
US8133672B2 (en) 2008-03-31 2012-03-13 Pacific Biosciences Of California, Inc. Two slow-step polymerase enzyme systems and methods
EP2271751B1 (en) 2008-03-31 2015-07-22 Pacific Biosciences of California, Inc. Generation of modified polymerases for improved accuracy in single molecule sequencing
US8420366B2 (en) 2008-03-31 2013-04-16 Pacific Biosciences Of California, Inc. Generation of modified polymerases for improved accuracy in single molecule sequencing
US8999676B2 (en) 2008-03-31 2015-04-07 Pacific Biosciences Of California, Inc. Recombinant polymerases for improved single molecule sequencing
CN102084003A (en) 2008-04-04 2011-06-01 生命科技公司 Scanning system and method for imaging and sequencing
US9182406B2 (en) * 2008-08-04 2015-11-10 Biodesy, Inc. Nonlinear optical detection of molecules comprising an unnatural amino acid possessing a hyperpolarizability
WO2010084953A1 (en) * 2009-01-22 2010-07-29 コニカミノルタホールディングス株式会社 Plasmon excitation sensor and method of assay using same
JP5298876B2 (en) * 2009-01-22 2013-09-25 コニカミノルタ株式会社 Plasmon excitation sensor and assay method using the same
JP5298877B2 (en) * 2009-01-22 2013-09-25 コニカミノルタ株式会社 Assay method using plasmon excitation sensor
JP5245125B2 (en) * 2009-02-06 2013-07-24 コニカミノルタ株式会社 Assay method using surface plasmon
US9778188B2 (en) 2009-03-11 2017-10-03 Industrial Technology Research Institute Apparatus and method for detection and discrimination molecular object
JP5462548B2 (en) * 2009-08-12 2014-04-02 株式会社日立ハイテクノロジーズ Nucleic acid analyzer and nucleic acid analyzer using the same
US20110059864A1 (en) * 2009-09-07 2011-03-10 Caerus Molecular Diagnostics Incorporated Sequence Determination By Use Of Opposing Forces
EP2933629B1 (en) 2010-02-19 2019-04-10 Pacific Biosciences Of California, Inc. System for measuring analytical reactions comprising a socket for an optode array chip
US8994946B2 (en) 2010-02-19 2015-03-31 Pacific Biosciences Of California, Inc. Integrated analytical system and method
US9482615B2 (en) 2010-03-15 2016-11-01 Industrial Technology Research Institute Single-molecule detection system and methods
US9670243B2 (en) 2010-06-02 2017-06-06 Industrial Technology Research Institute Compositions and methods for sequencing nucleic acids
US8865077B2 (en) 2010-06-11 2014-10-21 Industrial Technology Research Institute Apparatus for single-molecule detection
US8865078B2 (en) 2010-06-11 2014-10-21 Industrial Technology Research Institute Apparatus for single-molecule detection
WO2012009206A2 (en) 2010-07-12 2012-01-19 Pacific Biosciences Of California, Inc. Sequencing reactions with alkali metal cations for pulse width control
WO2012031234A2 (en) * 2010-09-03 2012-03-08 Life Technologies Corporation Methods, systems and apparatus for sequencing
GB2503604B (en) 2011-03-21 2020-04-22 Biodesy Llc Classification of kinase inhibitors using second harmonic optical techniques
FR2986668B1 (en) * 2012-02-02 2014-02-21 Ecole Polytech MULTI-COLOR EXCITATION MODULE FOR A MULTI-PHOTONIC IMAGING SYSTEM, SYSTEM AND METHOD THEREOF
GB2559073A (en) 2012-06-08 2018-07-25 Pacific Biosciences California Inc Modified base detection with nanopore sequencing
US9372308B1 (en) * 2012-06-17 2016-06-21 Pacific Biosciences Of California, Inc. Arrays of integrated analytical devices and methods for production
WO2014047737A1 (en) * 2012-09-27 2014-04-03 Nanospeed Diagnostics Inc. Microfluidic chip for multi-analyte detection
US9399766B2 (en) 2012-10-01 2016-07-26 Pacific Biosciences Of California, Inc. Recombinant polymerases for incorporation of protein shield nucleotide analogs
EP2936222B1 (en) 2012-12-18 2019-07-03 Pacific Biosciences Of California, Inc. An optical analytical device
MX362545B (en) * 2013-02-18 2019-01-24 Theranos Ip Co Llc Image analysis and measurement of biological samples.
WO2014130900A1 (en) 2013-02-22 2014-08-28 Pacific Biosciences Of California, Inc. Integrated illumination of optical analytical devices
WO2014165554A1 (en) * 2013-04-03 2014-10-09 Life Technologies Corporation Systems and methods for genetic sequencing
GB2531213B (en) 2014-06-30 2020-09-16 Biodesy Inc Systems and methods for high throughput analysis of conformation in biological entities
CN107003241B (en) 2014-08-27 2022-01-11 加利福尼亚太平洋生物科学股份有限公司 Integrated analytical device array
EP3237906B8 (en) 2014-12-23 2020-10-28 Bluelight Therapeutics, Inc. Attachment of proteins to interfaces for use in nonlinear optical detection
CN113064236B (en) 2015-03-16 2022-11-01 加利福尼亚太平洋生物科学股份有限公司 Integrated device and system for free space optical coupling
US10672502B2 (en) 2015-04-02 2020-06-02 Biodesy, Inc. Methods for determining protein structure using a surface-selective nonlinear optical technique
CA2983882C (en) 2015-05-07 2023-10-03 Scott E. Helgesen Multiprocessor pipeline architecture
AU2016276980B2 (en) 2015-06-12 2021-09-23 Pacific Biosciences Of California, Inc. Integrated target waveguide devices and systems for optical coupling
CN111133294B (en) * 2017-07-24 2024-05-24 宽腾矽公司 Light-inhibiting photonic structures
TWI664397B (en) * 2018-07-10 2019-07-01 精準基因生物科技股份有限公司 Sensing apparatus
US12535420B2 (en) 2020-02-18 2026-01-27 Pacific Biosciences Of California, Inc. Highly multiplexed nucleic acid sequencing systems
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CN117554349B (en) * 2024-01-11 2024-03-19 中国科学院苏州生物医学工程技术研究所 Nano integrated optical chip for single molecule sensing and fluorescence detection method

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Also Published As

Publication number Publication date
US20080105831A1 (en) 2008-05-08
WO2007137060A2 (en) 2007-11-29
EP2027442A2 (en) 2009-02-25
JP2009537148A (en) 2009-10-29
US7709808B2 (en) 2010-05-04
US20100178691A1 (en) 2010-07-15

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