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WO2003000920A3 - Methods for characterization of nucleic acid molecules - Google Patents

Methods for characterization of nucleic acid molecules Download PDF

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Publication number
WO2003000920A3
WO2003000920A3 PCT/US2002/019766 US0219766W WO03000920A3 WO 2003000920 A3 WO2003000920 A3 WO 2003000920A3 US 0219766 W US0219766 W US 0219766W WO 03000920 A3 WO03000920 A3 WO 03000920A3
Authority
WO
WIPO (PCT)
Prior art keywords
nucleic acid
local
acid molecule
modified
molecule
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/US2002/019766
Other languages
French (fr)
Other versions
WO2003000920A9 (en
WO2003000920A2 (en
Inventor
Daniel Branton
Hui Wang
Stephen Laderman
Jeffrey Sampson
Zohar Yakhani
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.)
Agilent Technologies Inc
Harvard University
Original Assignee
Agilent Technologies Inc
Harvard University
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 Agilent Technologies Inc, Harvard University filed Critical Agilent Technologies Inc
Priority to EP02747942A priority Critical patent/EP1478771A4/en
Priority to AU2002318386A priority patent/AU2002318386A1/en
Publication of WO2003000920A2 publication Critical patent/WO2003000920A2/en
Publication of WO2003000920A9 publication Critical patent/WO2003000920A9/en
Anticipated expiration legal-status Critical
Publication of WO2003000920A3 publication Critical patent/WO2003000920A3/en
Ceased legal-status Critical Current

Links

Classifications

    • 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
    • C12Q1/6825—Nucleic acid detection involving sensors
    • 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
    • G—PHYSICS
    • G01—MEASURING; TESTING
    • G01N—INVESTIGATING OR ANALYSING MATERIALS BY DETERMINING THEIR CHEMICAL OR PHYSICAL PROPERTIES
    • G01N33/00—Investigating or analysing materials by specific methods not covered by groups G01N1/00 - G01N31/00
    • G01N33/48—Biological material, e.g. blood, urine; Haemocytometers
    • G01N33/483—Physical analysis of biological material
    • G01N33/487—Physical analysis of biological material of liquid biological material
    • G01N33/48707—Physical analysis of biological material of liquid biological material by electrical means
    • G01N33/48721—Investigating individual macromolecules, e.g. by translocation through nanopores
    • H—ELECTRICITY
    • H04—ELECTRIC COMMUNICATION TECHNIQUE
    • H04N—PICTORIAL COMMUNICATION, e.g. TELEVISION
    • H04N7/00—Television systems
    • H04N7/18—Closed-circuit television [CCTV] systems, i.e. systems in which the video signal is not broadcast
    • 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

Landscapes

  • Chemical & Material Sciences (AREA)
  • Life Sciences & Earth Sciences (AREA)
  • Engineering & Computer Science (AREA)
  • Health & Medical Sciences (AREA)
  • Organic Chemistry (AREA)
  • Physics & Mathematics (AREA)
  • Analytical Chemistry (AREA)
  • Proteomics, Peptides & Aminoacids (AREA)
  • Zoology (AREA)
  • Wood Science & Technology (AREA)
  • Biophysics (AREA)
  • Molecular Biology (AREA)
  • General Health & Medical Sciences (AREA)
  • Immunology (AREA)
  • Biomedical Technology (AREA)
  • Biochemistry (AREA)
  • Bioinformatics & Cheminformatics (AREA)
  • Biotechnology (AREA)
  • Microbiology (AREA)
  • Genetics & Genomics (AREA)
  • General Engineering & Computer Science (AREA)
  • Hematology (AREA)
  • Spectroscopy & Molecular Physics (AREA)
  • Nanotechnology (AREA)
  • Urology & Nephrology (AREA)
  • Food Science & Technology (AREA)
  • Medicinal Chemistry (AREA)
  • General Physics & Mathematics (AREA)
  • Pathology (AREA)
  • Multimedia (AREA)
  • Signal Processing (AREA)
  • Measuring Or Testing Involving Enzymes Or Micro-Organisms (AREA)

Abstract

To probe the characteristics of a target nucleic acid molecule or a population of target nucleic acid molecules, a local cross-sectional area, local charge, or local chemistry of a molecule is modified. The modified nucleic acid is contacted with a substrate that includes a detector that is responsive to the modification in the local cross-sectional area, local charge, or local chemistry of the nucleic acid molecule. The modified nucleic acid molecule traverses a defined and preferably molecular dimensioned volume on the substrate so that nucleotides of the modified nucleic acid molecule interact with the detector in sequential order, whereby data correlating with the cross-sectional area, local charge, or local chemistry of the nucleic acid molecule are obtained. The nucleic acid molecule may be modified in a number of locations along the molecule's length. Because the individual nucleotides of the nucleic acid molecule interact with the detector in sequential order, information regarding the location and composition of a plurality of modified sites along a single molecule can be obtained.
PCT/US2002/019766 2001-06-21 2002-06-21 Methods for characterization of nucleic acid molecules Ceased WO2003000920A2 (en)

Priority Applications (2)

Application Number Priority Date Filing Date Title
EP02747942A EP1478771A4 (en) 2001-06-21 2002-06-21 PROCESS FOR CHARACTERIZING NUCLEIC ACID MOLECULES
AU2002318386A AU2002318386A1 (en) 2001-06-21 2002-06-21 Methods for characterization of nucleic acid molecules

Applications Claiming Priority (2)

Application Number Priority Date Filing Date Title
US29987001P 2001-06-21 2001-06-21
US60/299,870 2001-06-21

Publications (3)

Publication Number Publication Date
WO2003000920A2 WO2003000920A2 (en) 2003-01-03
WO2003000920A9 WO2003000920A9 (en) 2003-03-20
WO2003000920A3 true WO2003000920A3 (en) 2004-09-23

Family

ID=23156656

Family Applications (1)

Application Number Title Priority Date Filing Date
PCT/US2002/019766 Ceased WO2003000920A2 (en) 2001-06-21 2002-06-21 Methods for characterization of nucleic acid molecules

Country Status (3)

Country Link
EP (1) EP1478771A4 (en)
AU (1) AU2002318386A1 (en)
WO (1) WO2003000920A2 (en)

Families Citing this family (47)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
US6362002B1 (en) 1995-03-17 2002-03-26 President And Fellows Of Harvard College Characterization of individual polymer molecules based on monomer-interface interactions
US20120160687A1 (en) 1995-03-17 2012-06-28 President And Fellows Of Harvard College Characterization of individual polymer molecules based on monomer-interface interactions
US7410564B2 (en) * 2003-01-27 2008-08-12 Agilent Technologies, Inc. Apparatus and method for biopolymer identification during translocation through a nanopore
US7282130B2 (en) 2003-01-31 2007-10-16 Agilent Technologies, Inc. Apparatus and method for control of biopolymer translocation through a nanopore
US7846738B2 (en) 2003-08-15 2010-12-07 President And Fellows Of Harvard College Study of polymer molecules and conformations with a nanopore
US7238485B2 (en) 2004-03-23 2007-07-03 President And Fellows Of Harvard College Methods and apparatus for characterizing polynucleotides
GB0713143D0 (en) * 2007-07-06 2007-08-15 Ucl Business Plc Nucleic acid detection method
EP2201136B1 (en) 2007-10-01 2017-12-06 Nabsys 2.0 LLC Nanopore sequencing by hybridization of probes to form ternary complexes and variable range alignment
US8262879B2 (en) 2008-09-03 2012-09-11 Nabsys, Inc. Devices and methods for determining the length of biopolymers and distances between probes bound thereto
JP5717634B2 (en) 2008-09-03 2015-05-13 ナブシス， インコーポレイテッド Use of longitudinally displaced nanoscale electrodes for voltage sensing of biomolecules and other analytes in fluid channels
US9650668B2 (en) 2008-09-03 2017-05-16 Nabsys 2.0 Llc Use of longitudinally displaced nanoscale electrodes for voltage sensing of biomolecules and other analytes in fluidic channels
US20100243449A1 (en) * 2009-03-27 2010-09-30 Oliver John S Devices and methods for analyzing biomolecules and probes bound thereto
AU2010326349B2 (en) 2009-12-01 2015-10-29 Oxford Nanopore Technologies Limited Biochemical analysis instrument
US9005425B2 (en) 2010-03-05 2015-04-14 University Of Utah Research Foundation Detection of nucleic acid lesions and adducts using nanopores
EP2580588B1 (en) 2010-06-08 2014-09-24 President and Fellows of Harvard College Nanopore device with graphene supported artificial lipid membrane
CA2805247C (en) 2010-07-14 2021-08-10 The Curators Of The University Of Missouri Nanopore-facilitated single molecule detection of nucleic acids
US8715933B2 (en) 2010-09-27 2014-05-06 Nabsys, Inc. Assay methods using nicking endonucleases
EP2622343B1 (en) 2010-10-01 2016-01-20 Oxford Nanopore Technologies Limited Biochemical analysis apparatus using nanopores
EP2640849B1 (en) 2010-11-16 2016-04-06 Nabsys 2.0 LLC Methods for sequencing a biomolecule by detecting relative positions of hybridized probes
US11274341B2 (en) 2011-02-11 2022-03-15 NABsys, 2.0 LLC Assay methods using DNA binding proteins
WO2012177792A2 (en) 2011-06-24 2012-12-27 Sequenom, Inc. Methods and processes for non-invasive assessment of a genetic variation
GB2498021A (en) * 2011-09-07 2013-07-03 Univ Utah Res Found Detection of Nucleic acid lesions and adducts using nanopores
US10424394B2 (en) 2011-10-06 2019-09-24 Sequenom, Inc. Methods and processes for non-invasive assessment of genetic variations
US9984198B2 (en) 2011-10-06 2018-05-29 Sequenom, Inc. Reducing sequence read count error in assessment of complex genetic variations
US20140242588A1 (en) 2011-10-06 2014-08-28 Sequenom, Inc Methods and processes for non-invasive assessment of genetic variations
US9367663B2 (en) 2011-10-06 2016-06-14 Sequenom, Inc. Methods and processes for non-invasive assessment of genetic variations
US10196681B2 (en) 2011-10-06 2019-02-05 Sequenom, Inc. Methods and processes for non-invasive assessment of genetic variations
US8688388B2 (en) 2011-10-11 2014-04-01 Sequenom, Inc. Methods and processes for non-invasive assessment of genetic variations
PL2805280T3 (en) 2012-01-20 2022-11-21 Sequenom, Inc. Diagnostic processes that factor experimental conditions
US9920361B2 (en) 2012-05-21 2018-03-20 Sequenom, Inc. Methods and compositions for analyzing nucleic acid
US10504613B2 (en) 2012-12-20 2019-12-10 Sequenom, Inc. Methods and processes for non-invasive assessment of genetic variations
US10497461B2 (en) 2012-06-22 2019-12-03 Sequenom, Inc. Methods and processes for non-invasive assessment of genetic variations
US10482994B2 (en) 2012-10-04 2019-11-19 Sequenom, Inc. Methods and processes for non-invasive assessment of genetic variations
US9914966B1 (en) 2012-12-20 2018-03-13 Nabsys 2.0 Llc Apparatus and methods for analysis of biomolecules using high frequency alternating current excitation
WO2014113557A1 (en) 2013-01-18 2014-07-24 Nabsys, Inc. Enhanced probe binding
US20130309666A1 (en) 2013-01-25 2013-11-21 Sequenom, Inc. Methods and processes for non-invasive assessment of genetic variations
EP2971118B1 (en) 2013-03-15 2019-10-02 The Curators of the University of Missouri Encoded nanopore sensor for multiplex nucleic acids detection
US10930368B2 (en) 2013-04-03 2021-02-23 Sequenom, Inc. Methods and processes for non-invasive assessment of genetic variations
EP3578670B1 (en) 2013-05-24 2025-07-02 Sequenom, Inc. Methods and processes for non-invasive assessment of genetic variations
KR102447079B1 (en) 2013-06-21 2022-09-23 시쿼넘, 인코포레이티드 Methods and Processes for Non-Invasive Assessment of Genetic Variation
AU2014329493B2 (en) 2013-10-04 2020-09-03 Sequenom, Inc. Methods and processes for non-invasive assessment of genetic variations
EP3495496B1 (en) 2013-10-07 2020-11-25 Sequenom, Inc. Methods and processes for non-invasive assessment of chromosome alterations
US20160034640A1 (en) 2014-07-30 2016-02-04 Sequenom, Inc. Methods and processes for non-invasive assessment of genetic variations
WO2016154337A2 (en) * 2015-03-23 2016-09-29 The University Of North Carolina At Chapel Hill Method for identification and enumeration of nucleic acid sequences, expression, splice variant, translocation, copy, or dna methylation changes using combined nuclease, ligase, polymerase, terminal transferase, and sequencing reactions
EP3491560A1 (en) 2016-07-27 2019-06-05 Sequenom, Inc. Genetic copy number alteration classifications
EP3574424A1 (en) 2017-01-24 2019-12-04 Sequenom, Inc. Methods and processes for assessment of genetic variations
EP3998350B1 (en) 2017-03-17 2025-05-07 Sequenom, Inc. Methods and processes for assessment of genetic mosaicism

Citations (2)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
US5795782A (en) * 1995-03-17 1998-08-18 President & Fellows Of Harvard College Characterization of individual polymer molecules based on monomer-interface interactions
US20030104428A1 (en) * 2001-06-21 2003-06-05 President And Fellows Of Harvard College Method for characterization of nucleic acid molecules

Family Cites Families (6)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
US6362002B1 (en) * 1995-03-17 2002-03-26 President And Fellows Of Harvard College Characterization of individual polymer molecules based on monomer-interface interactions
WO1998035012A2 (en) * 1997-02-12 1998-08-13 Chan Eugene Y Methods and products for analyzing polymers
US6537755B1 (en) * 1999-03-25 2003-03-25 Radoje T. Drmanac Solution-based methods and materials for sequence analysis by hybridization
EP1192103A1 (en) * 1999-06-22 2002-04-03 President And Fellows of Harvard College Control of solid state dimensional features
ATE316582T1 (en) * 1999-09-07 2006-02-15 Univ California METHOD FOR DETECTING THE PRESENCE OF DOUBLE STRANDED DNA IN A SAMPLE
WO2002042496A2 (en) * 2000-11-27 2002-05-30 The Regents Of The University Of California Methods and devices for characterizing duplex nucleic acid molecules

Patent Citations (2)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
US5795782A (en) * 1995-03-17 1998-08-18 President & Fellows Of Harvard College Characterization of individual polymer molecules based on monomer-interface interactions
US20030104428A1 (en) * 2001-06-21 2003-06-05 President And Fellows Of Harvard College Method for characterization of nucleic acid molecules

Non-Patent Citations (1)

* Cited by examiner, † Cited by third party
Title
See also references of EP1478771A4 *

Also Published As

Publication number Publication date
AU2002318386A1 (en) 2003-01-08
EP1478771A2 (en) 2004-11-24
WO2003000920A9 (en) 2003-03-20
EP1478771A4 (en) 2005-06-15
WO2003000920A2 (en) 2003-01-03

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