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WO1996032504A3 - Solid phase sequencing of biopolymers - Google Patents

Solid phase sequencing of biopolymers Download PDF

Info

Publication number
WO1996032504A3
WO1996032504A3 PCT/US1996/005136 US9605136W WO9632504A3 WO 1996032504 A3 WO1996032504 A3 WO 1996032504A3 US 9605136 W US9605136 W US 9605136W WO 9632504 A3 WO9632504 A3 WO 9632504A3
Authority
WO
WIPO (PCT)
Prior art keywords
probes
nucleic acid
target
nucleic acids
determined
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/US1996/005136
Other languages
French (fr)
Other versions
WO1996032504A2 (en
Inventor
Charles R Cantor
Hubert Koster
Cassandra L Smith
Dong-Jing Fu
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.)
Boston University
Original Assignee
Boston 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
Priority claimed from US08/614,151 external-priority patent/US6436635B1/en
Application filed by Boston University filed Critical Boston University
Priority to AU55446/96A priority Critical patent/AU5544696A/en
Priority to EP96912743A priority patent/EP0830460A1/en
Priority to JP8531243A priority patent/JPH11503611A/en
Publication of WO1996032504A2 publication Critical patent/WO1996032504A2/en
Publication of WO1996032504A3 publication Critical patent/WO1996032504A3/en
Anticipated expiration legal-status Critical
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
    • C12Q1/6869—Methods for sequencing
    • C12Q1/6872—Methods for sequencing involving mass spectrometry
    • 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
    • C12Q1/6874—Methods for sequencing involving nucleic acid arrays, e.g. sequencing by hybridisation

Landscapes

  • Life Sciences & Earth Sciences (AREA)
  • Proteomics, Peptides & Aminoacids (AREA)
  • Chemical & Material Sciences (AREA)
  • Organic Chemistry (AREA)
  • Health & Medical Sciences (AREA)
  • Zoology (AREA)
  • Engineering & Computer Science (AREA)
  • Wood Science & Technology (AREA)
  • Physics & Mathematics (AREA)
  • Biochemistry (AREA)
  • General Health & Medical Sciences (AREA)
  • Molecular Biology (AREA)
  • Immunology (AREA)
  • Biotechnology (AREA)
  • Analytical Chemistry (AREA)
  • Biophysics (AREA)
  • Bioinformatics & Cheminformatics (AREA)
  • General Engineering & Computer Science (AREA)
  • Microbiology (AREA)
  • Genetics & Genomics (AREA)
  • Spectroscopy & Molecular Physics (AREA)
  • Measuring Or Testing Involving Enzymes Or Micro-Organisms (AREA)
  • Saccharide Compounds (AREA)
  • Electron Tubes For Measurement (AREA)
  • Investigating Or Analysing Biological Materials (AREA)
  • Apparatus Associated With Microorganisms And Enzymes (AREA)

Abstract

This invention relates to methods for detecting and sequencing target nucleic acid sequences, and double-stranded nucleic acid sequences, to nucleic acid probes, to mass modified nucleic acid probes, to arrays of probes useful in these methods and to kits and systems which contain these probes. Useful methods involve hybridizing the nucleic acids or nucleic acids which represent complementary or homologous sequences of the target to an array of nucleic acid probes. These probes comprise a single-stranded portion, an optional double-stranded portion and a variable sequence within the single-stranded portion. The molecular weights of the hybridized nucleic acids of the set can be determined by mass spectroscopy, and the sequence of the target determined from the molecular weights of the fragments. Nucleic acids whose sequences can be determined include DNA or RNA in biological samples such as patient biopsies and environmental samples. Probes may be fixed to a solid support such as a hybridization chip to facilitate automated molecular weight analysis and identification of the target sequence.
PCT/US1996/005136 1995-04-11 1996-04-10 Solid phase sequencing of biopolymers Ceased WO1996032504A2 (en)

Priority Applications (3)

Application Number Priority Date Filing Date Title
AU55446/96A AU5544696A (en) 1995-04-11 1996-04-10 Solid phase sequencing of biopolymers
EP96912743A EP0830460A1 (en) 1995-04-11 1996-04-10 Solid phase sequencing of biopolymers
JP8531243A JPH11503611A (en) 1995-04-11 1996-04-10 Solid-phase sequencing of biopolymers

Applications Claiming Priority (6)

Application Number Priority Date Filing Date Title
US42000995A 1995-04-11 1995-04-11
US41999495A 1995-04-11 1995-04-11
US08/614,151 US6436635B1 (en) 1992-11-06 1996-03-12 Solid phase sequencing of double-stranded nucleic acids
US08/420,009 1996-03-12
US08/419,994 1996-03-12
US08/614,151 1996-03-12

Publications (2)

Publication Number Publication Date
WO1996032504A2 WO1996032504A2 (en) 1996-10-17
WO1996032504A3 true WO1996032504A3 (en) 1996-11-14

Family

ID=27411260

Family Applications (1)

Application Number Title Priority Date Filing Date
PCT/US1996/005136 Ceased WO1996032504A2 (en) 1995-04-11 1996-04-10 Solid phase sequencing of biopolymers

Country Status (5)

Country Link
EP (1) EP0830460A1 (en)
JP (1) JPH11503611A (en)
AU (1) AU5544696A (en)
CA (1) CA2218188A1 (en)
WO (1) WO1996032504A2 (en)

Cited By (18)

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US6949633B1 (en) 1995-05-22 2005-09-27 Sequenom, Inc. Primers useful for sizing nucleic acids
US6991903B2 (en) 1992-11-06 2006-01-31 Sequenom, Inc. Solid phase sequencing of double-stranded nucleic acids
US7074563B2 (en) 1995-03-17 2006-07-11 Sequenom, Inc. Mass spectrometric methods for detecting mutations in a target nucleic acid
US7108974B2 (en) 2001-03-02 2006-09-19 Isis Pharmaceuticals, Inc. Method for rapid detection and identification of bioagents
US7132519B2 (en) 1996-12-10 2006-11-07 Sequenom, Inc. Releasable nonvolatile mass-label molecules
US7198893B1 (en) 1996-11-06 2007-04-03 Sequenom, Inc. DNA diagnostics based on mass spectrometry
US7217510B2 (en) 2001-06-26 2007-05-15 Isis Pharmaceuticals, Inc. Methods for providing bacterial bioagent characterizing information
US7285422B1 (en) 1997-01-23 2007-10-23 Sequenom, Inc. Systems and methods for preparing and analyzing low volume analyte array elements
US7332275B2 (en) 1999-10-13 2008-02-19 Sequenom, Inc. Methods for detecting methylated nucleotides
US7432342B2 (en) 2002-05-03 2008-10-07 Sequenom, Inc. Kinase anchor protein muteins, peptides thereof and related documents
US7608394B2 (en) 2004-03-26 2009-10-27 Sequenom, Inc. Methods and compositions for phenotype identification based on nucleic acid methylation
USRE41005E1 (en) 1996-11-06 2009-11-24 Sequenom, Inc. Beads bound to a solid support and to nucleic acids
US8993271B2 (en) 1997-04-01 2015-03-31 Illumina, Inc. Method of nucleic acid amplification
US8999266B2 (en) 2000-10-30 2015-04-07 Agena Bioscience, Inc. Method and apparatus for delivery of submicroliter volumes onto a substrate
US9034798B2 (en) 2003-01-16 2015-05-19 Caprotec Bioanalytics Gmbh Capture compounds, collections thereof and methods for analyzing the proteome and complex compositions
US9249456B2 (en) 2004-03-26 2016-02-02 Agena Bioscience, Inc. Base specific cleavage of methylation-specific amplification products in combination with mass analysis
US9394565B2 (en) 2003-09-05 2016-07-19 Agena Bioscience, Inc. Allele-specific sequence variation analysis
US9512478B2 (en) 2007-02-02 2016-12-06 Illumina Cambridge Limited Methods for indexing samples and sequencing multiple polynucleotide templates

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US6117634A (en) * 1997-03-05 2000-09-12 The Reagents Of The University Of Michigan Nucleic acid sequencing and mapping
US6197557B1 (en) 1997-03-05 2001-03-06 The Regents Of The University Of Michigan Compositions and methods for analysis of nucleic acids
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US6207370B1 (en) 1997-09-02 2001-03-27 Sequenom, Inc. Diagnostics based on mass spectrometric detection of translated target polypeptides
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US6104028A (en) 1998-05-29 2000-08-15 Genetrace Systems Inc. Volatile matrices for matrix-assisted laser desorption/ionization mass spectrometry
US7270958B2 (en) 1998-09-10 2007-09-18 The Regents Of The University Of Michigan Compositions and methods for analysis of nucleic acids
AR021833A1 (en) 1998-09-30 2002-08-07 Applied Research Systems METHODS OF AMPLIFICATION AND SEQUENCING OF NUCLEIC ACID
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JP2001204463A (en) * 2000-01-27 2001-07-31 Toyo Kohan Co Ltd Carrier for nucleotide immobilization
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Cited By (21)

* Cited by examiner, † Cited by third party
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US6991903B2 (en) 1992-11-06 2006-01-31 Sequenom, Inc. Solid phase sequencing of double-stranded nucleic acids
US7074563B2 (en) 1995-03-17 2006-07-11 Sequenom, Inc. Mass spectrometric methods for detecting mutations in a target nucleic acid
US7419787B2 (en) 1995-03-17 2008-09-02 Sequenom, Inc. Mass spectrometric methods for detecting mutations in a target nucleic acid
US6949633B1 (en) 1995-05-22 2005-09-27 Sequenom, Inc. Primers useful for sizing nucleic acids
US7501251B2 (en) 1996-11-06 2009-03-10 Sequenom, Inc. DNA diagnostics based on mass spectrometry
US7198893B1 (en) 1996-11-06 2007-04-03 Sequenom, Inc. DNA diagnostics based on mass spectrometry
USRE44693E1 (en) 1996-11-06 2014-01-07 Sequenom, Inc. Beads bound to a solid support and to nucleic acids
USRE41005E1 (en) 1996-11-06 2009-11-24 Sequenom, Inc. Beads bound to a solid support and to nucleic acids
US7132519B2 (en) 1996-12-10 2006-11-07 Sequenom, Inc. Releasable nonvolatile mass-label molecules
US7285422B1 (en) 1997-01-23 2007-10-23 Sequenom, Inc. Systems and methods for preparing and analyzing low volume analyte array elements
US8993271B2 (en) 1997-04-01 2015-03-31 Illumina, Inc. Method of nucleic acid amplification
US7332275B2 (en) 1999-10-13 2008-02-19 Sequenom, Inc. Methods for detecting methylated nucleotides
US8999266B2 (en) 2000-10-30 2015-04-07 Agena Bioscience, Inc. Method and apparatus for delivery of submicroliter volumes onto a substrate
US7108974B2 (en) 2001-03-02 2006-09-19 Isis Pharmaceuticals, Inc. Method for rapid detection and identification of bioagents
US7217510B2 (en) 2001-06-26 2007-05-15 Isis Pharmaceuticals, Inc. Methods for providing bacterial bioagent characterizing information
US7432342B2 (en) 2002-05-03 2008-10-07 Sequenom, Inc. Kinase anchor protein muteins, peptides thereof and related documents
US9034798B2 (en) 2003-01-16 2015-05-19 Caprotec Bioanalytics Gmbh Capture compounds, collections thereof and methods for analyzing the proteome and complex compositions
US9394565B2 (en) 2003-09-05 2016-07-19 Agena Bioscience, Inc. Allele-specific sequence variation analysis
US7608394B2 (en) 2004-03-26 2009-10-27 Sequenom, Inc. Methods and compositions for phenotype identification based on nucleic acid methylation
US9249456B2 (en) 2004-03-26 2016-02-02 Agena Bioscience, Inc. Base specific cleavage of methylation-specific amplification products in combination with mass analysis
US9512478B2 (en) 2007-02-02 2016-12-06 Illumina Cambridge Limited Methods for indexing samples and sequencing multiple polynucleotide templates

Also Published As

Publication number Publication date
CA2218188A1 (en) 1996-10-17
EP0830460A1 (en) 1998-03-25
AU5544696A (en) 1996-10-30
WO1996032504A2 (en) 1996-10-17
JPH11503611A (en) 1999-03-30

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