Solid phase sequencing of biopolymers

Cantor, Charles R.; Koster, Hubert

Title: Solid phase sequencing of biopolymers

Abstract

This invention relates to methods for detecting and sequencing target nucleic acid sequences, to mass modified nucleic acid probes and 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. Probes may be affixed to a solid support such as a hybridization chip to facilitate automated molecular weight analysis and identification of the target sequence.

Inventors:: Cantor, Charles R.; Koster, Hubert

Issue Date:: 2014-06-24

Research Org.:: Sequenom, Inc., San Diego, CA (USA)

Sponsoring Org.:: USDOE

OSTI Identifier:: 1135918

Patent Number(s):: 8758995

Application Number:: 12/852,336

Assignee:: Sequenom, Inc. (San Diego, CA)

Patent Classifications (CPCs):: C - CHEMISTRY C12 - BIOCHEMISTRY C12Q - MEASURING OR TESTING PROCESSES INVOLVING ENZYMES, NUCLEIC ACIDS OR MICROORGANISMS

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C - CHEMISTRY C12 - BIOCHEMISTRY C12Q - MEASURING OR TESTING PROCESSES INVOLVING ENZYMES, NUCLEIC ACIDS OR MICROORGANISMS
C12Q2531/119 - Strand displacement amplification [SDA]
C12Q2565/627 - being a mass spectrometer
C12Q2521/301 - Endonuclease
C12Q2565/501 - being an array of oligonucleotides
C12Q1/6874 - involving nucleic acid arrays, e.g. sequencing by hybridisation
C12Q2531/113 - PCR
C12Q2521/525 - Phosphatase
C12Q1/6872 - involving mass spectrometry
C12Q2523/301 - Sonication
C12Q2531/149 - Replicase based amplification, e.g. Q beta replicase
C12Q2531/137 - Ligase Chain Reaction [LCR]

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DOE Contract Number:: FG02-93ER61609

Resource Type:: Patent

Resource Relation:: Patent File Date: 2010 Aug 06

Country of Publication:: United States

Language:: English

Subject:: 59 BASIC BIOLOGICAL SCIENCES

Citation Formats


                    Cantor, Charles R., and Koster, Hubert. Solid phase sequencing of biopolymers.  United States: N. p., 2014. 
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                    Cantor, Charles R., & Koster, Hubert. Solid phase sequencing of biopolymers.  United States.

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                    Cantor, Charles R., and Koster, Hubert. Tue .  
        "Solid phase sequencing of biopolymers".  United States.  https://www.osti.gov/servlets/purl/1135918.

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@article{osti_1135918,

  title        = {Solid phase sequencing of biopolymers},

  author       = {Cantor, Charles R. and Koster, Hubert},

  abstractNote = {This invention relates to methods for detecting and sequencing target nucleic acid sequences, to mass modified nucleic acid probes and 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. Probes may be affixed to a solid support such as a hybridization chip to facilitate automated molecular weight analysis and identification of the target sequence.},

  doi          = {},

  journal      = {},
number       = ,

  volume       = ,

  place        = {United States},

  year         = {2014},

  month        = {6}

}

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Abstract

Citation Formats

Magnetic bead purification of M13 DNA sequencing templates journal, February 1992

New methods to sequence DNA by mass spectrometry conference, July 1990

An improved procedure for derivatization of controlled-pore glass beads for solid-phase oligonucleotide synthesis journal, January 1990

Fabrication of patterned DNA surfaces journal, August 1996

Analyzing and comparing nucleic acid sequences by hybridization to arrays of oligonucleotides: Evaluation using experimental models journal, August 1992

Two-dimensional electrophoretic analysis of proteins expressed by normal and cancerous human crypts: Application of mass spectrometry to peptide-mass fingerprinting journal, January 1994

Pulsed-Field Gel Electrophoresis of Very Large DNA Molecules journal, June 1988

Direct detection of nucleic acid hybridization on the surface of a charge coupled device journal, January 1994

DNA chips: An array of possibilities journal, January 1998

Synthesis of some pyrimidine 2'-amino-2'-deoxynucleosides journal, January 1971

Matrix-assisted laser desorption/ionization mass spectrometry of nucleic acids with wavelengths in the ultraviolet and infrared journal, December 1992

Solid-phase synthesis of protected peptide fragments using a trialkoxy-diphenyl-methylester resin. journal, January 1987

Probing the solution structure of the DNA-binding protein Max by a combination of proteolysis and mass spectrometry: Probing the solution structure of Max journal, June 1995

A new simpler photoaffinity analogue of peptidyl tRNA journal, January 1974

Enhanced DNA sequencing by hybridization. journal, April 1994

Coaxial continuous flow fast atom bombardment for higher-molecular-weight peptides: Comparison with static fast atom bombardment and electrospray ionization journal, December 1991

Reliable Hybridization of Oligonucleotides as Short as Six Nucleotides journal, September 1990

Covalent immobilization of DNA onto polystyrene microwells: The molecules are only bound at the 5′ end journal, October 1991

Effect of Impurities on the Matrix-Assisted Laser Desorption Mass Spectra of Single-Stranded Oligodeoxynucleotides journal, January 1996

Mid-infrared matrix assisted laser desorption ionization with a water/glycerol matrix journal, May 1998

A Streptavidin–Protein a Chimera that allows one–step production of a variety of Specific Antibody Conjugates journal, December 1991

Identification of multiple structural domains regulating viroid pathogenicity. journal, November 1992

Improved Chips for Sequencing by Hybridization journal, October 1991

Well-Defined Insoluble Primers for the Enzymatic Synthesis of Oligo- and Polynucleotides journal, January 1978

DNA Probes: Applications of the Principles of Nucleic Acid Hybridization journal, January 1991

Beaded polymer supports and gels: II. Physico-chemical criteria and functionalization journal, November 1991

Preparation of base-modified nucleosides suitable for non-radioactive label attachment and their incorporation into synthetic oligodeoxyribonucleotides journal, January 1987

Rapid screening of genetic polymorphisms using buccal cell DNA with detection by matrix-assisted laser desorption/ionization mass spectrometry journal, January 1995

Sequencing exons 5 to 8 of the p53 gene by MALDI-TOF mass spectrometry journal, April 1998

Infrared MALDI Mass Spectrometry of Large Nucleic Acids journal, July 1998

N-acyl protecting groups for deoxynucleosides journal, January 1981

Purification of Mbo II methylase (GAAG m A from Moraxella bovis: site specific cleavage of DNA at nine and ten base pair sequences journal, January 1985

Encoded combinatorial chemistry. journal, June 1992

Dna Sequencing After the Human Genome Project journal, May 1997

Optimal conditions for supercoil DNA sequencing with the Escherichia coli DNA polymerase I large fragment journal, March 1988

Synthesis of an amplifiable reporter RNA for bioassays journal, January 1986

Advances in DNA diagnostics journal, February 1998

DNA base-pair substitutions detected in double-stranded DNA with matrix-assisted laser desorption/ionization time-of-flight mass spectrometry journal, January 1995

Negative ion FAB mass spectrometric analysis of non-charged key intermediates in oligonucleotide synthesis: Rapid identification of partially protected dinucleoside monophosphates journal, March 1987

Sequence-selective recognition of DNA by strand displacement with a thymine-substituted polyamide journal, December 1991

High-Speed DNA Sequencing: An Approach Based Upon Fluorescence Detection of Single Molecules journal, October 1989

Synthesis and properties of dithymidine phosphate analogues containing 3′-thiothymidine journal, January 1990

Oligonucleotides and analogues: A practical approach journal, May 1992

Covalent attachment of oligonucleotides to solid supports journal, January 1987

Mass spectrometry from miniaturized arrays for full comparative DNA analysis journal, December 1997

The Facile Synthesis of 5′-Nucleotides by the Selective Phosphorylation of a Primary Hydroxyl Group of Nucleosides with Phosphoryl Chloride journal, July 1975

An Algorithm for the DNA Sequence Generation from k-Tuple Word Contents of the Minimal Number of Random Fragments journal, April 1991

The synthesis of protected 5′-mercapto-2′,5′-dideoxyribonucleoside-3′-0-phosphorainidites; uses of 5′-mercapto-oligodeoxyribonucleotides journal, January 1987

Determination of oligonucleotide composition from mass spectrometrically measured molecular weight journal, March 1993

Beaded polymer supports and gels: I. Manufacturing techniques journal, November 1991

β-Cyanoethyl N,N-dialkylamino/N-morpholinomonochloro phosphoamidites, new phosphitylating agents facilitating ease of deprotection and work-up of synthesized oligonucleotides journal, January 1983

Verification of 50- to 100-mer DNA and RNA sequences with high-resolution mass spectrometry. journal, March 1995

Universal restriction endonucleases: designing novel cleavage specificities by combining adapter oligodeoxynucleotide and enzyme moieties journal, January 1985

Solid phase DNA sequencing using the biotin-avidin system journal, January 1988

Efficient methods for attaching non-radioactive labels to the 5′ ends of synthetic oligodeoxyribonucleotides journal, January 1986

The thermodynamic advantage of DNA oligonucleotide 'stacking hybridization' reactions: energetics of a DNA nick journal, February 1997

The determination of protein, oligonucleotide and peptide molecular weights by ion-spray mass spectrometry journal, November 1988

Application of nested PCR and mass spectrometry for DNA-based virus detection: HBV-DNA detected in the majority of isolated anti-HBc positive sera journal, January 1998

Capillary zone electrophoresis-mass spectrometry using an electrospray ionization interface journal, March 1988

An oligonucleotide hybridization approach to DNA sequencing journal, October 1989

The Use of 96-Well Polystyrene Plates for DNA Hybridization-Based Assays: An Evaluation of Different Approaches to Oligonucleotide Immobilization journal, May 1995

Megabase-scale mapping of the HLA gene complex by pulsed field gel electrophoresis journal, March 1987

Molecular cloning and nucleotide sequence of the streptavidin gene journal, January 1986

Expression vectors for streptavidin-containing chimeric proteins journal, April 1991

A new method for sequencing DNA. journal, February 1977

1-Tuple DNA Sequencing: Computer Analysis journal, August 1989

Quantitative multiplex sequence analysis of mutational hot spots. Frequency and specificity of mutations induced by a site-specific ethenocytosine in M13 viral DNA journal, April 1993

A system for rapid DNA sequencing with fluorescent chain-terminating dideoxynucleotides journal, October 1987

DNA sequencing by hybridization: 100 bases read by a non-gel-based method. journal, November 1991

Matrix-Assisted Laser Desorption/Ionization Time-of-Flight Mass Spectrometry for the Detection of Polymerase Chain Reaction Products Containing 7-Deazapurine Moieties journal, December 1996

Mass spectrometric techniques in nucleic acid research journal, September 1990

Matrix-assisted laser desorption/ionization mass spectrometry of immobilized duplex DNA probes journal, January 1995

Capillary gel electrophoresis for rapid, high resolution DNA sequencing journal, January 1990

A strategy for rapid and efficient DNA sequencing by mass spectrometry journal, September 1996

Detection of RET proto-oncogene codon 634 mutations using mass spectrometry journal, October 1997

Configurationally defined phosphorothioate-containing oligoribonucleotides in the study of the mechanism of cleavage of hammerhead ribozymes journal, January 1991

Improvement of the dideoxy chain termination method of DNA sequencing by use of deoxy-7-deazaguanosine triphosphate in place of dGTP journal, January 1986

Magnetic bead purification of M13 DNA sequencing templates
journal, February 1992

New methods to sequence DNA by mass spectrometry
conference, July 1990

An improved procedure for derivatization of controlled-pore glass beads for solid-phase oligonucleotide synthesis
journal, January 1990

Fabrication of patterned DNA surfaces
journal, August 1996

Analyzing and comparing nucleic acid sequences by hybridization to arrays of oligonucleotides: Evaluation using experimental models
journal, August 1992

Two-dimensional electrophoretic analysis of proteins expressed by normal and cancerous human crypts: Application of mass spectrometry to peptide-mass fingerprinting
journal, January 1994

Pulsed-Field Gel Electrophoresis of Very Large DNA Molecules
journal, June 1988

Direct detection of nucleic acid hybridization on the surface of a charge coupled device
journal, January 1994

DNA chips: An array of possibilities
journal, January 1998

Synthesis of some pyrimidine 2'-amino-2'-deoxynucleosides
journal, January 1971

Matrix-assisted laser desorption/ionization mass spectrometry of nucleic acids with wavelengths in the ultraviolet and infrared
journal, December 1992

Solid-phase synthesis of protected peptide fragments using a trialkoxy-diphenyl-methylester resin.
journal, January 1987

Probing the solution structure of the DNA-binding protein Max by a combination of proteolysis and mass spectrometry: Probing the solution structure of Max
journal, June 1995

A new simpler photoaffinity analogue of peptidyl tRNA
journal, January 1974

Enhanced DNA sequencing by hybridization.
journal, April 1994

Coaxial continuous flow fast atom bombardment for higher-molecular-weight peptides: Comparison with static fast atom bombardment and electrospray ionization
journal, December 1991

Reliable Hybridization of Oligonucleotides as Short as Six Nucleotides
journal, September 1990

Covalent immobilization of DNA onto polystyrene microwells: The molecules are only bound at the 5′ end
journal, October 1991

Effect of Impurities on the Matrix-Assisted Laser Desorption Mass Spectra of Single-Stranded Oligodeoxynucleotides
journal, January 1996

Mid-infrared matrix assisted laser desorption ionization with a water/glycerol matrix
journal, May 1998

A Streptavidin–Protein a Chimera that allows one–step production of a variety of Specific Antibody Conjugates
journal, December 1991

Identification of multiple structural domains regulating viroid pathogenicity.
journal, November 1992

Improved Chips for Sequencing by Hybridization
journal, October 1991

Well-Defined Insoluble Primers for the Enzymatic Synthesis of Oligo- and Polynucleotides
journal, January 1978

DNA Probes: Applications of the Principles of Nucleic Acid Hybridization
journal, January 1991

Beaded polymer supports and gels: II. Physico-chemical criteria and functionalization
journal, November 1991

Preparation of base-modified nucleosides suitable for non-radioactive label attachment and their incorporation into synthetic oligodeoxyribonucleotides
journal, January 1987

Rapid screening of genetic polymorphisms using buccal cell DNA with detection by matrix-assisted laser desorption/ionization mass spectrometry
journal, January 1995

Sequencing exons 5 to 8 of the p53 gene by MALDI-TOF mass spectrometry
journal, April 1998

Infrared MALDI Mass Spectrometry of Large Nucleic Acids
journal, July 1998

N-acyl protecting groups for deoxynucleosides
journal, January 1981

Purification of Mbo II methylase (GAAG ^m A from Moraxella bovis: site specific cleavage of DNA at nine and ten base pair sequences
journal, January 1985

Encoded combinatorial chemistry.
journal, June 1992

Dna Sequencing After the Human Genome Project
journal, May 1997

Optimal conditions for supercoil DNA sequencing with the Escherichia coli DNA polymerase I large fragment
journal, March 1988

Synthesis of an amplifiable reporter RNA for bioassays
journal, January 1986

Advances in DNA diagnostics
journal, February 1998

DNA base-pair substitutions detected in double-stranded DNA with matrix-assisted laser desorption/ionization time-of-flight mass spectrometry
journal, January 1995

Negative ion FAB mass spectrometric analysis of non-charged key intermediates in oligonucleotide synthesis: Rapid identification of partially protected dinucleoside monophosphates
journal, March 1987

Sequence-selective recognition of DNA by strand displacement with a thymine-substituted polyamide
journal, December 1991

High-Speed DNA Sequencing: An Approach Based Upon Fluorescence Detection of Single Molecules
journal, October 1989

Synthesis and properties of dithymidine phosphate analogues containing 3′-thiothymidine
journal, January 1990

Oligonucleotides and analogues: A practical approach
journal, May 1992

Covalent attachment of oligonucleotides to solid supports
journal, January 1987

Mass spectrometry from miniaturized arrays for full comparative DNA analysis
journal, December 1997

The Facile Synthesis of 5′-Nucleotides by the Selective Phosphorylation of a Primary Hydroxyl Group of Nucleosides with Phosphoryl Chloride
journal, July 1975

An Algorithm for the DNA Sequence Generation from k-Tuple Word Contents of the Minimal Number of Random Fragments
journal, April 1991

The synthesis of protected 5′-mercapto-2′,5′-dideoxyribonucleoside-3′-0-phosphorainidites; uses of 5′-mercapto-oligodeoxyribonucleotides
journal, January 1987

Determination of oligonucleotide composition from mass spectrometrically measured molecular weight
journal, March 1993

Beaded polymer supports and gels: I. Manufacturing techniques
journal, November 1991

β-Cyanoethyl N,N-dialkylamino/N-morpholinomonochloro phosphoamidites, new phosphitylating agents facilitating ease of deprotection and work-up of synthesized oligonucleotides
journal, January 1983

Verification of 50- to 100-mer DNA and RNA sequences with high-resolution mass spectrometry.
journal, March 1995

Universal restriction endonucleases: designing novel cleavage specificities by combining adapter oligodeoxynucleotide and enzyme moieties
journal, January 1985

Solid phase DNA sequencing using the biotin-avidin system
journal, January 1988

Efficient methods for attaching non-radioactive labels to the 5′ ends of synthetic oligodeoxyribonucleotides
journal, January 1986

The thermodynamic advantage of DNA oligonucleotide 'stacking hybridization' reactions: energetics of a DNA nick
journal, February 1997

The determination of protein, oligonucleotide and peptide molecular weights by ion-spray mass spectrometry
journal, November 1988

Application of nested PCR and mass spectrometry for DNA-based virus detection: HBV-DNA detected in the majority of isolated anti-HBc positive sera
journal, January 1998

Capillary zone electrophoresis-mass spectrometry using an electrospray ionization interface
journal, March 1988

An oligonucleotide hybridization approach to DNA sequencing
journal, October 1989

The Use of 96-Well Polystyrene Plates for DNA Hybridization-Based Assays: An Evaluation of Different Approaches to Oligonucleotide Immobilization
journal, May 1995

Megabase-scale mapping of the HLA gene complex by pulsed field gel electrophoresis
journal, March 1987

Molecular cloning and nucleotide sequence of the streptavidin gene
journal, January 1986

Expression vectors for streptavidin-containing chimeric proteins
journal, April 1991

A new method for sequencing DNA.
journal, February 1977

1-Tuple DNA Sequencing: Computer Analysis
journal, August 1989

Quantitative multiplex sequence analysis of mutational hot spots. Frequency and specificity of mutations induced by a site-specific ethenocytosine in M13 viral DNA
journal, April 1993

A system for rapid DNA sequencing with fluorescent chain-terminating dideoxynucleotides
journal, October 1987

DNA sequencing by hybridization: 100 bases read by a non-gel-based method.
journal, November 1991

Matrix-Assisted Laser Desorption/Ionization Time-of-Flight Mass Spectrometry for the Detection of Polymerase Chain Reaction Products Containing 7-Deazapurine Moieties
journal, December 1996

Mass spectrometric techniques in nucleic acid research
journal, September 1990

Matrix-assisted laser desorption/ionization mass spectrometry of immobilized duplex DNA probes
journal, January 1995

Capillary gel electrophoresis for rapid, high resolution DNA sequencing
journal, January 1990

A strategy for rapid and efficient DNA sequencing by mass spectrometry
journal, September 1996

Detection of RET proto-oncogene codon 634 mutations using mass spectrometry
journal, October 1997

Configurationally defined phosphorothioate-containing oligoribonucleotides in the study of the mechanism of cleavage of hammerhead ribozymes
journal, January 1991

Improvement of the dideoxy chain termination method of DNA sequencing by use of deoxy-7-deazaguanosine triphosphate in place of dGTP
journal, January 1986

DNA Sequence Analysis of Human Chromosome 21 Notl Linking Clones
journal, November 1993

Liquid-phase hybridization and capture of hepatitis B virus DNA with magnetic beads and fluorescence detection of PCR product
journal, December 1994

Applications of Delayed Extraction Matrix-Assisted Laser Desorption Ionization Time-of-Flight Mass Spectrometry to Oligonucleotide Analysis
journal, January 1996