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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:
;
Issue Date:
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
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. Web.
Cantor, Charles R., & Koster, Hubert. Solid phase sequencing of biopolymers. United States.
Cantor, Charles R., and Koster, Hubert. Tue . "Solid phase sequencing of biopolymers". United States. https://www.osti.gov/servlets/purl/1135918.
@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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Works referenced in this record:

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


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


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


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


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


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


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


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


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


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


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 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


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


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


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


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


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


Analysis of Single Mammalian Cell Lysates by Mass Spectrometry
journal, January 1996


Fluorescence detection in automated DNA sequence analysis
journal, June 1986


Efficient methods for attachment of thiol specific probes to the 3′-ends of synthetic oligodeoxyribonucleotides
journal, January 1987


Microfabrication and array technologies for DNA sequencing and diagnostics
journal, December 1996


Preparation and manipulation of large DNA molecules: advances and applications
journal, January 1987


Budgeting the genome
journal, January 1992


Sequence-specific artificial photo-induced endonucleases based on triple helix-forming oligonucleotides
journal, March 1990


Matrix-assisted laser desorption time-of-flight mass spectrometry of oligonucleotides using 3-hydroxypicolinic acid as an ultraviolet-sensitive matrix
journal, February 1993


Sequencing of megabase plus DNA by hybridization: Theory of the method
journal, February 1989


Improved Resolution and Very High Sensitivity in MALDI TOF of Matrix Surfaces Made by Fast Evaporation
journal, October 1994


7-Deaza purine bases offer a higher ion stability in the analysis of dna by matrix-assisted laser desorption/ionization mass spectrometry
journal, January 1995


DNA Sequencing by Hybridization to Oligonucleotide Matrix. Calculation of Continuous Stacking Hybridization Efficiency
journal, February 1994


Time-of-flight mass spectrometry of nucleic acids by laser ablation and ionization from a frozen aqueous matrix
journal, September 1990


Hybridization methods for DNA sequencing
journal, October 1991


Matrix-assisted laser-desorption mass spectrometry of DNA using an infrared free-electron laser
conference, July 1993

  • Haglund, Jr., Richard F.; Tang, Kai; Hillenkamp, Franz
  • OE/LASE'93: Optics, Electro-Optics, & Laser Applications in Science& Engineering, SPIE Proceedings
  • https://doi.org/10.1117/12.148034

Multiplex DNA sequencing
journal, April 1988


Detection of 500-nucleotide DNA by laser desorption mass spectrometry
journal, September 1994


Ion stability of nucleic acids in infrared matrix-assisted laser desorption/ionization mass spectrometry
journal, January 1993


Applications of mass spectrometry to DNA sequencing
journal, December 1991


Time-of-Flight Mass Spectrometry Of Underivatized Single-Stranded DNA Oligomers by Matrix-Assisted Laser Desorption
journal, May 1994


Rapid chromatographic technique for preparative separations with moderate resolution
journal, July 1978


Analysis of enzymatic DNA sequencing reactions by matrix-assisted laser desorption/ionization time-of-flight mass spectrometry
journal, January 1995


Detection of oligonucleotide duplex forms by ion-spray mass spectrometry
journal, February 1993


Investigations of the metastable decay of DNA under ultraviolet matrix-assisted laser desorption/ionization conditions with post-source-decay analysis and hydrogen/deuterium exchange
journal, September 1998


A method for DNA sequencing by hybridization with oligonucleotide matrix
journal, January 1991


The emergence of mass spectrometry in biochemical research.
journal, November 1994


Direct detection of synthetic and biologically generated double-stranded DNA by MALDI-TOF MS
journal, December 1997


Analytical strategies for the use of DNA probes
journal, February 1988


Volatilization of high molecular weight DNA by pulsed laser ablation of frozen aqueous solutions
journal, December 1989


Improved electrospray ionization of synthetic oligodeoxynucleotides
journal, August 1991


Improved Analysis of Microsatellites Using Mass Spectrometry
journal, November 1997


Attomole-Sensitivity Electrospray Source for Large-Molecule Mass Spectrometry
journal, October 1995


Sequencing double-stranded DNA by strand displacement
journal, February 1997


Use of combined mass spectrometry methods for the characterization of a new variant of human hemoglobin: The double mutant hemoglobin villeparisis β77(EF1) His → Tyr, β 80 (EF4) Asn → Ser
journal, February 1996


Efficient preparation of short DNA sequence ladders potentially suitable for MALDI-TOF DNA sequencing
journal, January 1996


A versatile acid-labile linker for modification of synthetic biomolecules
journal, January 1990


Identification of denatured double-stranded DNA by matrix-assisted laser desorption/ionization time-of-flight mass spectrometry
journal, January 1995


Analysis of Ligase Chain Reaction Products via Matrix-Assisted Laser Desorption/Ionization Time-of-Flight–Mass Spectrometry
journal, June 1996


DNA diagnostics--molecular techniques and automation
journal, October 1988


Matrix-assisted laser desorption mass spectrometry of oligodeoxythmidylic acids
journal, March 1992


Detection of hepatitis B virus DNA in serum samples via nested PCR and MALDI-TOF mass spectrometry
journal, September 1996


Genetic Bit Analysis: a solid phase method for typing single nucleotide polymorphisms
journal, January 1994


Applications of resonance ionization spectroscopy for semiconductor, environmental and biomedical analysis, and for DNA sequencing
conference, July 1991

  • Arlinghaus, Heinrich F.; Spaar, M. T.; Thonnard, N.
  • Optics, Electro-Optics, and Laser Applications in Science and Engineering, SPIE Proceedings
  • https://doi.org/10.1117/12.44228

A 2prime;-O-thiol tether in the ribose moiety of nucleic acids for conjugation chemistry
journal, November 1994


High-Resolution MALDI Fourier Transform Mass Spectrometry of Oligonucleotides
journal, January 1996


A general method of in vitro preparation and specific mutagenesis of DNA fragments: study of protein and DNA interactions
journal, January 1988


Variable-wavelength on-column fluorescence detector for open-tubular zone electrophoresis
journal, February 1986


A Filtration Method for Plasmid Isolation Using Microtiter Filter Plates
journal, September 1995


Electrospray ionization mass spectrometry of biomolecules
journal, June 1990


Initiator oligonucleotides for the combination of chemical and enzymatic RNA synthesis
journal, March 1992


The development of microfabricated arrays for DNA sequencing and analysis
journal, October 1996


Applications of dioxetane chemiluminescent probes to molecular biology
journal, November 1990


Mass spectrometry of laser-desorbed oligonucleotides
journal, June 1992


Direct sequencing of polymerase chain reaction amplified DNA fragments through the incorporation of deoxynucleoside α-thiotriphosphates
journal, January 1988


Matrix-assisted laser desorption/ionization of restriction enzyme-digested DNA
journal, February 1994


Time of flight mass spectrometry of DNA laser-ablated from frozen aqueous solutions: applications to the Human Genome Project
journal, February 1994


Detection of ΔF508 mutation of the cystic fibrosis gene by matrix-assisted laser desorption/ionization mass spectrometry
journal, January 1995


Matrix-assisted laser desorption/ionisation mass spectrometry of transfer ribonucleic acids isolated from yeast
journal, May 1997


HB Abruzzo [β143(H21)HIS→ARG] Identified by Mass Spectrometry and DNA Analysis
journal, January 1993


Rapid detection and sequencing of specific in vitro amplified DNA sequences using solid phase methods
journal, August 1990


High-Density, Covalent Attachment of DNA to Silicon Wafers for Analysis by MALDI-TOF Mass Spectrometry
journal, July 1997


Solid-phase method for the purification of DNA sequencing reactions
journal, November 1992


Chemiluminescent detection of DNA: application for DNA sequencing and hybridization
journal, January 1989


New developments in biochemical mass spectrometry: electrospray ionization
journal, May 1990


Genetic analysis of amplified DNA with immobilized sequence-specific oligonucleotide probes.
journal, August 1989


Templated Synthesis of Peptide Nucleic Acids via Sequence-Selective Base-Filling Reactions
journal, August 2009


DNA sequencing with chain-terminating inhibitors
journal, December 1977


High-throughput DNA analysis by time-of-flight mass spectrometry
journal, March 1997


Direct solid phase sequencing of genomic and plasmid DNA using magnetic beads as solid support
journal, January 1989


Immuno-PCR: very sensitive antigen detection by means of specific antibody-DNA conjugates
journal, October 1992


DNA sequence analysis by MALDI mass spectrometry
journal, June 1998


Covalent attachment of synthetic DNA to self-assembled monolayer films
journal, August 1996


Evolving strategies for making physical maps of mammalian chromosomes
journal, January 1989


New technologies for large-genome sequencing
journal, January 1989


DNA sequencing, automation, and the human genome
journal, March 1990


Nucleoside Phosphorothioates
journal, June 1985