Methods and compositions for efficient nucleic acid sequencing

Drmanac, Radoje

Title: Methods and compositions for efficient nucleic acid sequencing

Abstract

Disclosed are novel methods and compositions for rapid and highly efficient nucleic acid sequencing based upon hybridization with two sets of small oligonucleotide probes of known sequences. Extremely large nucleic acid molecules, including chromosomes and non-amplified RNA, may be sequenced without prior cloning or subcloning steps. The methods of the invention also solve various current problems associated with sequencing technology such as, for example, high noise to signal ratios and difficult discrimination, attaching many nucleic acid fragments to a surface, preparing many, longer or more complex probes and labelling more species.

Inventors:: Drmanac, Radoje

Issue Date:: 2006-07-04

Research Org.:: The University Of Chicago, Chicago, IL (United States); Argonne National Lab. (ANL), Argonne, IL (United States)

Sponsoring Org.:: USDOE

OSTI Identifier:: 1175815

Patent Number(s):: 7070927

Application Number:: 10/068,301

Assignee:: University of Chicago (Chicago, IL)

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
C12Q1/6874 - involving nucleic acid arrays, e.g. sequencing by hybridisation

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DOE Contract Number:: W-31-109-ENG-38

Resource Type:: Patent

Country of Publication:: United States

Language:: English

Subject:: 59 BASIC BIOLOGICAL SCIENCES

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                    Drmanac, Radoje. Methods and compositions for efficient nucleic acid sequencing.  United States: N. p., 2006. 
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                    Drmanac, Radoje. Methods and compositions for efficient nucleic acid sequencing.  United States.

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                    Drmanac, Radoje. Tue .  
        "Methods and compositions for efficient nucleic acid sequencing".  United States.  https://www.osti.gov/servlets/purl/1175815.

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@article{osti_1175815,

  title        = {Methods and compositions for efficient nucleic acid sequencing},

  author       = {Drmanac, Radoje},

  abstractNote = {Disclosed are novel methods and compositions for rapid and highly efficient nucleic acid sequencing based upon hybridization with two sets of small oligonucleotide probes of known sequences. Extremely large nucleic acid molecules, including chromosomes and non-amplified RNA, may be sequenced without prior cloning or subcloning steps. The methods of the invention also solve various current problems associated with sequencing technology such as, for example, high noise to signal ratios and difficult discrimination, attaching many nucleic acid fragments to a surface, preparing many, longer or more complex probes and labelling more species.},

  doi          = {},

  journal      = {},
number       = ,

  volume       = ,

  place        = {United States},

  year         = {2006},

  month        = {7}

}

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Similar Records

Title: Methods and compositions for efficient nucleic acid sequencing

Abstract

Citation Formats

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

DNA sequencing by hybridization — a megasequencing method and a diagnostic tool? journal, January 1994

Likelihood DNA Sequencing By Hybridization journal, December 1993

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

Nucleic acid hybridization assays employing dA-tailed capture probes. Single capture methods journal, June 1989

Light-directed, spatially addressable parallel chemical synthesis journal, February 1991

Rapid shotgeun cloning utillizing the two base recongition endonuclease Cvi JI journal, January 1992

Continuous, on-line DNA sequencing using oligodeoxynucleotide primers with multiple fluorophores. journal, August 1988

Specificity of the nick-closing activity of bacteriophage T4 DNA ligase journal, March 1989

Dissociation of Duplexes Formed by Hybridization of DNA with Gel-Immobilized Oligonucleotides journal, February 1994

Site-directed modification of DNA duplexes by chemical ligation journal, January 1988

A versatile solid support system for oligodeoxynucleotide probe-based hybridization assays journal, January 1991

Multiplex DNA sequencing journal, April 1988

Enhanced DNA sequencing by hybridization. journal, April 1994

Distribution of high mobility group proteins 1/2,E and 14/17 and linker histones H1 and H5 on transcribed and non-transcribed regions of chicken erythrocyte chromatin journal, January 1991

Light-generated oligonucleotide arrays for rapid DNA sequence analysis. journal, May 1994

An oligonucleotide hybridization approach to DNA sequencing journal, October 1989

Affinity chromatography of a sequence-specific DNA binding protein using teflon-linked oligonucleotides journal, February 1988

Proposal for sequencing DNA using ligation of hexamers to generate sequential elongation primers (SPEL-6) journal, May 1990

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

Rapid renaturation of complementary DNA strands mediated by cationic detergents: a role for high-probability binding domains in enhancing the kinetics of molecular assembly processes. journal, September 1991

A new method for sequencing DNA. journal, February 1977

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

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

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

DNA sequence determination by hybridization: a strategy for efficient large-scale sequencing journal, June 1993

Genomic Southern analysis with alkaline-phosphatase-conjugated oligonucleotide probes and the chemiluminescent substrate AMPPD journal, May 1991

DNA Sequence Confidence Estimation journal, February 1994

Inhibitory Effects of Human and Bovine Milk Constituents on Rotavirus Infections journal, December 2004

Quantification of picogram levels of specific DNA immobilized in microtiter wells journal, April 1985

Technique for maintaining and screening many microbial cultures journal, December 1989

Derivatization of unprotected polynucleotides journal, January 1983

Genomic sequencing. journal, April 1984

DNA sequencing by primer walking with strings of contiguous hexamers journal, December 1992

Improved Chips for Sequencing by Hybridization journal, October 1991

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

Selecting varieties using a series of trials and a combinatorial ordering method journal, January 1994

Constant denaturant capillary electrophoresis (CDCE): a high resolution approach to mutational anaylsis journal, January 1994

Low pressure DNA shearing: a method for random DNA sequence analysis journal, January 1990

One-step labelling of oligonucleotides with fluoresceine during automated synthesis journal, January 1990

Convergent Evolution of Alternative Splices at Domain Boundaries of the BK Channel journal, March 2009

Microarrays: their origins and applications journal, June 1999

DNA sequencing with chain-terminating inhibitors journal, December 1977

Microplate hybridization of amplified viral DNA segment. journal, January 1990

Worldwide Distribution of a Common Methylenetetrahydrofolate Reductase Mutation journal, May 1998

Sensitive detection of genes by sandwich hybridization and time-resolved fluorometry journal, June 1987

A universal nucleoside for use at ambiguous sites in DNA primers journal, June 1994

Fluorescent-labeled oligonucleotide probes: detection of hybrid formation in solution by fluorescence polarization spectroscopy journal, January 1991

Report on the sequencing by Hybridization workshop journal, August 1992

A novel method for nucleic acid sequence determination journal, December 1988

A ligase-mediated gene detection technique journal, August 1988

Sequencing by hybridization: Towards an automated sequencing of one million M13 clones arrayed on membranes journal, January 1992

Labelling oligonucleotides to high specific activity (I) journal, January 1989

Chemical ligation of DNA: the first non-enzymatic assembly of a biologically active gene journal, January 1991

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

DNA sequencing by hybridization — a megasequencing method and a diagnostic tool?
journal, January 1994

Likelihood DNA Sequencing By Hybridization
journal, December 1993

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

Nucleic acid hybridization assays employing dA-tailed capture probes. Single capture methods
journal, June 1989

Light-directed, spatially addressable parallel chemical synthesis
journal, February 1991

Rapid shotgeun cloning utillizing the two base recongition endonuclease Cvi JI
journal, January 1992

Continuous, on-line DNA sequencing using oligodeoxynucleotide primers with multiple fluorophores.
journal, August 1988

Specificity of the nick-closing activity of bacteriophage T4 DNA ligase
journal, March 1989

Dissociation of Duplexes Formed by Hybridization of DNA with Gel-Immobilized Oligonucleotides
journal, February 1994

Site-directed modification of DNA duplexes by chemical ligation
journal, January 1988

A versatile solid support system for oligodeoxynucleotide probe-based hybridization assays
journal, January 1991

Multiplex DNA sequencing
journal, April 1988

Enhanced DNA sequencing by hybridization.
journal, April 1994

Distribution of high mobility group proteins 1/2,E and 14/17 and linker histones H1 and H5 on transcribed and non-transcribed regions of chicken erythrocyte chromatin
journal, January 1991

Light-generated oligonucleotide arrays for rapid DNA sequence analysis.
journal, May 1994

An oligonucleotide hybridization approach to DNA sequencing
journal, October 1989

Affinity chromatography of a sequence-specific DNA binding protein using teflon-linked oligonucleotides
journal, February 1988

Proposal for sequencing DNA using ligation of hexamers to generate sequential elongation primers (SPEL-6)
journal, May 1990

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

Rapid renaturation of complementary DNA strands mediated by cationic detergents: a role for high-probability binding domains in enhancing the kinetics of molecular assembly processes.
journal, September 1991

A new method for sequencing DNA.
journal, February 1977

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

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

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

DNA sequence determination by hybridization: a strategy for efficient large-scale sequencing
journal, June 1993

Genomic Southern analysis with alkaline-phosphatase-conjugated oligonucleotide probes and the chemiluminescent substrate AMPPD
journal, May 1991

DNA Sequence Confidence Estimation
journal, February 1994

Inhibitory Effects of Human and Bovine Milk Constituents on Rotavirus Infections
journal, December 2004

Quantification of picogram levels of specific DNA immobilized in microtiter wells
journal, April 1985

Technique for maintaining and screening many microbial cultures
journal, December 1989

Derivatization of unprotected polynucleotides
journal, January 1983

Genomic sequencing.
journal, April 1984

DNA sequencing by primer walking with strings of contiguous hexamers
journal, December 1992

Improved Chips for Sequencing by Hybridization
journal, October 1991

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

Selecting varieties using a series of trials and a combinatorial ordering method
journal, January 1994

Constant denaturant capillary electrophoresis (CDCE): a high resolution approach to mutational anaylsis
journal, January 1994

Low pressure DNA shearing: a method for random DNA sequence analysis
journal, January 1990

One-step labelling of oligonucleotides with fluoresceine during automated synthesis
journal, January 1990

Convergent Evolution of Alternative Splices at Domain Boundaries of the BK Channel
journal, March 2009

Microarrays: their origins and applications
journal, June 1999

DNA sequencing with chain-terminating inhibitors
journal, December 1977

Microplate hybridization of amplified viral DNA segment.
journal, January 1990

Worldwide Distribution of a Common Methylenetetrahydrofolate Reductase Mutation
journal, May 1998

Sensitive detection of genes by sandwich hybridization and time-resolved fluorometry
journal, June 1987

A universal nucleoside for use at ambiguous sites in DNA primers
journal, June 1994

Fluorescent-labeled oligonucleotide probes: detection of hybrid formation in solution by fluorescence polarization spectroscopy
journal, January 1991

Report on the sequencing by Hybridization workshop
journal, August 1992

A novel method for nucleic acid sequence determination
journal, December 1988

A ligase-mediated gene detection technique
journal, August 1988

Sequencing by hybridization: Towards an automated sequencing of one million M13 clones arrayed on membranes
journal, January 1992

Labelling oligonucleotides to high specific activity (I)
journal, January 1989

Chemical ligation of DNA: the first non-enzymatic assembly of a biologically active gene
journal, January 1991