Quantitative DNA fiber mapping

Gray, Joe W; Weier, Heinz-Ulrich G

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Title: Quantitative DNA fiber mapping

Abstract

The present invention relates generally to the DNA mapping and sequencing technologies. In particular, the present invention provides enhanced methods and compositions for the physical mapping and positional cloning of genomic DNA. The present invention also provides a useful analytical technique to directly map cloned DNA sequences onto individual stretched DNA molecules.

Inventors:

Gray, Joe W ^[1]; Weier, Heinz-Ulrich G ^[2]

San Francisco, CA
Oakland, CA

Issue Date:: 1998-01-01

Research Org.:: Lawrence Berkeley National Laboratory (LBNL), Berkeley, CA (United States)

OSTI Identifier:: 872053

Patent Number(s):: 5851769

Assignee:: Regents of University of California (Oakland, 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
C12Q1/68 - involving nucleic acids
C12Q1/6834 - Enzymatic or biochemical coupling of nucleic acids to a solid phase

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Resource Type:: Patent

Country of Publication:: United States

Language:: English

Subject:: quantitative; dna; fiber; mapping; relates; sequencing; technologies; particular; provides; enhanced; methods; compositions; physical; positional; cloning; genomic; useful; analytical; technique; directly; map; cloned; sequences; individual; stretched; molecules; dna sequences; dna sequence; dna molecules; cloned dna; dna molecule; provides enhanced; enhanced method; physical mapping; analytical technique; /435/

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                    Gray, Joe W, and Weier, Heinz-Ulrich G. Quantitative DNA fiber mapping.  United States: N. p., 1998. 
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                    Gray, Joe W, & Weier, Heinz-Ulrich G. Quantitative DNA fiber mapping.  United States.

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                    Gray, Joe W, and Weier, Heinz-Ulrich G. Thu .  
        "Quantitative DNA fiber mapping".  United States.  https://www.osti.gov/servlets/purl/872053.

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@article{osti_872053,

  title        = {Quantitative DNA fiber mapping},

  author       = {Gray, Joe W and Weier, Heinz-Ulrich G},

  abstractNote = {The present invention relates generally to the DNA mapping and sequencing technologies. In particular, the present invention provides enhanced methods and compositions for the physical mapping and positional cloning of genomic DNA. The present invention also provides a useful analytical technique to directly map cloned DNA sequences onto individual stretched DNA molecules.},

  doi          = {},

  journal      = {},
number       = ,

  volume       = ,

  place        = {United States},

  year         = {1998},

  month        = {1}

}

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Human Molecular Genetics, Vol. 3, Issue 1
https://doi.org/10.1093/hmg/3.1.99

Similar Records in DOE Patents and OSTI.GOV collections:

Detection and quantitation of single nucleotide polymorphisms, DNA sequence variations, DNA mutations, DNA damage and DNA mismatches

Patent McCutchen-Maloney, Sandra L [Pleasanton, CA]

DNA mutation binding proteins alone and as chimeric proteins with nucleases are used with solid supports to detect DNA sequence variations, DNA mutations and single nucleotide polymorphisms. The solid supports may be flow cytometry beads, DNA chips, glass slides or DNA dips sticks. DNA molecules are coupled to solid supports to form DNA-support complexes. Labeled DNA is used with unlabeled DNA mutation binding proteins such at TthMutS to detect DNA sequence variations, DNA mutations and single nucleotide length polymorphisms by binding which gives an increase in signal. Unlabeled DNA is utilized with labeled chimeras to detect DNA sequence variations, DNAmore » « less
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Chimeric proteins for detection and quantitation of DNA mutations, DNA sequence variations, DNA damage and DNA mismatches

Patent McCutchen-Maloney, Sandra L [Pleasanton, CA]

Chimeric proteins having both DNA mutation binding activity and nuclease activity are synthesized by recombinant technology. The proteins are of the general formula A-L-B and B-L-A where A is a peptide having DNA mutation binding activity, L is a linker and B is a peptide having nuclease activity. The chimeric proteins are useful for detection and identification of DNA sequence variations including DNA mutations (including DNA damage and mismatches) by binding to the DNA mutation and cutting the DNA once the DNA mutation is detected.
Full Text Available
Magnetically-induced solid-phase microextraction fiber actuation system for quantitative headspace and liquid sampling

Patent Harvey, Chris; Carter, Jerry; Chambers, David M.

A magnetically-induced SPME fiber actuation system includes a SPME fiber holder and a SPME fiber holder actuator, for holding and magnetically actuating a SPME fiber assembly. The SPME fiber holder has a plunger with a magnetic material to which the SPME fiber assembly is connected, and the magnetic SPME fiber holder actuator has an elongated barrel with a loading chamber for receiving the SPME fiber assembly-connected SPME fiber holder, and an external magnet which induces axial motion of the magnetic material of the plunger to extend/retract the SPME fiber from/into the protective needle of the SPME fiber assembly.
Full Text Available
Spatially resolved quantitative mapping of thermomechanical properties and phase transition temperatures using scanning probe microscopy

Patent Jesse, Stephen; Kalinin, Sergei V; Nikiforov, Maxim P

An approach for the thermomechanical characterization of phase transitions in polymeric materials (polyethyleneterephthalate) by band excitation acoustic force microscopy is developed. This methodology allows the independent measurement of resonance frequency, Q factor, and oscillation amplitude of a tip-surface contact area as a function of tip temperature, from which the thermal evolution of tip-surface spring constant and mechanical dissipation can be extracted. A heating protocol maintained a constant tip-surface contact area and constant contact force, thereby allowing for reproducible measurements and quantitative extraction of material properties including temperature dependence of indentation-based elastic and loss moduli.
Full Text Available
Dual fiber microprobe for mapping elemental distributions in biological cells

Patent Martin, Rodger C [Powell, TN]; Martin, Madhavi Z [Powell, TN]

Laser-induced breakdown spectroscopy (LIBS) is applied on a microscale for in situ elemental analysis and spatial mapping in biological cells. A high power laser beam is focused onto a cell surface using a dual branching optical fiber probe for optical excitation of the cell constituents. Dual spectrometers and ICCD detectors capture the emission spectra from the excited cell(s). Repeated probing or repositioning of the laser beam with respect to the cell can provide 2-D or 3-D mapping of the cell.
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Similar Records

Title: Quantitative DNA fiber mapping

Abstract

Citation Formats

Rapid identification of yeast artificial chromosome clones by matrix pooling and crude Iysate PCR journal, January 1990

Generation of Five High-Complexity Painting Probe Libraries from Flow-Sorted Mouse Chromosomes journal, June 1994

PCR cloning of a repeated DNA fragment from Chinese hamster ovary (CHO) cell X chromosomes and mapping by fluorescence in situ hybridization journal, January 1993

Cytogenetic analysis by chromosome painting journal, March 1994

A high resolution physical map of 2.5 Mbp of the Down syndrome region on chromosome 21 journal, January 1994

Alignment and sensitive detection of DNA by a moving interface journal, September 1994

Evaluation of a cosmid contig physical map of human chromosome 16 journal, August 1992

Continuum of overlapping clones spanning the entire human chromosome 21q journal, October 1992

A physical map of the human Y-chromosome short arm journal, August 1990

Radiation hybrid mapping: a somatic cell genetic method for constructing high-resolution maps of mammalian chromosomes journal, October 1990

A new five-year plan for the U.S. Human Genome Project journal, October 1993

Construction of a 5.2-Megabase Physical Map of the Human X Chromosome at Xq22 Using Pulsed-Field Gel Electrophoresis and Yeast Artificial Chromosomes journal, March 1993

Order and genomic distances among members of the carcinoembryonic antigen (CEA) gene family determined by fluorescence in situ hybridization journal, April 1992

Construction and characterization of band-specific DNA libraries journal, May 1990

High resolution ordering of YAC contigs using extended chromatin and chromosomes journal, January 1994

A map of the distal region of the long arm of human chromosome 21 constructed by radiation hybrid mapping and pulsed-field gel electrophoresis journal, January 1991

Synthesis of Y chromosome-specific labeled DNA probes by in vitro DNA amplification. journal, March 1990

High-resolution in situ hybridization using DNA halo preparations journal, January 1992

Transposon-facilitated DNA sequencing. journal, February 1991

An integrated YAC-overlap and ‘cosmid-pocket’ map of the human chromosome 21 journal, January 1994

Semiautomated DNA probe mapping using digital imaging microscopy: II. System performance journal, January 1995

Semiautomated DNA probe mapping using digital imaging microscopy: I. System development journal, January 1995

Detection of APC region-specific signals by nonisotopic chromosomal in situ suppression (CISS)-hybridization using a microdissection library as a probe journal, August 1991

Preparation of immobilized proteins covalently coupled through silane coupling agents to inorganic supports journal, June 1993

Optimizing restriction fragment fingerprinting methods for ordering large genomic libraries journal, October 1990

High-Resolution Physical Mapping of Human 5q31-q33 Using Three Methods: Radiation Hybrid Mapping, Interphase Fluorescence in Situ Hybridization, and Pulsed-Field Gel Electrophoresis journal, November 1994

Ligation of oligonucleotides to nucleic acids or proteins via disulfide bonds journal, May 1988

Applications of polymerase chain reaction methods in genome mapping journal, June 1991

Multicolor fluorescence in situ hybridization on metaphase chromosomes and interphase Halo-preparations using cosmid and YAC clones for the simultaneous high resolution mapping of deletions in the dystrophin gene journal, March 1994

PCR probes for chromosome in situ hybridization of large-insert bacterial recombinants journal, January 1994

Physical and genetic map of 5q31: use of fluorescence in situ hybridization data to identify errors in the CEPH database journal, January 1994

Estimating genomic distance from DNA sequence location in cell nuclei by a random walk model journal, September 1992

Mapping the whole human genome by fingerprinting yeast artificial chromosomes journal, September 1992

Current methods for YAC clone characterization journal, September 1990

Cloning defined regions of the human genome by microdissection of banded chromosomes and enzymatic amplification journal, March 1989

A new system for high-resolution DNA sequence mapping in interphase pronuclei journal, May 1991

The ligation amplification reaction (LAR)—Amplification of specific DNA sequences using sequential rounds of template-dependent ligation journal, May 1989

Identification of CpG islands in a physical map encompassing the Friedreich's ataxia locus journal, January 1991

Physical and Genetic Maps for Chromosome 10 journal, May 1993

New RNA Polymerase from Escherichia coli infected with Bacteriophage T7 journal, October 1970

Systematic generation of sequence-tagged sites for physical mapping of human chromosomes: Application to the mapping of human chromosome 7 using yeast artificial chromosomes journal, November 1991

A radiation hybrid map of the region on human chromosome 22 containing the neurofibromatosis type 2 locus journal, November 1992

A positive selection vector for cloning high molecular weight DNA by the bacteriophage P1 system: improved cloning efficacy. journal, March 1992

Use of reference libraries and hybridisation fingerprinting for relational genome analysis journal, June 1993

High-resolution DNA Fiber-FISH for genomic DNA mapping and colour bar-coding of large genes journal, May 1995

FISH in genome research and molecular diagnostics journal, June 1995

Yeast artificial chromosomes: tools for mapping and analysis of complex genomes journal, January 1990

PCR amplification and analysis of yeast artificial chromosomes journal, August 1992

The human genome project. journal, May 1993

A Replicating RNA Molecule Suitable for a Detailed Analysis of Extracellular Evolution and Replication journal, October 1972

Induction of complete segregation of cellular DNA and non-encapsidated viral genomes in herpes simplex virus type 1 infected HeLa cells as revealed by in situ hybridization journal, April 1994

Generation of a Human Chromosome 18-Specific YAC Clone Collection and Mapping of 55 Unique YACs by FISH and Fingerprinting journal, August 1993

High resolution visual mapping of stretched DNA by fluorescent hybridization journal, September 1993

Fluorescence in Situ Hybridization Mapping of Human Chromosome 19: Cytogenetic Band Location of 540 Cosmids and 70 Genes or DNA Markers journal, January 1993

Comparative genomic hybridization for molecular cytogenetic analysis of solid tumors journal, October 1992

Human genome organization: Alu, LINES, and the molecular structure of metaphase chromosome bands journal, May 1988

Current trends in mapping human genes journal, January 1991

A second-generation linkage map of the human genome journal, October 1992

Detection and characterization of “Chimeric” yeast artificial chromosome clones by fluorescent in Situ suppression hybridization journal, October 1992

Systematic screening of yeast artificial-chromosome libraries by use of the polymerase chain reaction. journal, February 1990

The proximity of DNA sequences in interphase cell nuclei is correlated to genomic distance and permits ordering of cosmids spanning 250 kilobase pairs journal, November 1989

Distribution of moderately repetitive sequences pTR5 and LF1 in Xq24–q28 human DNA and their use in assembling YAC contigs journal, February 1992

Cytogenetic analysis by chromosome painting using dop-pcr amplified flow-sorted chromosomes journal, April 1992

Recently transposed Alu repeats result from multiple source genes journal, January 1990

A first-generation physical map of the human genome journal, December 1993

Extending the capabilities of interphase chromatin mapping journal, November 1992

Construction of a 2.6-Mb contig in yeast artificial chromosomes spanning the human dystrophin gene using an STS-based approach journal, March 1992

Alu and L1 Sequence Distributions in Xq24-q28 and Their Comparative Utility in YAC Contig Assembly and Verification journal, May 1993

Cloning and stable maintenance of 300-kilobase-pair fragments of human DNA in Escherichia coli using an F-factor-based vector. journal, September 1992

Amplification of 20q13 locus in breast cancer: -Defining the minimal region journal, October 1994

Rapid generation of region specific probes by chromosome microdissection and their application journal, April 1992

Assembly and analysis of cosmid contigs in the CEA-gene family region of human chromosome 19 journal, January 1992

Sequence-tagged site (STS) content mapping of human chromosomes: theoretical considerations and early experiences. journal, November 1991

Preparation and screening of an arrayed human genomic library generated with the P1 cloning system. journal, March 1994

Construction and characterization of a yeast artificial chromosome library containing seven haploid human genome equivalents. journal, June 1990

Construction of a YAC contig and a STS map spanning at least seven megabasepairs in chromosome 5q34-35 journal, January 1994

Rapid identification of yeast artificial chromosome clones by matrix pooling and crude Iysate PCR
journal, January 1990

Generation of Five High-Complexity Painting Probe Libraries from Flow-Sorted Mouse Chromosomes
journal, June 1994

PCR cloning of a repeated DNA fragment from Chinese hamster ovary (CHO) cell X chromosomes and mapping by fluorescence in situ hybridization
journal, January 1993

Cytogenetic analysis by chromosome painting
journal, March 1994

A high resolution physical map of 2.5 Mbp of the Down syndrome region on chromosome 21
journal, January 1994

Alignment and sensitive detection of DNA by a moving interface
journal, September 1994

Evaluation of a cosmid contig physical map of human chromosome 16
journal, August 1992

Continuum of overlapping clones spanning the entire human chromosome 21q
journal, October 1992

A physical map of the human Y-chromosome short arm
journal, August 1990

Radiation hybrid mapping: a somatic cell genetic method for constructing high-resolution maps of mammalian chromosomes
journal, October 1990

A new five-year plan for the U.S. Human Genome Project
journal, October 1993

Construction of a 5.2-Megabase Physical Map of the Human X Chromosome at Xq22 Using Pulsed-Field Gel Electrophoresis and Yeast Artificial Chromosomes
journal, March 1993

Order and genomic distances among members of the carcinoembryonic antigen (CEA) gene family determined by fluorescence in situ hybridization
journal, April 1992

Construction and characterization of band-specific DNA libraries
journal, May 1990

High resolution ordering of YAC contigs using extended chromatin and chromosomes
journal, January 1994

A map of the distal region of the long arm of human chromosome 21 constructed by radiation hybrid mapping and pulsed-field gel electrophoresis
journal, January 1991

Synthesis of Y chromosome-specific labeled DNA probes by in vitro DNA amplification.
journal, March 1990

High-resolution in situ hybridization using DNA halo preparations
journal, January 1992

Transposon-facilitated DNA sequencing.
journal, February 1991

An integrated YAC-overlap and ‘cosmid-pocket’ map of the human chromosome 21
journal, January 1994

Semiautomated DNA probe mapping using digital imaging microscopy: II. System performance
journal, January 1995

Semiautomated DNA probe mapping using digital imaging microscopy: I. System development
journal, January 1995

Detection of APC region-specific signals by nonisotopic chromosomal in situ suppression (CISS)-hybridization using a microdissection library as a probe
journal, August 1991

Preparation of immobilized proteins covalently coupled through silane coupling agents to inorganic supports
journal, June 1993

Optimizing restriction fragment fingerprinting methods for ordering large genomic libraries
journal, October 1990

High-Resolution Physical Mapping of Human 5q31-q33 Using Three Methods: Radiation Hybrid Mapping, Interphase Fluorescence in Situ Hybridization, and Pulsed-Field Gel Electrophoresis
journal, November 1994

Ligation of oligonucleotides to nucleic acids or proteins via disulfide bonds
journal, May 1988

Applications of polymerase chain reaction methods in genome mapping
journal, June 1991

Multicolor fluorescence in situ hybridization on metaphase chromosomes and interphase Halo-preparations using cosmid and YAC clones for the simultaneous high resolution mapping of deletions in the dystrophin gene
journal, March 1994

PCR probes for chromosome in situ hybridization of large-insert bacterial recombinants
journal, January 1994

Physical and genetic map of 5q31: use of fluorescence in situ hybridization data to identify errors in the CEPH database
journal, January 1994

Estimating genomic distance from DNA sequence location in cell nuclei by a random walk model
journal, September 1992

Mapping the whole human genome by fingerprinting yeast artificial chromosomes
journal, September 1992

Current methods for YAC clone characterization
journal, September 1990

Cloning defined regions of the human genome by microdissection of banded chromosomes and enzymatic amplification
journal, March 1989

A new system for high-resolution DNA sequence mapping in interphase pronuclei
journal, May 1991

The ligation amplification reaction (LAR)—Amplification of specific DNA sequences using sequential rounds of template-dependent ligation
journal, May 1989

Identification of CpG islands in a physical map encompassing the Friedreich's ataxia locus
journal, January 1991

Physical and Genetic Maps for Chromosome 10
journal, May 1993

New RNA Polymerase from Escherichia coli infected with Bacteriophage T7
journal, October 1970

Systematic generation of sequence-tagged sites for physical mapping of human chromosomes: Application to the mapping of human chromosome 7 using yeast artificial chromosomes
journal, November 1991

A radiation hybrid map of the region on human chromosome 22 containing the neurofibromatosis type 2 locus
journal, November 1992

A positive selection vector for cloning high molecular weight DNA by the bacteriophage P1 system: improved cloning efficacy.
journal, March 1992

Use of reference libraries and hybridisation fingerprinting for relational genome analysis
journal, June 1993

High-resolution DNA Fiber-FISH for genomic DNA mapping and colour bar-coding of large genes
journal, May 1995

FISH in genome research and molecular diagnostics
journal, June 1995

Yeast artificial chromosomes: tools for mapping and analysis of complex genomes
journal, January 1990

PCR amplification and analysis of yeast artificial chromosomes
journal, August 1992

The human genome project.
journal, May 1993

A Replicating RNA Molecule Suitable for a Detailed Analysis of Extracellular Evolution and Replication
journal, October 1972

Induction of complete segregation of cellular DNA and non-encapsidated viral genomes in herpes simplex virus type 1 infected HeLa cells as revealed by in situ hybridization
journal, April 1994

Generation of a Human Chromosome 18-Specific YAC Clone Collection and Mapping of 55 Unique YACs by FISH and Fingerprinting
journal, August 1993

High resolution visual mapping of stretched DNA by fluorescent hybridization
journal, September 1993

Fluorescence in Situ Hybridization Mapping of Human Chromosome 19: Cytogenetic Band Location of 540 Cosmids and 70 Genes or DNA Markers
journal, January 1993

Comparative genomic hybridization for molecular cytogenetic analysis of solid tumors
journal, October 1992

Human genome organization: Alu, LINES, and the molecular structure of metaphase chromosome bands
journal, May 1988

Current trends in mapping human genes
journal, January 1991

A second-generation linkage map of the human genome
journal, October 1992

Detection and characterization of “Chimeric” yeast artificial chromosome clones by fluorescent in Situ suppression hybridization
journal, October 1992

Systematic screening of yeast artificial-chromosome libraries by use of the polymerase chain reaction.
journal, February 1990

The proximity of DNA sequences in interphase cell nuclei is correlated to genomic distance and permits ordering of cosmids spanning 250 kilobase pairs
journal, November 1989

Distribution of moderately repetitive sequences pTR5 and LF1 in Xq24–q28 human DNA and their use in assembling YAC contigs
journal, February 1992

Cytogenetic analysis by chromosome painting using dop-pcr amplified flow-sorted chromosomes
journal, April 1992

Recently transposed Alu repeats result from multiple source genes
journal, January 1990

A first-generation physical map of the human genome
journal, December 1993

Extending the capabilities of interphase chromatin mapping
journal, November 1992

Construction of a 2.6-Mb contig in yeast artificial chromosomes spanning the human dystrophin gene using an STS-based approach
journal, March 1992

Alu and L1 Sequence Distributions in Xq24-q28 and Their Comparative Utility in YAC Contig Assembly and Verification
journal, May 1993

Cloning and stable maintenance of 300-kilobase-pair fragments of human DNA in Escherichia coli using an F-factor-based vector.
journal, September 1992

Amplification of 20q13 locus in breast cancer: -Defining the minimal region
journal, October 1994

Rapid generation of region specific probes by chromosome microdissection and their application
journal, April 1992

Assembly and analysis of cosmid contigs in the CEA-gene family region of human chromosome 19
journal, January 1992

Sequence-tagged site (STS) content mapping of human chromosomes: theoretical considerations and early experiences.
journal, November 1991

Preparation and screening of an arrayed human genomic library generated with the P1 cloning system.
journal, March 1994

Construction and characterization of a yeast artificial chromosome library containing seven haploid human genome equivalents.
journal, June 1990

Construction of a YAC contig and a STS map spanning at least seven megabasepairs in chromosome 5q34-35
journal, January 1994