Repeat sequence chromosome specific nucleic acid probes and methods of preparing and using

Weier, Heinz-Ulrich G; Gray, Joe W

Title: Repeat sequence chromosome specific nucleic acid probes and methods of preparing and using

Abstract

A primer directed DNA amplification method to isolate efficiently chromosome-specific repeated DNA wherein degenerate oligonucleotide primers are used is disclosed. The probes produced are a heterogeneous mixture that can be used with blocking DNA as a chromosome-specific staining reagent, and/or the elements of the mixture can be screened for high specificity, size and/or high degree of repetition among other parameters. The degenerate primers are sets of primers that vary in sequence but are substantially complementary to highly repeated nucleic acid sequences, preferably clustered within the template DNA, for example, pericentromeric alpha satellite repeat sequences. The template DNA is preferably chromosome-specific. Exemplary primers ard probes are disclosed. The probes of this invention can be used to determine the number of chromosomes of a specific type in metaphase spreads, in germ line and/or somatic cell interphase nuclei, micronuclei and/or in tissue sections. Also provided is a method to select arbitrarily repeat sequence probes that can be screened for chromosome-specificity.

Inventors:

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

Tracy, CA
San Francisco, CA

Publication Date:: 1995-01-01

Research Org.:: Lawrence Livermore National Laboratory (LLNL), Livermore, CA (United States)

OSTI Identifier:: 869950

Patent Number(s):: US 5427932

Assignee:: Reagents of University of California (Oakland, CA)

DOE Contract Number:: W-7405-ENG-48

Resource Type:: Patent

Country of Publication:: United States

Language:: English

Subject:: repeat; sequence; chromosome; specific; nucleic; acid; probes; methods; preparing; primer; directed; dna; amplification; method; isolate; efficiently; chromosome-specific; repeated; degenerate; oligonucleotide; primers; disclosed; produced; heterogeneous; mixture; blocking; staining; reagent; elements; screened; specificity; size; degree; repetition; parameters; sets; vary; substantially; complementary; highly; sequences; preferably; clustered; template; example; pericentromeric; alpha; satellite; exemplary; determine; chromosomes; type; metaphase; spreads; germ; line; somatic; cell; interphase; nuclei; micronuclei; tissue; sections; provided; select; arbitrarily; chromosome-specificity; acid probes; acid sequence; nucleic acid; acid sequences; chromosome specific; acid probe; chromosome-specific staining; specific nucleic; repeat sequences; repeat sequence; amplification method; germ line; substantially complementary; staining reagent; specific type; oligonucleotide primers; interphase nuclei; oligonucleotide primer; dna amplification; /435/436/999/

Citation Formats


                    Weier, Heinz-Ulrich G, and Gray, Joe W. Repeat sequence chromosome specific nucleic acid probes and methods of preparing and using.  United States: N. p., 1995. 
        Web.

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                    Weier, Heinz-Ulrich G, & Gray, Joe W. Repeat sequence chromosome specific nucleic acid probes and methods of preparing and using.  United States.

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                    Weier, Heinz-Ulrich G, and Gray, Joe W. 1995.  
        "Repeat sequence chromosome specific nucleic acid probes and methods of preparing and using".  United States.  https://www.osti.gov/servlets/purl/869950.

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@article{osti_869950,

  title        = {Repeat sequence chromosome specific nucleic acid probes and methods of preparing and using},

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

  abstractNote = {A primer directed DNA amplification method to isolate efficiently chromosome-specific repeated DNA wherein degenerate oligonucleotide primers are used is disclosed. The probes produced are a heterogeneous mixture that can be used with blocking DNA as a chromosome-specific staining reagent, and/or the elements of the mixture can be screened for high specificity, size and/or high degree of repetition among other parameters. The degenerate primers are sets of primers that vary in sequence but are substantially complementary to highly repeated nucleic acid sequences, preferably clustered within the template DNA, for example, pericentromeric alpha satellite repeat sequences. The template DNA is preferably chromosome-specific. Exemplary primers ard probes are disclosed. The probes of this invention can be used to determine the number of chromosomes of a specific type in metaphase spreads, in germ line and/or somatic cell interphase nuclei, micronuclei and/or in tissue sections. Also provided is a method to select arbitrarily repeat sequence probes that can be screened for chromosome-specificity.},

  doi          = {},

  url          = {https://www.osti.gov/biblio/869950},
  journal      = {},
number       = ,

  volume       = ,

  place        = {United States},

  year         = {1995},

  month        = {1}

}

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Title: Repeat sequence chromosome specific nucleic acid probes and methods of preparing and using

Abstract

Citation Formats

Isolation and characterization of a major tandem repeat family from the human X chromosome journal, January 1983

Identification and characterization of a gene encoding a kinesin-like protein in Drosophila journal, June 1990

Rapid plasmid insert amplification with polymerase chain reaction journal, January 1988

Cloning of human satellite III DNA: different components are on different chromosomes journal, January 1979

Human chromosome-specific repetitive DNA probes: Targeting in situ hybridization to chromosome 17 with a 42-base-pair alphoid DNA oligomer journal, May 1989

Nucleotide sequences of human α-DNA repeats journal, January 1987

Chromosome-specific alpha satellite DNA from human chromosome 1: Hierarchical structure and genomic organization of a polymorphic domain spanning several hundred kilobase pairs of centromeric DNA journal, September 1987

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

Chromosome-specific subfamilies within human alphoid repetitive DNA journal, January 1986

Hierarchical order in chromosome-specific human alpha satellite DNA journal, January 1987

Cloning regions of the Drosophila genome by microdissection of polytene chromosome DNA and PCR with nonspecific primer journal, January 1990

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

Structure, organization, and sequence of alpha satellite DNA from human chromosome 17: evidence for evolution by unequal crossing-over and an ancestral pentamer repeat shared with the human X chromosome. journal, September 1986

A hypervariable repeated sequence on human chromosome 1p36 journal, October 1987

PCR amplification of chromosome-specific alpha satellite DNA: Definition of centromeric STS markers and polymorphic analysis journal, October 1991

Sequence heterogeneity within the human alphoid repetitive DNA family journal, January 1986

Chromosome-specific alpha satellite DNA: nucleotide sequence analysis of the 2.0 kilobasepair repeat from the human X chromosome journal, January 1985

Oligonucleotide-priming methods for the chromosome-specific labelling of alpha satellite DNA in situ journal, October 1989

A human Y-chromosome specific repeated DNA family (DYZ1) consists of a tandem array of pentanucleotides journal, January 1986

Human alphoid family of tandemly repeated DNA journal, November 1985

Detection of chromosome aberrations in the human interphase nucleus by visualization of specific target DNAs with radioactive and non-radioactive in situ hybridization techniques: diagnosis of trisomy 18 with probe L1.84 journal, December 1986

Chromosome-specific alpha satellite DNA: Isolation and mapping of a polymorphic alphoid repeat from human chromosome 10 journal, July 1988

Generation of labeled RNA probes from enzymatically amplified DNA templates journal, January 1988

Isolation and characterization of alphoid DNA sequences specific for the pericentric regions of chromosomes 4, 5, 9, and 19 journal, January 1988

Isothermal, in vitro amplification of nucleic acids by a multienzyme reaction modeled after retroviral replication. journal, March 1990

Primer-directed enzymatic amplification of DNA with a thermostable DNA polymerase journal, January 1988

Localisation of satellite DNA sequences on human metaphase chromosomes using bromodeoxyuridine-labelled probes journal, September 1988

The distribution of interspersed repetitive DNA sequences in the human genome journal, April 1989

Nucleotide sequence heterogeneity of alpha satellite repetitive DNA: a survey of alphoid sequences from different human chromosomes journal, January 1987

Chromosome specificity of satellite DNAs: short- and long-range organization of a diverged dimeric subset of human alpha satellite from chromosome 3 journal, May 1989

Characterization of a cloned repetitive DNA sequence concentrated on the human X chromosome. journal, November 1982

A Programmable System to Perform the Polymerase Chain Reaction journal, July 1988

Fluorescence in situ hybridization with Alu and L1 polymerase chain reaction probes for rapid characterization of human chromosomes in hybrid cell lines. journal, September 1990

Repeated DNA of the human Y chromosome journal, March 1987

Isothermal in vitro amplification of DNA by a restriction enzyme/DNA polymerase system. journal, January 1992

Isolation and characterization of a major tandem repeat family from the human X chromosome
journal, January 1983

Identification and characterization of a gene encoding a kinesin-like protein in Drosophila
journal, June 1990

Rapid plasmid insert amplification with polymerase chain reaction
journal, January 1988

Cloning of human satellite III DNA: different components are on different chromosomes
journal, January 1979

Human chromosome-specific repetitive DNA probes: Targeting in situ hybridization to chromosome 17 with a 42-base-pair alphoid DNA oligomer
journal, May 1989

Nucleotide sequences of human α-DNA repeats
journal, January 1987

Chromosome-specific alpha satellite DNA from human chromosome 1: Hierarchical structure and genomic organization of a polymorphic domain spanning several hundred kilobase pairs of centromeric DNA
journal, September 1987

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

Chromosome-specific subfamilies within human alphoid repetitive DNA
journal, January 1986

Hierarchical order in chromosome-specific human alpha satellite DNA
journal, January 1987

Cloning regions of the Drosophila genome by microdissection of polytene chromosome DNA and PCR with nonspecific primer
journal, January 1990

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

Structure, organization, and sequence of alpha satellite DNA from human chromosome 17: evidence for evolution by unequal crossing-over and an ancestral pentamer repeat shared with the human X chromosome.
journal, September 1986

A hypervariable repeated sequence on human chromosome 1p36
journal, October 1987

PCR amplification of chromosome-specific alpha satellite DNA: Definition of centromeric STS markers and polymorphic analysis
journal, October 1991

Sequence heterogeneity within the human alphoid repetitive DNA family
journal, January 1986

Chromosome-specific alpha satellite DNA: nucleotide sequence analysis of the 2.0 kilobasepair repeat from the human X chromosome
journal, January 1985

Oligonucleotide-priming methods for the chromosome-specific labelling of alpha satellite DNA in situ
journal, October 1989

A human Y-chromosome specific repeated DNA family (DYZ1) consists of a tandem array of pentanucleotides
journal, January 1986

Human alphoid family of tandemly repeated DNA
journal, November 1985

Detection of chromosome aberrations in the human interphase nucleus by visualization of specific target DNAs with radioactive and non-radioactive in situ hybridization techniques: diagnosis of trisomy 18 with probe L1.84
journal, December 1986

Chromosome-specific alpha satellite DNA: Isolation and mapping of a polymorphic alphoid repeat from human chromosome 10
journal, July 1988

Generation of labeled RNA probes from enzymatically amplified DNA templates
journal, January 1988

Isolation and characterization of alphoid DNA sequences specific for the pericentric regions of chromosomes 4, 5, 9, and 19
journal, January 1988

Isothermal, in vitro amplification of nucleic acids by a multienzyme reaction modeled after retroviral replication.
journal, March 1990

Primer-directed enzymatic amplification of DNA with a thermostable DNA polymerase
journal, January 1988

Localisation of satellite DNA sequences on human metaphase chromosomes using bromodeoxyuridine-labelled probes
journal, September 1988

The distribution of interspersed repetitive DNA sequences in the human genome
journal, April 1989

Nucleotide sequence heterogeneity of alpha satellite repetitive DNA: a survey of alphoid sequences from different human chromosomes
journal, January 1987

Chromosome specificity of satellite DNAs: short- and long-range organization of a diverged dimeric subset of human alpha satellite from chromosome 3
journal, May 1989

Characterization of a cloned repetitive DNA sequence concentrated on the human X chromosome.
journal, November 1982

A Programmable System to Perform the Polymerase Chain Reaction
journal, July 1988

Fluorescence in situ hybridization with Alu and L1 polymerase chain reaction probes for rapid characterization of human chromosomes in hybrid cell lines.
journal, September 1990

Repeated DNA of the human Y chromosome
journal, March 1987

Isothermal in vitro amplification of DNA by a restriction enzyme/DNA polymerase system.
journal, January 1992