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US 2007/0190618 A1Published application
Methods and compositions for detecting viral nucleic acid in a cell
AssigneeAgilent Technologies, Inc.
InventorAnniek De Witte
Life of this patent
Estimating the term…
Abstract
Methods and compositions for identifying or detecting viral nucleic acids in a host cell are described. DNA fragments are bound to DNA-binding protein in a host cell and enriched using immunoprecipitation. The enriched fragments are then hybridized to a microarray containing sequences complementary to proviral DNA and genomic DNA.
Claims11
A method of determining whether a viral nucleic acid is present in a host cell, comprising the steps of:
- (a) producing a fragmented DNA sample from the host cell;
- (b) preparing a first target population of nucleic acids from a first portion of said fragmented DNA sample that is enriched for DNA fragments bound to DNA-binding protein, wherein said preparing comprises immunoprecipitation with an antibody or antigen-binding fragment of an antibody specific for the DNA-binding protein, wherein said immunoprecipitation is with an antibody or antigen-binding fragment of an antibody specific for RNA polymerase II or is with an antibody or antigen-binding fragment of an antibody specific for viral integrase;
- (c) preparing a second target population of nucleic acids from a second non-enriched portion of said fragmented DNA sample;
- and
- (d) contacting the first and second populations of target nucleic acids to an array of probe oligonucleotides, the array comprising probes specific for genomic DNA of the host cell and probes specific for viral nucleic acid;
- and
- (e) detecting hybridization of said first and second population of target nucleic acids to said array of probe oligonucleotides to determine whether said viral nucleic acid is present in said cell.
4 more elements
(canceled)
9-13. (canceled)
A method of determining whether a viral nucleic acid is present in a host cell, comprising the steps of:
- (a) producing a fragmented DNA sample from the host cell;
- (b) preparing a first target population of nucleic acids from a first portion of said fragmented DNA sample that is enriched for DNA fragments bound to DNA-binding protein, wherein said preparing comprises immunoprecipitation with an antibody or antigen-binding fragment of an antibody specific for the DNA-binding protein, wherein said immunoprecipitation is with an antibody or antigen-binding fragment of an antibody specific for viral integrase;
- (c) preparing a second target population of nucleic acids from a second non-enriched portion of said fragmented DNA sample;
- and
- (d) contacting the first and second populations of target nucleic acids to an array of probe oligonucleotides, the array comprising probes specific for genomic DNA of the host cell and probes specific for viral nucleic acid;
- and
- (e) detecting hybridization of said first and second population of target nucleic acids to said array of probe oligonucleotides to determine whether said viral nucleic acid is present in said cell.
4 more elements
A method of determining whether a viral nucleic acid is present in a host cell, comprising the steps of:
- (a) producing a fragmented DNA sample from the host cell;
- (b) preparing a first target population of nucleic acids from a first portion of said fragmented DNA sample that is enriched for DNA fragments bound to DNA-binding protein, wherein said preparing comprises immunoprecipitation with an antibody or antigen-binding fragment of an antibody specific for RNA polymerase II;
- (c) preparing a second target population of nucleic acids from a second non-enriched portion of said fragmented DNA sample;
- and
- (d) contacting the first and second populations of target nucleic acids to an array of probe oligonucleotides, the array comprising probes specific for genomic DNA of the host cell and probes specific for viral nucleic acid;
- and
- (e) detecting hybridization of said first and second population of target nucleic acids to said array of probe oligonucleotides to determine whether said viral nucleic acid is present in said cell.
4 more elements
Dependencies are inferred from the claim text.