Competitive oligonucleotides

• US 20070238104A1
• Filed: 04/07/2006
• Published: 10/11/2007
• Est. Priority Date: 04/07/2006
• Status: Abandoned Application

• Current Assignee: Agilent Technologies, Inc.
• Original Assignee: Agilent Technologies, Inc.
• Inventors: Caren, Michael P., Barrett, Michael Thomas
• Application Number:
  US11/400,475
• Publication Number:
  US 20070238104A1
• Time in Patent Office: Days
• US Class Current: 435/6
• CPC Class Codes: C12Q 1/6816 characterised by the detection means C12Q1/6804 takes precedence
• CPC Class Codes: C12Q 2525/186 incorporating a non-extendable or blocking moiety

Abstract

The present invention generally relates to competitive oligonucleotides and, in some embodiments, to competitive oligonucleotides for use in comparative genomic hybridization (CGH) and related techniques. One aspect is generally directed to a blocking composition constructed and arranged to be used in an assay of a nucleic acid. The blocking composition may comprise oligonucleotides comprising sequences selected to hybridize to the nucleic acid used in the assay. Another aspect is generally directed to performing CGH assays and similar techniques on genomic DNA, in the absence of a Cot-1 fraction, such that the genomic DNA does not substantially cross-hybridize. Yet other aspects of the invention are directed to devices or kits for making or using competitive oligonucleotides, methods of promoting such competitive oligonucleotides, or the like.

Claims

1. An article, comprising:

a blocking composition, constructed and arranged to be used in an assay of a nucleic acid, the blocking composition comprising a solution comprising a plurality of oligonucleotides, including at least a first oligonucleotide and a second oligonucleotide different from the first oligonucleotide, wherein each of the first and second oligonucleotides comprises respective first and second sequences each selected to hybridize to the nucleic acid used in the assay.

2. The article of claim 1, wherein the first oligonucleotide has a length of between 80 nucleotides and 200 nucleotides and the second oligonucleotide has a length of between 80 nucleotides and 200 nucleotides.

3. The article of claim 2, wherein the first oligonucleotide has a length of between 100 nucleotides and 200 nucleotides and the second oligonucleotide has a length of between 100 nucleotides and 200 nucleotides.

4. The article of claim 1, wherein the first sequence of the first oligonucleotide selected to hybridize to the nucleic acid has a length of at least 50 nucleotides.

5. The article of claim 1, wherein the first oligonucleotide and the second oligonucleotide are synthesized from a substrate.

6. The article of claim 1, wherein the first sequence of the first oligonucleotide selected to hybridize to the nucleic acid is perfectly complementary to a portion of the nucleic acid.

7. The article of claim 1 wherein the first oligonucleotide and the second oligonucleotide are designed using a computer.

8. A method, comprising:

providing a sample comprising a nucleic acid;

exposing the sample to a blocking composition comprising a plurality of oligonucleotides, including at least a first oligonucleotide and a second oligonucleotide different from the first oligonucleotide, wherein each of the first and second oligonucleotides comprises respective first and second sequences each selected to hybridize to the nucleic acid.

9. The method of claim 8, further comprising determining hybridization of the plurality of oligonucleotides with the nucleic acid.

10. The method of claim 8, further comprising analyzing the nucleic acid in the presence of the blocking composition.

11. A method of blocking at least a portion of a genome, comprising:

identifying a nucleic acid sequence; and

designing at least a first oligonucleotide and a second oligonucleotide different from the first oligonucleotide, wherein each of the first and second oligonucleotides comprises respective first and second sequences each selected to hybridize the nucleic acid.

12. The method of claim 11, wherein the act of designing comprises designing using a computer.

13. The method of claim 11, wherein the nucleic acid sequence is part of a genome.

14. A kit for use within an assay of a nucleic acid to block at least a portion of a nucleic acid, the kit comprising:

a first oligonucleotide; and

a second oligonucleotide different from the first oligonucleotide,

wherein each of the first and second oligonucleotides comprises respective first and second sequences each selected to hybridize a sequence that is suspected be present within the nucleic acid.

15. A method of performing comparative genomic hybridization (CGH), comprising acts of:

performing a CGH assay on a genomic DNA sample, in the absence of a Cot-1 fraction, such that the genomic DNA does not substantially cross-hybridize.

16. The method of claim 15, comprising performing the CGH assay on the genomic DNA sample, in the absence of competitor DNA.

17. The method of claim 15, comprising exposing the genomic DNA sample to a plurality of oligonucleotides.

18. A method of performing comparative genomic hybridization (CGH), comprising acts of:

exposing a sample comprising genomic DNA to a plurality of synthetic oligonucleotides, at least some of which are not identical; and

performing a CGH assay on the sample such that the DNA does not substantially cross-hybridize.

19. An article, comprising:

a solution comprising a plurality of oligonucleotides, at least some of which are not identical,

wherein, for at least some of the plurality of oligonucleotides, each of the oligonucleotides of the at least some oligonucleotides comprises at least two copies of a repetitive sequence.

20. The article of claim 19, wherein at least about 50% of the plurality of oligonucleotides comprises at least two copies of a repetitive sequence.