Target determination using compound probes

• US 20070259345A1
• Filed: 05/03/2006
• Published: 11/08/2007
• Est. Priority Date: 05/03/2006
• Status: Abandoned Application

• Current Assignee: Agilent Technologies, Inc.
• Original Assignee: Agilent Technologies, Inc.
• Inventors: Sampas, Nicholas M.
• Application Number:
  US11/417,324
• Publication Number:
  US 20070259345A1
• Time in Patent Office: Days
• US Class Current: 435/6
• CPC Class Codes: C12Q 1/6837 using probe arrays or probe chips C12Q1/6874 takes precedence
• CPC Class Codes: C12Q 2525/197 incorporating a spacer/coupling moiety
• CPC Class Codes: C12Q 2565/507 characterised by the density of the capture oligonucleotide

Abstract

The present invention generally relates to systems and methods for identifying and/or quantifying targets such as nucleic acid targets using compound probes (e.g., oligonucleotide probes), which can comprise first and second sequences able to hybridize to one or more nucleic acids or portions thereof. In one aspect, a nucleic acid (e.g., one or more genomes or chromosomes) may be fragmented, and the fragments exposed to a compound probe. By suitably labeling of the fragments, the amount of binding of each of the fragments to the compound probe may be determined. In some cases, the fragments may be distinguishably labeled, and in certain embodiments, the fragments may be sorted (e.g., via size or charge) prior to exposure to the compound probe.

Claims

1. A method, comprising:

providing an oligonucleotide probe;

exposing the oligonucleotide probe to a first nucleic acid labeled with a first detection entity such that at least a portion of the first nucleic acid hybridizes to a first sequence of the oligonucleotide probe; and

exposing the oligonucleotide probe to a second nucleic acid, different from the first nucleic acid and labeled with a second detection entity, such that at least a portion of the second nucleic acid hybridizes to a second sequence of the oligonucleotide probe.

2. The method of claim 1, wherein the act of exposing the oligonucleotide probe to the first nucleic acid and the act of exposing the oligonucleotide probe to the second nucleic acid occurs essentially simultaneously.

3. The method of claim 1, further comprising cleaving a precursor nucleic acid to produce the first nucleic acid and the second nucleic acid.

4. The method of claim 3, comprising:

separating the first nucleic acid and the second nucleic acid;

thereafter, labeling the first nucleic acid with the first detection entity and the second nucleic acid with the second detection entity.

5. The method of claim 3, further comprising identifying one or more restriction sites within the precursor nucleic acid by determining hybridization of the first nucleic acid with the oligonucleotide probe, and hybridization of the second nucleic acid with the oligonucleotide probe.

6. The method of claim 1, wherein the oligonucleotide probe is immobilized relative to a surface.

7. The method of claim 1, wherein the oligonucleotide probe has a length of at least 60 nucleotides.

8. The method of claim 1, wherein the first detection entity is fluorescent.

9. The method of claim 1, comprising providing a plurality of oligonucleotide probes, at least some of which are non-identical, and exposing the plurality of oligonucleotide probes to the first and second nucleic acids.

10. The method of claim 9, comprising providing at least 100 non-identical oligonucleotide probes.

11. The method of claim 9, wherein the plurality of oligonucleotide probes are each immobilized relative to a surface at a density of at least about 0.01 pmol/mm².

12. The method of claim 1, further comprising comparing hybridization of the first nucleic acid with the oligonucleotide probe, and hybridization of the second nucleic acid with the oligonucleotide probe.

13. The method of claim 12, further comprising determining a ratio of concentration of the first nucleic acid to the second nucleic acid.

14. An article, comprising:

a composition, constructed and arranged to be used in an assay of a sample comprising a first nucleic acid labeled with a first detection entity and a second nucleic acid, different from the first nucleic acid and labeled with a second detection entity, the composition comprising an oligonucleotide probe able to hybridize to at least portions of each of the first nucleic acid and the second acid such that each of the first detection entity and the second detection entity can be determined.

15. An article, comprising:

an array comprising a plurality of oligonucleotide probes, at least some of which each comprise a first nucleotide sequence able to hybridize to a first portion of a chromosome and a second nucleotide sequence able to hybridize to a second portion of the chromosome.

16. An article, comprising:

a composition comprising a first oligonucleotide probe comprising a first nucleotide sequence able to hybridize to a first portion of a first chromosome and a second nucleotide sequence able to hybridize to a second portion of the first chromosome, and a second oligonucleotide probe comprising a first nucleotide sequence able to hybridize to a first portion of a second chromosome and a second nucleotide sequence able to hybridize to a second portion of the second chromosome.

17. A method, comprising:

cleaving a nucleic acid into a plurality of nucleic acid fragments;

separating the nucleic acid fragments into at least a first sample and a second sample;

labeling at least some of the fragments of the first sample with a first detection entity and at least some of the fragments of the second sample with a second detection entity; and

exposing at least some of the nucleic acid fragments of the first and second samples to at least one compound probe.

18. A method, comprising:

cleaving a nucleic acid into a plurality of nucleic acid fragments, each having a first end and a second end;

labeling the first end of at least some of the nucleic acid fragments with a first detection label and the second end of at least some of the nucleic acid fragments with a second detection label; and

exposing at least some of the nucleic acid fragments to at least one compound probe.

19. A method, comprising:

labeling one or more portions of a first chromosome with a first detection entity and one or more portions of a second chromosome with a second detection entity;

fragmenting each of the first chromosome and the second chromosome to produce a plurality of chromosome fragments; and

exposing the chromosome fragments to one or more compound probes.

20. The method of claim 19, wherein the acts are performed in the order recited.

21. The method of claim 19, wherein at least some of the one or more compound probes comprises a first sequence able to hybridize the first chromosome but not the second chromosome, and a second sequence able to hybridize the second chromosome but not the first chromosome.

22. The method of claim 19, further comprising determining whether a compound probe of the one or more compound probes has hybridized to both a portion of a first chromosome and a portion of a second chromosome.

23. The method of claim 22, further comprising identifying a translocation between the first and second chromosomes based on hybridization of the compound probe.