Methods for controlling cross-hybridization in analysis of nucleic acid sequences

• US 6,461,816 B1
• Filed: 07/09/1999
• Issued: 10/08/2002
• Est. Priority Date: 07/09/1999
• Status: Expired due to Fees

• Current Assignee: Agilent Technologies, Inc.
• Original Assignee: Agilent Technologies, Inc.
• Inventors: Kincaid, Robert H., Wolber, Paul K.
• Primary Examiner(s): Brusca, John S.
• Assistant Examiner(s): KIM, YOUNG J
• Application Number:
  US09/350,969
• Time in Patent Office: 1,187 Days
• Field of Search: 435/6, 435/91.1, 536/24.3, 536/23.1
• US Class Current: 435/6.12
• CPC Class Codes: C12Q 1/6813 Hybridisation assays

Abstract

Methods, reagents and kits are disclosed for selecting target-specific oligonucleotide probes, which may be used in analyzing a target nucleic acid sequence. In one aspect the present invention is directed to selecting a set of target-specific oligonucleotide probes. A cross-hybridization oligonucleotide probe is identified based on a candidate target-specific oligonucleotide probe for the target nucleic acid sequence. The cross-hybridization oligonucleotide probe measures the extent of occurrence of a cross-hybridization event having a predetermined probability. Cross-hybridization results are determined employing the cross-hybridization oligonucleotide probe and the target-specific oligonucleotide probe. The target-specific oligonucleotide probe is selected or rejected for the set based on the cross-hybridization results.

Claims

1. A method for selecting a set of target-specific oligonucleotide probes for use in analyzing a target nucleic acid sequence, said method comprising:

(a) identifying a cross-hybridization oligonucleotide probe based on a candidate target-specific oligonucleotide probe for said target nucleic acid sequence wherein said cross-hybridization oligonucleotide probe measures the extent of occurrence of a cross-hybridization event, having a predetermined probability, to an interfering nucleic acid sequence,

(b) determining cross-hybridization results employing said cross-hybridization oligonucleotide probe and said target-specific oligonucleotide probe wherein said cross-hybridization results are determined by a hybridization study of a sample suspected of containing a target nucleic acid sequence using said target-specific oligonucleotide probe and said cross-hybridization probe and

(c) selecting or rejecting said target-specific oligonucleotide probe for said set of target specific oligonucleotide probes based on said cross-hybridization results.

2. A method according to claim 1 wherein said cross-hybridization oligonucleotide probe is a single probe obtained from a homology algorithm.

3. A method according to claim 1 wherein said cross-hybridization probe is part of a set of oligonucleotide probes wherein the cross-hybridization result obtained with said set of oligonucleotide probes measures the extent of occurrence of hybridization events that have a predetermined probability.

4. The method of claim 1 wherein steps (a)-(c) are repeated.

5. A method according to claim 1 wherein said identifying of a cross-hybridization oligonucleotide probe in step (a) is carried out by a process comprising determining homologous sequences to target genes that meet predetermined criteria with respect to said oligonucleotide probe specific for said target nucleic acid sequence.

6. A method according to claim 5 wherein said criteria comprise a predetermined number of mismatches between said target-specific oligonucleotide probe and said cross-hybridization oligonucleotide probe derived from said homologous sequences.

7. A method according to claim 5 wherein said criteria comprise a distribution of mismatches between said target-specific oligonucleotide probe and said probe derived from said homologous sequences.

8. A method according to claim 5 wherein said criteria comprise accepting or rejecting said homologous sequences on the basis of a predicted free energy compared to a predetermined predicted free energy of the hybridizing of said target-specific oligonucleotide probe with said target nucleic acid sequence.

9. A method according to claim 1 wherein said identifying of step (a) is carried out by a process comprising incorporating a selected combination of possible nucleotide substitutions at one or more positions in a single cross-hybridization oligonucleotide probe.

10. A method according to claim 9 wherein said identifying of step (a) is carried out by a process comprising deleting nucleotides at one or more positions in a single cross-hybridization oligonucleotide probe.

11. A method according to claim 9 wherein said identifying of step (a) is carried out by a process comprising inserting nucleotides at one or more positions in a single cross-hybridization oligonucleotide probe.

19. A kit for analyzing a target nucleic acid sequence, said kit comprising in packaged combination:

(a) an oligonucleotide probe specific for said target nucleic acid sequence,

(b) a set of cross-hybridization oligonucleotide probes based on said target nucleic acid sequence wherein cross-hybridization results obtained with said set measures the extent of the occurrence of cross-hybridization events, having a predetermined probability, between an interfering nucleic acid sequence and said oligonucleotide probe specific for said target nucleic sequence and wherein said predetermined probability is a threshold level based on information about said target nucleic acid sequence and said oligonucleotide specific for a target nucleic acid sequence,

(c) a written description of a method according to claim 1.

20. A kit according to claim 19 wherein said set of cross-hybridization oligonucleotide probes is obtained from a homology algorithm.

21. A kit according to claim 19 wherein said target-specific oligonucleotide probe comprises a label.

22. A kit according to claim 19 wherein said target-specific oligonucleotide probe is bound to a support.

23. A kit according to claim 22 wherein said support comprises an array of different target-specific oligonucleotide probes.

12. A method for selecting a set of target-specific oligonucleotide probes for use in analyzing a target nucleic acid sequence, said method comprising:

(a) identifying a cross-hybridization oligonucleotide probe based on said target nucleic acid sequence by a process comprising determining homologous sequences in target genes that meet predetermined criteria with respect to said oligonucleotide probe specific for said target nucleic acid sequence,

(b) determining cross-hybridization results employing said cross-hybridization oligonucleotide probe and target-specific oligonucleotide probe wherein said cross-hybridization results are determined by a hybridization study of a sample suspected of containing a target nucleic acid sequence using said target-specific oligonucleotide probe and said cross-hybridization probe and

(c) selecting or rejecting said target-specific oligonucleotide probe for said set based on said cross-hybridization results.

13. A method according to claim 12 wherein said criteria comprise a predetermined number of mismatches between said target-specific oligonucleotide probe and said probe derived from said homologous sequences.

14. A method according to claim 12 wherein said criteria comprise a distribution of mismatches between said target-specific oligonucleotide probe and said probe derived from said homologous sequences.

15. A method according to claim 12 wherein said criteria comprise homologous sequences having a predicted free energy substantially the same as a predetermined predicted free energy of the hybridizing of said target-specific oligonucleotide probe with said target nucleic acid sequence.

16. A method for selecting a set of target-specific oligonucleotide probes for use in analyzing a target nucleic acid sequence, said method comprising:

(a) identifying a cross-hybridization oligonucleotide probe based on said target nucleic acid sequence by a process comprising incorporating a selected combination of possible nucleotide substitutions at one or more positions in a single cross-hybridization oligonucleotide probe,

(b) determining cross-hybridization results employing said cross-hybridization oligonucleotide probe and target-specific oligonucleotide probe and

(c) selecting or rejecting said target-specific oligonucleotide probe for said set based on said cross-hybridization results.

17. A method for selecting a set of target-specific oligonucleotide probes for use in analyzing a target nucleic acid sequence, said method comprising:

(a) identifying a cross-hybridization oligonucleotide probe based on said target nucleic acid sequence by a process comprising deleting nucleotides at one or more positions in a single cross-hybridization oligonucleotide probe,

(b) determining cross-hybridization results employing said cross-hybridization oligonucleotide probe and target-specific oligonucleotide probe and

(c) selecting or rejecting said target-specific oligonucleotide probe for said set based on said cross-hybridization results.

18. A method for selecting a set of target-specific oligonucleotide probes for use in analyzing a target nucleic acid sequence, said method comprising:

(a) identifying a cross-hybridization oligonucleotide probe based on said target nucleic acid sequence by a process comprising inserting nucleotides at one or more positions in a single cross-hybridization oligonucleotide probe,

(b) determining cross-hybridization results employing said cross-hybridization oligonucleotide probe and target-specific oligonucleotide probe and

(c) selecting or rejecting said target-specific oligonucleotide probe for said set based on said cross-hybridization results.

24. A computer based method for selecting a set of target-specific oligonucleotide probes for use in analyzing a target nucleic acid sequence, said method comprising:

(a) identifying under computer control a cross-hybridization oligonucleotide probe based on said target nucleic acid sequence wherein said cross-hybridization oligonucleotide probe measures the extent of the occurrence of a cross-hybridization event, having a predetermined probability, to an interfering nucleic acid sequence,

(b) determining under computer control cross-hybridization results employing said cross-hybridization oligonucleotide probe and target-specific oligonucleotide probe wherein said cross-hybridization results are determined by a hybridization study of a sample suspected of containing a target nucleic acid sequence using said target-specific oligonucleotide probe and said cross-hybridization probe and

(c) selecting or rejecting under computer control said target-specific oligonucleotide probe for said set of target specific oligonucleotide probes based on said cross-hybridization results.

25. A computer system for selecting a set of target-specific oligonucleotide probes for use in analyzing a target nucleic acid sequence, said system comprising:

(a) input means for introducing a target nucleotide sequence into said computer system,

(b) means for determining a cross-hybridization oligonucleotide probe based on said target nucleic acid sequence wherein said cross-hybridization oligonucleotide probe measures the extent of the occurrence of a cross-hybridization event, having a predetermined probability, to an interfering nucleic acid sequence wherein said cross-hybridization results are determined by a hybridization study of a sample suspected of containing a target nucleic acid sequence using said target-specific oligonucleotide probe and said cross-hybridization probe,

(c) memory means for determining cross-hybridization results employing said cross-hybridization oligonucleotide probe and target-specific oligonucleotide probe,

(d) means for storing said cross-hybridization results,

(e) means for controlling said computer system to select or reject said target-specific oligonucleotide probe for said set of target specific oligonucleotide probes based on said cross-hybridization results,

(f) means for storing selection results from step (e), and

(g) means for outputting data relating to said selection results.

26. A computer program product comprising a computer readable storage medium having a computer program stored thereon which, when loaded into a computer, selects a set of target-specific oligonucleotide probes for use in analyzing a target nucleic acid sequence by performing steps comprising:

(a) identifying under computer control a cross-hybridization oligonucleotide probe based on said target nucleic acid sequence wherein said cross-hybridization oligonucleotide probe measures the extent of the occurrence of a cross-hybridization event, having a predetermined probability, to an interfering nucleic acid sequence,

(b) determining under computer control cross-hybridization results employing said cross-hybridization oligonucleotide probe and target-specific oligonucleotide probe wherein said cross-hybridization results are determined by a hybridization study of a sample suspected of containing a target nucleic acid sequence using said target-specific oligonucleotide probe and said cross-hybridization probe and

(c) selecting or rejecting under computer control said target-specific oligonucleotide probe for said set of target specific oligonucleotide probes based on said cross-hybridization results.

27. A computer program product according to claim 26 wherein said identifying of step (a) is carried out by a process comprising determining homologous sequences in target genes that meet predetermined criteria with respect to said oligonucleotide probe specific for said target nucleic acid sequence.

28. A computer program product according to claim 27 wherein said criteria comprise a predetermined number of mismatches between said target-specific oligonucleotide probe and said cross-hybridization oligonucleotide probe derived from said homologous sequences.