Method for identifying suitable nucleic acid probe sequences for use in nucleic acid arrays

• US 20040002070A1
• Filed: 06/26/2002
• Published: 01/01/2004
• Est. Priority Date: 06/26/2002
• Status: Active Grant

• Current Assignee: Agilent Technologies, Inc.
• Original Assignee: Agilent Technologies, Inc.
• Inventors: Kincaid, Robert
• Granted Patent: US 7,894,998 B2
• Time in Patent Office: Days
• US Class Current: 435/6
• CPC Class Codes: G16B 25/00 ICT specially adapted for hybridisation; ICT specially adapted for gene or protein expression
• CPC Class Codes: G16B 25/20 Polymerase chain reaction [PCR]; Primer or probe design; Probe optimisation
• CPC Class Codes: G16B 30/00 ICT specially adapted for sequence analysis involving nucleotides or amino acids

Abstract

Methods of identifying regions of a nucleic acid sequence suitable for use as probes in nucleic acid arrays, as well as compositions of matter for practicing such methods, are provided. The subject methods include: (a) providing a set of known, undesirable probe sequences; (b) comparing a nucleic acid sequence to each member of the set; and (c) identifying regions of the nucleic acid sequence that substantially match a sequence of a member of the probe set as undesirable regions. The subject methods also include marking the undesirable regions of the nucleic acid sequence to identify regions of the nucleic acid sequence that are suitable for use as probes in a nucleic acid array. The subject invention also includes an algorithm and kits for carrying out the subject methods. Also provided are nucleic acid arrays produced with the identified suitable probes, and methods for using the same.

Claims

1. A method of identifying regions of a nucleic acid sequence as suitable for use as probes in a nucleic acid array, said method comprising:

(a) providing a set of known, undesirable probe sequences;

(b) comparing said nucleic acid sequence to each member of said set of known, undesirable probe sequences; and

(c) identifying regions of said nucleic acid sequence as undesirable regions, wherein said undesirable regions have a sequence that substantially matches a sequence of a member of said known, undesirable probe set,

whereby regions of said nucleic acid sequence that are suitable for use as probes in a nucleic acid array are identified.

2. The method according to claim 1, further comprising marking said undesirable regions of said nucleic acid sequence, whereby unmarked regions that are suitable for use as probes in a nucleic acid array are identified.

3. The method according to claim 2, further comprising synthesizing probe nucleic acids identified by said marking step, whereby nucleic acid probes are not synthesized according to any of said marked regions.

4. The method according to claim 3, whereby, prior to synthesizing said probe nucleic acids, further computationally analyzing said unmarked probe sequences to determine suitability as probe sequences, whereby said marked undesirable regions are not further computationally analyzed for consideration as suitable probes.

5. The method according to claim 4, further comprising expanding said set of known, undesirable probe sequences with probe sequences determined unsuitable according to said computational analysis.

6. The method according to claim 3, further comprising testing said probe nucleic acids in an array hybridization assay to confirm that said probe nucleic acids actually work in a nucleic acid array.

7. The method according to claim 6, further comprising expanding said set of known, undesirable probe sequences with probe sequences determined unsuitable according to said array hybridization assay.

8. The method according to claim 6, wherein said step of testing comprises determining at least one of the signal strength, binding specificity, melting temperature and hybridization energies of said probe nucleic acids.

9. The method according to claim 1, wherein said nucleic acid sequence is present in text format representative of the nucleotide sequence of said nucleic acid sequence.

10. The method according to claim 1, further comprising expanding said set of known, undesirable probe sequences with an additional undesirable probe sequence.

11. The method according to claim 1, further comprising determining whether a probe sequence is undesirable for use as a probe.

12. The method according to claim 11, wherein a probe sequence determined to be undesirable for use as a probe is added to said set of undesirable probe sequences.

13. The method according to claim 11, wherein said determining whether a probe sequence is undesirable for use as a probe is accomplished using experimental analysis.

14. The method according to claim 11, wherein said determining whether a probe sequence is undesirable for use as a probe is accomplished using computational analysis.

15. The method according to claim 11, wherein said determining whether a probe sequence is undesirable for use as a probe is based at least in part on undesirability for a particular sample type.

16. A method of synthesizing an array of nucleic acids according to the method of claim 15, whereby an array comprising probes that are suitable for a particular sample type is produced.

17. The method according to claim 16, further comprising performing a hybridization assay with said array and said particular sample type.

18. A method of synthesizing an array of nucleic acids, said method comprising:

producing at least two different probe nucleic acids immobilized on a surface of a solid support, where said at least two different probe nucleic acids each comprise a sequence of nucleotides identified as suitable according to the method of claim 1.

19. The method according to claim 18, wherein said at least two different probe nucleic acids are produced on said surface of said solid support by synthesizing said probe nucleic acids on said surface.

20. The method according to claim 18, wherein said at least two different probe nucleic acids are produced on said surface of said solid support by depositing said at least two different probe nucleic acids onto said surface of said solid support.

21. The method according to claim 18, further comprising employing said nucleic acid array in a hybridization assay, wherein said array is contacted with a sample and any resultant duplex nucleic acids on said surface of said array following said contact are detected.

22. The method according to claim 21, wherein said resultant duplexes are detected by reading said array.

23. A method comprising forwarding a result of a reading obtained by the method of claim 22 to a remote location.

24. A method comprising transmitting data representing a result of a reading obtained by the method of claim 22.

25. A method comprising receiving data representing a result of a reading obtained by the method of claim 22.

26. An algorithm that performs the method according to claim 1, wherein said algorithm is present on a computer readable medium.

27. A kit for identifying regions of a nucleic acid sequence as suitable for use as probes in a nucleic acid array, said kit comprising:

(a) an algorithm that performs the method according to claim 1, wherein said algorithm is present on a computer readable medium; and

(b) instructions for using said algorithm to identify regions of said nucleic acid sequence as suitable for use as probes in a nucleic acid array

28. The kit according to claim 27, further comprising a data set of known, undesirable probes stored on a computer readable media.

29. The kit according to claim 27, wherein said kit further comprises a substrate for use in a nucleic acid array.

30. The kit according to claim 27, further comprising hybridization buffer.

31. The kit according to claim 27, further comprising wash medium.