Mycobacterial rpoB sequences

• US 20060147964A1
• Filed: 12/22/2005
• Published: 07/06/2006
• Est. Priority Date: 04/03/1998
• Status: Abandoned Application

• Current Assignee: Affymetrix, Inc. (Thermo Fisher Scientific Incorporated)
• Original Assignee: Affymetrix, Inc. (Thermo Fisher Scientific Incorporated)
• Inventors: Drenkow, Jorg, Gingeras, Thomas R.
• Application Number:
  US11/313,718
• Publication Number:
  US 20060147964A1
• Time in Patent Office: Days
• US Class Current: 435/6
• CPC Class Codes: C12Q 1/689 for bacteria
• CPC Class Codes: C12Q 2600/156 Polymorphic or mutational markers

Abstract

This invention provides polynucleotide probes, sequences and methods for speciating and phenotyping organisms, for example, using probes based on the Mycobacterium tuberculosis rpoB gene. The groups or species to which an organism belongs may be determined by comparing hybridization patterns of target nucleic acid from the organism to hybridization patterns in a database.

Claims

1-19. -19. (canceled)

20. A polynucleotide probe or primer that hybridizes under stringent hybridization conditions to a mycobacterial rpoB sequence selected from the group consisting of SEQ ID NOS:

2, 3, 4, 5, 6 and 9 or its complement without hybridizing to the M. tuberculosis sequence of SEQ ID NO;

1 or its complement, wherein said stringent hybridization conditions comprise 5×

SSPE and a temperature of 25-30°

C.

21. The polynucleotide of claim 20 that is a probe.

22. The polynucleotide of claim 21, wherein a central position of the probe aligns with one or more bases of a sequence selected from the group consisting of SEQ ID NOS:

2, 3, 4, 5, 6 and 9 which differ from the corresponding one or more bases in SEQ ID NO;

1 when the sequences are maximally aligned.

23. The sequence-specific polynucleotide of claim 20 that is a primer.

24. The polynucleotide of claim 23, wherein the 3′

end of the primer aligns with one or more bases of a sequence selected from the group consisting of SEQ ID NOS;

2, 3, 4, 5, 6 and 9 which differ from the corresponding one or more bases in SEQ ID NO;

1 when the sequences are maximally aligned.

25. The polynucleotide of claim 20 that hybridizes under stringent hybridization conditions to at least 100 contiguous bases of a mycobacterial rpoB sequence selected from the group consisting of SEQ ID NOS:

2, 3, 4, 5, 6 and 9 or its complement without hybridizing to the M. tuberculosis sequence of SEQ ID NO;

1 or its complement, wherein said stringent hybridization conditions comprise 5×

SSPE and a temperature of 25-30°

C.

26. A polynucleotide probe or primer that hybridizes under stringent hybridization conditions to at least 100 contiguous bases of a mycobacterial rpoB sequence selected from the group consisting of SEQ ID NOS:

8 and 10 or its complement without hybridizing to the M. tuberculosis sequence of SEQ ID NO;

1 or its complement, wherein said stringent hybridization conditions comprise 5×

SSPE and a temperature of 25-30°

C.

27. The polynucleotide of claim 26, wherein the polynucleotide is a probe, and wherein a central position of the probe aligns with one or more bases of a sequence selected from the group consisting of SEQ ID NOS:

8 and 10 which differ from the corresponding one or more bases in SEQ ID NO;

1 when the sequences are maximally aligned.

28. The polynucleotide of claim 26, wherein the polynucleotide is a primer, and wherein the 3′

end of the primer aligns with one or more bases of a sequence selected from the group consisting of SEQ ID NOS;

8 and 10 which differ from the corresponding one or more bases in SEQ ID NO;

1 when the sequences are maximally aligned.