COMPOSITIONS AND METHODS FOR DETERMINING THE PRESENCE OF CHLAMYDOPHILA PNEUMONIAE IN A TEST SAMPLE

• US 20090220981A1
• Filed: 02/02/2009
• Published: 09/03/2009
• Est. Priority Date: 06/06/2005
• Status: Active Grant

• Current Assignee: Gen-Probe Incorporated (Hologic Incorporated)
• Original Assignee: Gen-Probe Incorporated (Hologic Incorporated)
• Inventors: CUNNINGHAM, Melissa M.
• Granted Patent: US 7,858,347 B2
• Time in Patent Office: Days
• US Class Current: 435/6
• CPC Class Codes: C12Q 1/689 for bacteria

Abstract

Oligonucleotides for use in determining the presence of Chlamydophila pneumoniae in a test sample. The oligonucleotides are incorporated into detection probes, capture probes, and amplification oligonucleotides, and can be used in various combinations thereof.

Claims

1. A detection probe for use in determining the presence of Chlamydophila pneumoniae in a test sample, said probe being up to 50 bases in length and comprising a target binding region that forms a probe:

target hybrid stable for detection with a target sequence contained within a target region selected from the group consisting of SEQ ID NO;

1, SEQ ID NO;

2, SEQ ID NO;

3 and SEQ ID NO;

4 under stringent hybridization conditions, wherein said target binding region comprises the nucleotide base sequence of SEQ ID NO;

13, SEQ ID NO;

14, SEQ ID NO;

15 or SEQ ID NO;

16, and wherein said probe does not form a hybrid stable for detection with nucleic acid derived from Chlamydia trachomatis or Chlamydophila psittaci under said conditions.

2. The detection probe of claim 1, wherein said probe is up to 40 bases in length.

3. The detection probe of claim 1, wherein said probe is up to 35 bases in length.

4. The detection probe of claim 1, wherein said probe is up to 30 bases in length.

5. The detection probe of claim 1, wherein said probe is up to 25 bases in length.

6. The detection probe of claim 1, wherein said probe is up to 20 bases in length.

7. The detection probe of claim 1, wherein said probe fully hybridizes to said target region.

8. The detection probe of claim 7, wherein said target binding region consists of the base sequence of SEQ ID NO:

13, SEQ ID NO;

14, SEQ ID NO;

15 or SEQ ID NO;

16.

9. The detection probe of claim 1, wherein the base sequence of said probe consists of the base sequence of SEQ ID NO:

13, SEQ ID NO;

14, SEQ ID NO;

15 or SEQ ID NO;

16.

10. The detection probe of claim 1, wherein said probe includes a detectable label.

11. The detection probe of claim 1, wherein said probe is a self-hybridizing probe under said conditions and in the absence of said target sequence.

12. The detection probe of claim 1, wherein said probe comprises a pair of interacting labels.

13. The detection probe of claim 1, wherein said target binding region includes at least one 2′

-O-methyl ribonucleotide.

14. The detection probe of claim 1, wherein said conditions include a temperature of about 60°

C. and a salt concentration of about 0.6 M to about 0.9 M.

15. A composition comprising said probe of claim 1 hybridized to nucleic acid derived from Chlamydophila pneumoniae under said conditions.

16. A method for determining the presence of Chlamydophila pneumoniae in a test sample, said method comprising the steps of:

(a) contacting a test sample with said probe of claim 1 under said conditions; and

(b) determining whether said probe;

target hybrid is present in said test sample as indication of the presence of Chlamydophila pneumoniae in said test sample.

17. The method of claim 16, wherein said probe is up to 40 bases in length.

18. The method of claim 16, wherein said probe is up to 35 bases in length.

19. The method of claim 16, wherein said probe is up to 30 bases in length.

20. The method of claim 16, wherein said probe is up to 25 bases in length.

21. The method of claim 16, wherein said probe is up to 20 bases in length.

22. The method of claim 16, wherein said probe fully hybridizes to said target region.

23. The method of claim 22, wherein said target binding region consists of the base sequence of SEQ ID NO:

13, SEQ ID NO;

14, SEQ ID NO;

15 or SEQ ID NO;

16.

24. The method of claim 16, wherein the base sequence of said probe consists of the base sequence of SEQ ID NO:

13, SEQ ID NO;

14, SEQ ID NO;

15 or SEQ ID NO;

16.

25. The method of claim 16, wherein said probe includes a detectable label.

26. The method of claim 16, wherein said probe is a self-hybridizing probe under said conditions and in the absence of said target sequence.

27. The method of claim 26, wherein said probe comprises a pair of interacting labels.

28. The method of claim 16, wherein said target binding region includes at least one 2′

-O-methyl ribonucleotide.