Compositions and methods for determining the presence of
View Patent ↗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.
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 fully hybridizes to said target region.
7. The detection probe of claim 6 , 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.
8. 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.
9. The detection probe of claim 1 , wherein said probe includes a detectable label.
10. 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.
11. The detection probe of claim 1 , wherein said probe comprises a pair of interacting labels.
12. The detection probe of claim 1 ,wherein said target binding region includes at least one 2′-O-methyl ribonucleotide.
13. 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.
14. A composition comprising said probe of claim 1 hybridized to nucleic acid derived from Chlamydophila pneumoniae under said conditions.
15. 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.
16. The method of claim 15 , wherein said probe is up to 40 bases in length.
17. The method of claim 15 , wherein said probe is up to 35 bases in length.
18. The method of claim 15 , wherein said probe is up to 30 bases in length.
19. The method of claim 15 , wherein said probe is up to 25 bases in length.
20. The method of claim 15 , wherein said probe fully hybridizes to said target region.
21. The method of claim 20 , 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.
22. The method of claim 15 , 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.
23. The method of claim 15 , wherein said probe includes a detectable label.
24. The method of claim 15 , wherein said probe is a self-hybridizing probe under said conditions and in the absence of said target sequence.
25. The method of claim 24 , wherein said probe comprises a pair of interacting labels.
26. The method of claim 15 , wherein said target binding region includes at least one 2′-O-methyl ribonucleotide.