PNA Probes, Probe Sets, Methods and Kits Pertaining to the Detection of Candida

• US 20150176086A1
• Filed: 12/15/2014
• Published: 06/25/2015
• Est. Priority Date: 05/18/2001
• Status: Active Grant

• Current Assignee: Applied Biosystems LLC (Thermo Fisher Scientific Incorporated)
• Original Assignee: Applied Biosystems LLC (Thermo Fisher Scientific Incorporated)
• Inventors: Hyldig-Nielsen, Jens J., Stender, Henrik, Oliveira, Kenneth M., Rigby, Susan
• Granted Patent: US 9,765,405 B2
• Time in Patent Office: Days
• US Class Current: 1/1
• CPC Class Codes: C07K 14/003 Peptide-nucleic acids (PNAs)
• CPC Class Codes: C12Q 1/689 for bacteria
• CPC Class Codes: C12Q 1/6895 for plants, fungi or algae
• CPC Class Codes: C12Q 2525/107 incorporating a peptide nucleic acid

Abstract

This invention is related to novel PNA probes, probe sets, methods and kits pertaining to the detection of one or more species of Candida yeast. Non-limiting examples of probing nucleobase sequences that can be used for the probes of this invention can be selected from the group consisting of: AGA-GAG-CAG-CAT-GCA (Seq. Id. No. 1), AGA-GAG-CAA-CAT-GCA (Seq. Id. No. 2), ACA-GCA-GAA-GCC-GTG (Seq. Id. No. 3), CAT-AAA-TGG-CTA-CCA-GA (Seq. Id. No. 4), CAT-AAA-TGG-CTA-CCC-AG (Seq. Id. No. 5), ACT-TGG-AGT-CGA-TAG (Seq. Id. No. 6), CCA-AGG-CTT-ATA-CTC-GC (Seq. Id. No. 7), CCC-CTG-AAT-CGG-GAT (Seq. Id. No. 8), GAC-GCC-AAA-GAC-GCC (Seq. Id. No. 9), ATC-GTC-AGA-GGC-TAT-AA (Seq. Id. No. 10), TAG-CCA-GAA-GAA-AGG (Seq. Id. No. 11), CAT-AAA-TGG-CTA-GCC-AG (Seq. Id. No. 12), CTC-CGA-TGT-GAC-TGC-G (Seq. Id. No. 13), TCC-CAG-ACT-GCT-CGG (Seq. Id. No. 14), TCC-AAG-AGG-TCG-AGA (Seq. Id. No. 15), GCC-AAG-CCA-CAA-GGA (Seq. Id. No. 16), GCC-GCC-AAG-CCA-CA (Seq. Id. No. 17), GGA-CTT-GGG-GTT-AG (Seq. Id. No. 18), CCG-GGT-GCA-TTC-CA (Seq. Id. No. 19), ATG-TAG-AAC-GGA-ACT-A (Seq. Id. No. 20), GAT-TCT-CGG-CCC-CAT-G (Seq. Id. No. 21), CTG-GTT-CGC-CAA-AAA-G (Seq. Id. No. 22) and AGT-ACG-CAT-CAG-AAA (Seq. Id. No. 23).

Claims

1-11. -11. (canceled)

12. A PNA probe set suitable for detecting, identifying or quantitating one or more species of Candida yeast in a sample, wherein at least one PNA probe of the set comprises a probing nucleobase sequence wherein at least a portion is at least ninety percent homologous to the nucleobase sequences, or their complements, selected from the group consisting of:

13. The probe set of claim 12, wherein a PNA probe for C. albicans is selected from the group consisting of:

14. The probe set of claim 12, wherein a PNA probe for C. dubliniesis is selected from the group consisting of:

15. The probe set of claim 12, wherein a PNA probe for C. glabrata is selected from the group consisting of:

16. The probe set of claim 12, wherein a PNA probe for C. krusei is selected from the group consisting of:

17. The probe set of claim 12, wherein at least one probe of the set is unlabeled.

19. The probe set of claim 12, wherein at least one probe is labeled with a detectable moiety.

21. The probe set of claim 19, wherein the detectable moiety or moieties are selected from the group consisting of:

a dextran conjugate, a branched nucleic acid detection system, a chromophore, a fluorophore, a spin label, a radioisotope, an enzyme, a hapten, an acridinium ester and a chemiluminescent compound.

18. (canceled)

20. (canceled)

22-27. -27. (canceled)

28. A method for detecting, identifying and/or quantitating one or more species of Candida yeast in a sample;

said method comprising the steps of;

a) contacting the sample with one or more PNA probes, wherein the one or more PNA probes have a probing nucleobase sequence that is at least ninety percent homologous to the nucleobase sequences, or their complements, selected from the group consisting of;

31. The method of claim 28, wherein at least one PNA probe is labeled with a detectable moiety.

34. The method of claim 28, wherein at least one PNA probe is labeled with at least two independently detectable moieties.

36. The method of claim 31, wherein in situ hybridization using a fluorophore or enzyme-linked probe is used to determine the presence, absence or number of organisms of Candida yeast in the sample.

37. The method of claim 28, wherein a set of at least two PNA probes is used in the assay.

38. The method of claim 37, wherein two or more PNA probes are independently detectable.

41. The method of claim 28, wherein at least one PNA probe is self-indicating.

42. The method of claim 28, wherein at least one PNA probe is support bound.

29-30. -30. (canceled)

32-33. -33. (canceled)

35. (canceled)

39-40. -40. (canceled)

43. A kit suitable for performing an assay that determines the presence, absence or quantity of one or more species of Candida yeast in a sample, wherein said kit comprises:

a) one or more PNA probes, wherein the PNA probes comprise a probing nucleobase sequence such that at least a portion is at least ninety percent homologous to the nucleobase sequences, or their complements, selected from the group consisting of;

51. The kit of claim 43, wherein hybridization of the probing nucleobase sequence of the probe to the nucleic acid of the organism of interest is detected using an antibody or antibody fragment, wherein the antibody or antibody fragment specifically binds to the PNA/nucleic acid complex.

52. The kit of claim 51, further comprising an antibody labeled with a detectable moiety.

54. The kit of claim 43, further comprising buffers and/or other reagents suitable for performing a PNA-ISH or PNA-FISH assay.

44-50. -50. (canceled)

53. (canceled)

55-56. -56. (canceled)