PNA probes, probe sets, methods and kits pertaining to the detection of Candida

• US 9,765,405 B2
• Filed: 12/15/2014
• Issued: 09/19/2017
• Est. Priority Date: 05/18/2001
• Status: Expired due to Term

• 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
• Primary Examiner(s): GOLDBERG, JEANINE ANNE
• Application Number:
  US14/571,080
• Publication Number:
  US 20150176086A1
• Time in Patent Office: 1,009 Days
• Field of Search: None
• 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. A PNA probe set suitable for detecting, identifying or quantitating one or more species of Candida yeast in a sample, wherein the probe set comprises PNA probes with probing nucleobase sequences 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), and CCC-CTG-AAT-CGG-GAT (Seq. Id. No.

     8), or their complements.

2. The probe set of claim 1, wherein at least one probe of the set is unlabeled.

3. The probe set of claim 1, wherein at least one probe is labeled with a detectable moiety.

4. The probe set of claim 3, 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.

5. The probe set of claim 1, wherein all the probes of the set are labeled with one or more detectable labels.

6. The probe set of claim 1, wherein two or more probes are independently detectable.

7. The probe set of claim 1, wherein at least one probe of the set is self-indicating.

8. The probe set of claim 1, wherein at least one probe of the set is support bound.

9. 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) a combination of PNA probes, wherein the PNA probes comprise probing nucleobase sequences 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) , and CCC-CTG-AAT-CGG-GAT (Seq. Id. No.

     8), or their complements; and

b) other reagents or compositions necessary to perform the assay.

10. The kit of claim 9, further comprising an antibody or antibody fragment which specifically binds to the PNA/nucleic acid complex.

11. The kit of claim 10, wherein the antibody is labeled with a detectable moiety.

12. The kit of claim 11, wherein the detectable moiety is 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.

13. The kit of claim 9, further comprising buffers and/or other reagents suitable for performing a PNA-ISH or PNA-FISH assay.

14. The kit of claim 9, wherein the PNA probes of the kit are unlabeled.

15. The kit of claim 9, wherein at least one PNA probe is labeled with a detectable moiety.

16. The kit of claim 9, wherein two or more PNA probes are labeled with independently detectable moieties.

17. The kit of claim 16, wherein the independently detectable moieties are independently detectable fluorophores.

18. The kit of claim 9, wherein at least one PNA probe is labeled with at least two independently detectable moieties.

19. The kit of claim 9, further comprising buffers and/or other reagents suitable for performing a nucleic acid amplification reaction.

20. The kit of claim 9, wherein at least one PNA probe is self-indicating.