Compositions for detecting group A streptococci

• US 8,202,978 B2
• Filed: 10/16/2008
• Issued: 06/19/2012
• Est. Priority Date: 11/09/2004
• Status: Active Grant

• Current Assignee: Gen-Probe Incorporated (Hologic Incorporated)
• Original Assignee: Gen-Probe Incorporated (Hologic Incorporated)
• Inventors: Pollner, Reinhold B., Darby, Paul M.
• Primary Examiner(s): Sitton, Jehanne
• Application Number:
  US12/253,090
• Publication Number:
  US 20090170104A1
• Time in Patent Office: 1,342 Days
• Field of Search: None
• US Class Current: 536/24.3
• CPC Class Codes: C12Q 1/689 for bacteria

Abstract

Compositions, methods and kits for detecting Group A streptococci. Particularly described are oligonucleotides that are useful as amplification primers and hybridization probes for detecting very low levels of Group A streptococci nucleic acids.

Claims

1. A composition for amplifying in a transcription associated amplification reaction and detecting in real time a Streptococcus pyogenes target nucleic acid sequence, said composition comprising:

a first primer, the base sequence of which consists of a 3′

terminal target-complementary sequence and, optionally, a first primer upstream promoter sequence that is non-complementary to a nucleic acid containing said target nucleic acid sequence or its complement, said 3′

terminal target-complementary sequence of said first primer being selected from the group consisting of SEQ ID NO;

9, SEQ ID NO;

10, SEQ ID NO;

11, SEQ ID NO;

12 and SEQ ID NO;

13, allowing for the presence of RNA equivalents and nucleotide analogs;

a second primer, the base sequence of which consists of a 3′

terminal target-complementary sequence and, optionally, a second primer upstream promoter sequence that is non-complementary to a nucleic acid containing said target nucleic acid sequence or its complement, said 3′

terminal target-complementary sequence of said second primer being selected from the group consisting of SEQ ID NO;

4, SEQ ID NO;

5, SEQ ID NO;

6, and SEQ ID NO;

7, allowing for the presence of RNA equivalents and nucleotide analogs; and

a molecular beacon probe, the base sequence of which consists of a target-complementary sequence and a pair of mutually complementary base sequences that are non-complementary to a nucleic acid containing said target nucleic acid sequence or its complement, said target-complementary sequence of said probe being selected from the group consisting of SEQ ID NO;

23, SEQ ID NO;

24 and SEQ ID NO;

25, allowing for the presence of DNA equivalents and nucleotide analogs.

2. The composition of claim 1, wherein said first primer comprises said first primer upstream promoter sequence.

3. The composition of claim 2, wherein said first primer upstream promoter sequence comprises a promoter sequence for T7 RNA polymerase.

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

5. The composition of claim 1, wherein said probe further comprises a fluorophore moiety and a quencher moiety.

6. The composition claim 1, wherein said probe further comprises a detectable label.

7. The composition of claim 6, wherein said detectable label of said probe is selected from the group consisting of a chemiluminescent label and a fluorescent label.

8. The composition of claim 1, wherein the base sequence of said first primer is selected from the group consisting of SEQ ID NO:

14, SEQ ID NO;

15, SEQ ID NO;

16, SEQ ID NO;

17 and SEQ ID NO;

18, allowing for the presence of RNA equivalents and nucleotide analogs.

9. The composition of claim 1, wherein the base sequence of said second primer is selected from the group consisting of SEQ ID NO:

4, SEQ ID NO;

5, SEQ ID NO;

6, and SEQ ID NO;

7, allowing for the presence of RNA equivalents and nucleotide analogs.

10. The composition of claim 1, wherein the base sequence of said probe is selected from the group consisting of SEQ ID NO:

26, SEQ ID NO;

27 and SEQ ID NO;

28, allowing for the presence of DNA equivalents and nucleotide analogs.

11. The composition of claim 1, wherein:

the base sequence of said first primer is selected from the group consisting of SEQ ID NO;

14, SEQ ID NO;

15, SEQ ID NO;

16, SEQ ID NO;

17 and SEQ ID NO;

18, allowing for the presence of RNA equivalents and nucleotide analogs;

the base sequence of said second primer is selected from the group consisting of SEQ ID NO;

4, SEQ ID NO;

5, SEQ ID NO;

6, and SEQ ID NO;

7, allowing for the presence of RNA equivalents and nucleotide analogs; and

the base sequence of said probe is selected from the group consisting of SEQ ID NO;

26, SEQ ID NO;

27 and SEQ ID NO;

28, allowing for the presence of DNA equivalents and nucleotide analogs.

12. The composition of claim 1, wherein:

the base sequence of said first primer is selected from the group consisting of SEQ ID NO;

14, SEQ ID NO;

15, SEQ ID NO;

16, SEQ ID NO;

17 and SEQ ID NO;

18;

the base sequence of said second primer is selected from the group consisting of SEQ ID NO;

4, SEQ ID NO;

5, SEQ ID NO;

6, and SEQ ID NO;

7; and

the base sequence of said probe is selected from the group consisting of SEQ ID NO;

26, SEQ ID NO;

27 and SEQ ID NO;

28.