Claims
- 1. An oligomer comprising a base sequence of SEQ ID NO: 1, SEQ ID NO: 2, SEQ ID NO: 3, SEQ ID NO: 4, SEQ ID NO: 5, SEQ ID NO: 6, SEQ ID NO: 10, SEQ ID NO: 17, SEQ ID NO: 18, SEQ ID NO: 19, SEQ ID NO: 20, SEQ ID NO: 21, SEQ ID NO: 42, SEQ ID NO: 45, SEQ ID NO: 46, SEQ ID NO: 47, SEQ ID NO: 50, SEQ ID NO: 51, SEQ ID NO: 52 or SEQ ID NO: 57.
- 2. An oligomer of claim 1, wherein the base sequence is that of SEQ ID NO: 2, SEQ ID NO: 4, SEQ ID NO: 6, SEQ ID NO: 10, SEQ ID NO: 17, SEQ ID NO: 18 or SEQ ID NO: 45.
- 3. An oligomer of claim 1, further comprising a backbone that includes at least one 2′-methoxy RNA group, at least one 2′ fluoro-substituted RNA group, at least one peptide nucleic acid linkage, at least one phosphorothioate linkage, at least one methylphosphonate linkage or any combination thereof.
- 4. An oligomer of claim 3, wherein the base sequence comprises the sequence of SEQ ID NO: 1, SEQ ID NO: 2, SEQ ID NO: 3, SEQ ID NO: 4, SEQ ID NO: 5, SEQ ID NO: 6, SEQ ID NO: 17, SEQ ID NO: 18, SEQ ID NO: 19, SEQ ID NO: 20 or SEQ ID NO: 45, and the backbone comprises at least one 2′-methoxy RNA group.
- 5. An oligomer consisting of a base sequence of SEQ ID NO: 7, SEQ ID NO: 8, SEQ ID NO: 9, SEQ ID NO :11, SEQ ID NO: 12, SEQ ID NO: 13, SEQ ID NO: 16, SEQ ID NO: 22, SEQ ID NO: 23, SEQ ID NO: 24, SEQ ID NO: 25, SEQ ID NO: 26, SEQ ID NO: 27, SEQ ID NO: 28, SEQ ID NO: 29, SEQ ID NO: 30, SEQ ID NO: 31, SEQ ID NO: 32, SEQ ID NO: 33, SEQ ID NO: 34, SEQ ID NO: 35, SEQ ID NO: 36, SEQ ID NO: 37, SEQ ID NO: 38, SEQ ID NO: 39, SEQ ID NO: 40, SEQ ID NO: 41, SEQ ID NO: 43, SEQ ID NO: 44, SEQ ID NO: 48, SEQ ID NO: 49, SEQ ID NO: 54, SEQ ID NO: 55 or SEQ ID NO: 56.
- 6. The oligomer of claim 5, wherein the base sequence is SEQ ID NO: 8, SEQ ID NO: 9, SEQ ID NO: 11, SEQ ID NO: 13 or SEQ ID NO: 16.
- 7. An oligomer of claim 5, wherein the base sequence is joined by a backbone that includes at least one 2′-methoxy RNA group, at least one 2′ fluoro-substituted RNA group, at least one peptide nucleic acid linkage, at least one phosphorothioate linkage, at least one methylphosphonate linkage or any combination thereof.
- 8. A labeled oligomer comprising:
a base sequence of SEQ ID NO: 16, SEQ ID NO: 17, SEQ ID NO: 18, SEQ ID NO: 39, SEQ ID NO: 40, SEQ ID NO: 41, SEQ ID NO: 46, SEQ ID NO: 47, SEQ ID NO: 48, SEQ ID NO: 49, SEQ ID NO: 50, SEQ ID NO: 51, SEQ ID NO: 52, SEQ ID NO: 53, SEQ ID NO: 54, SEQ ID NO: 55 or SEQ ID NO: 56; and a detectable label joined directly or indirectly to the base sequence.
- 9. The labeled oligomer of claim 8, wherein the detectable label is a luminescent compound.
- 10. The labeled oligomer of claim 8, wherein the base sequence is joined by a backbone comprising at least one 2′-methoxy RNA group.
- 11. The labeled oligomer of claim 10, wherein the base sequence is SEQ ID NO: 16, SEQ ID NO: 17 or SEQ ID NO: 18, and the label is a chemiluminescent compound.
- 12. The labeled oligomer of claim 11, wherein the base sequence is SEQ ID NO: 16 containing an inosine at residue 7, and the label is an acridinium ester compound.
- 13. A method of detecting HIV-1 RNA in a biological sample, comprising the steps of:
providing a biological sample containing HIV-1 RNA; contacting the biological sample with at least one capture oligomer comprising a base sequence that hybridizes specifically to a target region in LTR or pol sequences of HIV-1 RNA, thus forming a capture oligomer:HIV-1 RNA complex; separating the capture oligomer:HIV-1 RNA complex from the biological sample; then amplifying the LTR or pol sequences, or a cDNA made therefrom, using a nucleic acid polymerase in vitro to produce an amplified product; and detecting the amplified product using a labeled detection probe that hybridizes specifically with the amplified product.
- 14. The method of claim 13, wherein the contacting step uses a capture oligomer further comprising a tail sequence that binds to a complementary sequence immobilized on a solid support.
- 15. The method of claim 13, wherein the base sequence of the capture oligomer that hybridizes specifically to a target region in LTR or pol sequences comprises a sequence of SEQ ID NO: 1, SEQ ID NO: 3, SEQ ID NO: 5, SEQ ID NO: 19 or SEQ ID NO: 57.
- 16. The method of claim 13, wherein the capture oligomer comprises the base sequence of at least one of SEQ ID NO: 2, SEQ ID NO: 4, SEQ ID NO: 6, SEQ ID NO: 20 or SEQ ID NO: 45, or is any combination of oligomers of SEQ ID NO: 2, SEQ ID NO: 4, SEQ ID NO: 6, SEQ ID NO: 20 or SEQ ID NO: 45.
- 17. The method of claim 16, wherein the capture oligomer is any combination of at least two oligomers having base sequences selected from the group of SEQ ID NO: 2, SEQ ID NO: 4 and SEQ ID NO: 6.
- 18. The method of claim 16, wherein the capture oligomer is a combination of oligomers having base sequences of SEQ ID NO: 20 and SEQ ID NO: 6, or SEQ ID NO: 45 and SEQ ID NO: 6.
- 19. The method of claim 13, wherein the amplifying step uses at least two amplification oligomers that bind specifically to LTR or pol sequences or complementary sequences thereof.
- 20. The method of claim 19, wherein the amplifying step uses at least two amplification oligomers for amplifying LTR sequences selected from the group consisting of: SEQ ID NO: 7, SEQ ID NO: 8, SEQ ID NO: 9, SEQ ID NO: 21, SEQ ID NO: 22, SEQ ID NO: 23, SEQ ID NO: 24, SEQ ID NO: 25, SEQ ID NO: 26, SEQ ID NO: 27, SEQ ID NO: 28, SEQ ID NO: 29, SEQ ID NO: 30, SEQ ID NO: 31, SEQ ID NO: 32, SEQ ID NO: 33, SEQ ID NO: 34, SEQ ID NO: 35, SEQ ID NO: 36, SEQ ID NO: 37 and SEQ ID NO: 38.
- 21. The method of claim 19, wherein the amplifying step uses at least two amplification oligomers for amplifying pol sequences selected from the group consisting of:
SEQ ID NO: 10, SEQ ID NO: 11, SEQ ID NO: 12, SEQ ID NO: 13, SEQ ID NO: 14, SEQ ID NO: 15, SEQ ID NO: 42, SEQ ID NO: 43 and SEQ ID NO: 44.
- 22. The method of claim 13, wherein the amplifying step comprises a transcription-associated amplification method that includes:
at least one promoter-primer comprising a promoter sequence that is recognized by an RNA polymerase when the promoter sequence is double stranded, wherein the promoter sequence is covalently attached to the 5′ end of
a LTR-specific sequence selected from the group consisting of SEQ ID NO: 7, SEQ ID NO: 21, SEQ ID NO: 23, SEQ ID NO: 25, SEQ ID NO: 27, SEQ ID NO: 29, SEQ ID NO: 31 and SEQ ID NO: 33, or a pol-specific sequence selected from the group consisting of SEQ ID NO: 12 and SEQ ID NO: 14; and at least one primer comprising
a LTR-specific sequence selected from the group consisting of SEQ ID NO: 9, SEQ ID NO: 35, SEQ ID NO: 36, SEQ ID NO: 37 and SEQ ID NO: 38, or a pol-specific sequence selected from the group consisting of SEQ ID NO: 10, SEQ ID NO: 11 and SEQ ID NO: 42, provided that at least one LTR-specific promoter-primer is combined with at least one LTR-specific primer for amplifying a LTR target region, or at least one pol-specific promoter-primer is combined with at least one pol-specific primer for amplifying a pol target region.
- 23. The method of claim 13, wherein the amplifying step comprises a transcription-associated amplification method that includes:
at least one promoter-primer having:
a LTR-specific sequence selected from the group consisting of SEQ ID NO: 8, SEQ ID NO: 22, SEQ ID NO: 24, SEQ ID NO: 26, SEQ ID NO: 28, SEQ ID NO: 30, SEQ ID NO: 32 and SEQ ID NO: 34, or a pol-specific sequence selected from the group consisting of SEQ ID NO: 13, SEQ ID NO: 15, SEQ ID NO: 43 and SEQ ID NO: 44; and at least one primer having
a LTR-specific sequence selected from the group consisting of SEQ ID NO: 9, SEQ ID NO: 35, SEQ ID NO: 36, SEQ ID NO: 37 and SEQ ID NO: 38, or a pol-specific sequence selected from the group consisting of SEQ ID NO: 10, SEQ ID NO: 11 and SEQ ID NO: 42, provided that at least one LTR-specific promoter-primer is combined with at least one LTR-specific primer for amplifying a LTR target region, or at least one pol-specific promoter-primer is combined with at least one pol-specific primer for amplifying a pol target region.
- 24. The method of claim 23, wherein the amplifying step uses any of the following combinations of promoter-primers and primers:
promoter-primers of SEQ ID NO: 13 and SEQ ID NO: 15, with primers of SEQ ID NO: 10 and SEQ ID NO: 11; promoter-primers of SEQ ID NO: 13 and SEQ ID NO: 15, with primers of SEQ ID NO: 42 and SEQ ID NO: 11; promoter-primers of SEQ ID NO: 43 and SEQ ID NO: 15, with primers of SEQ ID NO: 10 and SEQ ID NO: 11; promoter-primers of SEQ ID NO: 13 and SEQ ID NO: 44, with primers of SEQ ID NO: 10 and SEQ ID NO: 11; promoter-primers of SEQ ID NO: 7, SEQ ID NO: 13 and SEQ ID NO: 15, with primers of SEQ ID NO: 9, SEQ ID NO: 10 and SEQ ID NO: 11; a promoter-primer of SEQ ID NO: 8, and a primer of SEQ ID NO: 9; a promoter-primer of SEQ ID NO: 8, and a primer of SEQ ID NO: 35; a promoter-primer of SEQ ID NO: 8, and a primer of SEQ ID NO: 36; a promoter-primer of SEQ ID NO: 30, and a primer of SEQ ID NO: 9; a promoter-primer of SEQ ID NO: 30, and a primer of SEQ ID NO: 36; a promoter-primer of SEQ ID NO: 32, and a primer of SEQ ID NO: 9; a promoter-primer of SEQ ID NO: 34, and a primer of SEQ ID NO: 36; a promoter-primer of SEQ ID NO: 13, and a primer of SEQ ID NO: 10; or a promoter-primer of SEQ ID NO: 7, and a primer of SEQ ID NO: 9.
- 25. The method of claim 13, wherein the detecting step uses at least one labeled detection probe having a base sequence selected from:
the LTR-specific group consisting of SEQ ID NO: 16, SEQ ID NO: 39, SEQ ID NO: 40 and SEQ ID NO: 41, or the pol-specific group consisting of SEQ ID NO: 17, SEQ ID NO: 18, SEQ ID NO: 46, SEQ ID NO: 47, SEQ ID NO: 48, SEQ ID NO: 49, SEQ ID NO: 50, SEQ ID NO: 51, SEQ ID NO: 52, SEQ ID NO: 53, SEQ ID NO: 54, SEQ ID NO: 55 and SEQ ID NO: 56, or a combination thereof.
- 26. The method of claim 13, wherein the detecting step uses a combination of at least two labeled detection probes having the base sequences of SEQ ID NO: 16, SEQ ID NO: 17 or SEQ ID NO: 18.
- 27. The method of claim 26, wherein the labeled detection probe of SEQ ID NO: 16 has an inosine at position 7.
- 28. The method of claim 13, wherein the detecting step uses at least one labeled detection probe having a base sequence selected from the LTR-specific group consisting of SEQ ID NO: 16, SEQ ID NO: 39, SEQ ID NO: 40 and SEQ ID NO: 41.
- 29. The method of claim 13, wherein the detecting step uses at least one labeled detection probe having a base sequence selected from the pol-specific group consisting of SEQ ID NO: 17, SEQ ID NO: 18, SEQ ID NO: 46, SEQ ID NO: 47, SEQ ID NO: 48, SEQ ID NO: 49, SEQ ID NO: 50, SEQ ID NO: 51, SEQ ID NO: 52, SEQ ID NO: 53, SEQ ID NO: 54, SEQ ID NO: 55 and SEQ ID NO: 56.
- 30. The method of claim 13, wherein the detecting step uses at least one labeled detection probe that includes at least one 2′-methoxy backbone linkage.
- 31. The method of claim 13, wherein:
the contacting step uses capture oligomers having the sequences of SEQ ID NO: 2, SEQ ID NO: 4 and SEQ ID NO: 6; the amplifying step uses promoter-primers having the sequences of SEQ ID NO: 8, SEQ ID NO: 13 and SEQ ID NO: 15 and primers having the sequences of SEQ ID NO: 9, SEQ ID NO: 10 and SEQ ID NO: 11; and the detecting step uses labeled detection probes having the sequences of SEQ ID NO: 16, SEQ ID NO: 17 and SEQ ID NO: 18.
- 32. The method of claim 13, wherein:
the contacting step uses at least two capture oligomers that hybridize to different sequences in the target region; the amplifying step uses at least two different promoter-primers that hybridize to a first set of sequences within the target region and at least two different primers that hybridize to a second set of sequences within the target region; and the detecting step uses at least two labeled probes that bind specifically to different sequences located between the first set and second set of sequences within the target region.
- 33. The method of claim 32, wherein
the contacting step uses capture oligomers having the sequences of SEQ ID NO: 4 and SEQ ID NO: 6; the amplifying step uses promoter-primers having the sequences of SEQ ID NO: 13 and SEQ ID NO: 15 and primers having the sequences of SEQ ID NO: 10 and SEQ ID NO: 11; and the detecting step uses labeled probes having the sequences of SEQ ID NO: 17 and SEQ ID NO: 18.
- 34. The method of claim 32, wherein the amplifying step uses at least two promoter-primers that hybridize to a first set of overlapping sequences within the target region, at least two primers that hybridize to a second set of overlapping sequences within the target region, or a combination thereof.
- 35. A kit comprising a plurality of oligomers having the sequences of SEQ ID NO: 10, SEQ ID NO: 11, SEQ ID NO: 13, SEQ ID NO: 15, SEQ ID NO: 17 and SEQ ID NO: 18, wherein the oligomers having the sequences of SEQ ID NO: 17 and SEQ ID NO: 18 are labeled with a detectable label.
- 36. The kit of claim 35, further comprising oligomers having the sequences of SEQ ID NO: 8, SEQ ID NO: 9 and SEQ ID NO: 16, wherein the oligomer having the sequence of SEQ ID NO: 16 is labeled with a detectable label.
RELATED APPLICATION
[0001] This application is a divisional of U.S. application Ser. No. 09/611,627, filed Jul. 7, 2000, and claims the benefit under 35 U.S.C. §119(e) of U.S. Provisional Application Serial No. 60/143,072, filed Jul. 9, 1999, the contents of both of which are hereby incorporated by reference.
Provisional Applications (1)
|
Number |
Date |
Country |
|
60143072 |
Jul 1999 |
US |
Divisions (1)
|
Number |
Date |
Country |
Parent |
09611627 |
Jul 2000 |
US |
Child |
10632658 |
Aug 2003 |
US |