Compositions and methods for detecting C1orf43 nucleic acid
This disclosure provides oligomers, combinations of oligomers, compositions, kits, uses, and methods for detecting a C1orf43 nucleic acid, such as C1orf43 mRNA, such as human C1orf43 mRNA, in a sample.
1. A method of detecting the presence or absence of a C1orf43 nucleic acid in a sample, comprising:
contacting the sample with a combination of oligomers comprising at least first and second amplification oligomers,
performing a nucleic acid amplification reaction which produces at least a first amplicon in the presence of the C1orf43 nucleic acid,
and detecting the presence or absence of the first amplicon,
wherein:
the first amplicon is produced through extension of the first and second amplification oligomers in the presence of the C1orf43 nucleic acid; and
wherein the first and second amplification oligomers are reverse and forward amplification oligomers, respectively; and are configured to
specifically hybridize to first and second sites in the sequence of SEQ ID NO: 39, respectively, wherein the first site is in the complement of SEQ ID NO: 52 and the first amplification oligomer comprises the sequence of SEQ ID NO:53 or SEQ ID NO:54; and
wherein the second site is in the complement of SEQ ID NO: 46 and the second amplification oligomer comprises the sequence of SEQ ID NO: 47 or SEQ ID NO:48.
2. The method of claim 1 , wherein at least one of the amplification oligomers is a promoter-primer.
3. The method of claim 2 , wherein the first amplification oligomer is a promoter-primer.
4. The method of claim 3 , wherein the promoter-primer comprises a T7 promoter which is located 5′ of a target-hybridizing sequence and wherein the T7 promoter comprises the sequence of SEQ ID NO: 58.
5. The method of claim 2 , wherein the first amplification oligomer comprises a target-hybridizing sequence comprising the sequence of SEQ ID NO: 27, 29, 31, or 33.
6. The method of claim 5 , wherein the first amplification oligomer comprises the sequence of SEQ ID NO: 26, 28, 30, or 32.
7. The method of claim 1 , wherein the second amplification oligomer comprises a target-hybridizing sequence comprising the sequence of SEQ ID NO: 34, 35, 36, 37, or 38.
8. The method of claim 1 , wherein the combination further comprises at least one probe oligomer that comprises at least 10 nucleotides and is configured to specifically hybridize to an amplicon produced from the first and second amplification oligomers.
9. The method of claim 8 , wherein the probe oligomer is configured to specifically hybridize to a detection site in a nucleic acid having the sequence of SEQ ID NO: 49 and wherein the probe oligomer comprises a target hybridizing sequence comprising the sequence of SEQ ID NO: 50 or SEQ ID NO:51.
10. The method of claim 8 , wherein the probe oligomer comprises a target hybridizing sequence comprising the sequence of SEQ ID NO: 15, 17, 19, 21, 23, or 25, with up to two mismatches.
11. The method of claim 10 , wherein the probe oligomer comprises the sequence of SEQ ID NO: 14, 16, 18, 20, 22, or 24.
12. The method of claim 8 , wherein the probe oligomer comprises a target hybridizing sequence comprising the sequence of SEQ ID NO: 59, 60, 64, 66, 67, 68, 69, 70, 71, or 72, with up to two mismatches.
13. The method of claim 8 , wherein the probe oligomer comprises 2′-O-methyl-ribose in its backbone.
14. The method of claim 13 , wherein at least half, at least 90%, or all of the sugars in the probe oligomer are 2′-O-methyl-ribose.
15. The method of claim 8 , wherein at least one probe oligomer comprises a non-nucleotide detectable label.
16. The method of claim 15 , wherein the non-nucleotide detectable label is a fluorescent label.
17. The method of claim 16 , wherein the probe oligomer comprises a quencher.
18. The method of claim 15 , wherein the non-nucleotide detectable label is a chemiluminescent label.
19. A method of isolating C1orf43 nucleic acid from a sample, comprising:
contacting the sample with at least one capture oligomer under conditions permissive for forming one or more complexes of a capture oligomer and the C1orf43 nucleic acid, thereby forming a composition, wherein the capture oligomer comprises a target hybridizing sequence comprising the sequence of SEQ ID NO: 56 or SEQ ID NO:57 and is configured to specifically hybridize to a capture site in the sequence of SEQ ID NO: 55; and
isolating the capture oligomer from the composition.
20. The method, of claim 19 , wherein the capture oligomer comprises a target hybridizing sequence comprising the sequence of SEQ ID NO: 5, 7, 9, 11, or 13.
21. The method of claim 20 , wherein the capture oligomer comprises the sequence of SEQ ID NO: 4, 6, 8, 10, or 12.