Amplification and detection of ribonucleic acids
Compositions, methods, and kits for detecting one or more species of RNA molecules are disclosed. In one embodiment, a first adaptor and a second adaptor are ligated to the RNA molecule using a polypeptide comprising double-strand specific RNA ligase activity, without an intervening purification step. The ligated product is reverse transcribed, then at least some of the ribonucleosides in the reverse transcription product are removed. Primers are added and amplified products are generated. In certain embodiments, the sequence of at least part of at least one species of amplified product is determined and at least part of the corresponding RNA molecule is determined. In some embodiments, at least some of the amplified product species are detected, directly or indirectly, allowing the presence and/or quantity of the RNA molecule of interest to be determined.
1. A method for detecting an RNA molecule, comprising:
(a) forming a single ligation reaction mixture containing
(i) a plurality of RNA molecules, and
(ii) a plurality of a first double-stranded nucleic acid adaptor, and
(iii) a plurality of a second double-stranded nucleic acid adaptor, and
(iv) an RNA ligase,
wherein a first strand of the first double-stranded nucleic acid adaptors of the plurality include at least two ribonucleosides at the 3′ end, and a second strand of the first double-stranded nucleic acid adaptors of the plurality include a first single-stranded portion at the 5′ end, and
wherein a first strand of the second double-stranded nucleic acid adaptors of the plurality include a terminal 5′ phosphate group, and a second strand of the second double-stranded nucleic acid adaptors of the plurality include a second single-stranded portion at the 3′ end, and wherein the first single-stranded portion contains a degenerate nucleotide sequence that hybridizes to a first region of a first RNA molecule of the plurality of RNA molecules, and
wherein the second single-stranded portion contains a degenerate nucleotide sequence that hybridizes to a second region of the first RNA molecule; and
(b) producing at least one RNA ligation product by ligating the first double-stranded adaptor to a first end of the first RNA molecule and ligating the second double-stranded adaptor to the other end of the first RNA molecule.
2. The method of claim 1 further comprising:
(a) producing a first strand cDNA product by reverse transcribing the at least one RNA ligation product;
(b) producing a plurality of amplification products by amplifying the first strand cDNA product; and
(c) detecting at least one amplification product of the plurality of amplification products.
3. The method of claim 2 , wherein the reverse transcribing of step (a) comprises contacting the at least one RNA ligation product with triphosphate nucleotides, and (i) an RNA-dependent DNA polymerase, (ii) a DNA polymerase having DNA-dependent DNA polymerase activity and RNA-dependent DNA polymerase activity, or (iii) an RNA-dependent DNA polymerase and a DNA-dependent DNA polymerase.
4. The method of claim 2 , wherein the amplifying in step (b) comprises PCR amplifying with at least one forward amplification primer and at least one reverse amplification primer.
5. The method of claim 2 , wherein the amplifying in step (b) comprises contacting the first strand cDNA product with at least one forward amplification primer and at least one reverse amplification primer.
6. The method of claim 5 , wherein the at least one forward amplification primer or the at least one reverse amplification primer includes a unique identification sequence.
7. The method of claim 5 , wherein the at least one forward amplification primer or the at least one reverse amplification primer includes a library-specific barcode sequence.
8. The method of claim 5 , wherein the at least one forward amplification primer or the at least one reverse amplification primer includes a promoter sequence selected from the group consisting of a T3 RNA polymerase promoter sequence, a T7 RNA polymerase promoter sequence and an SP6 RNA polymerase promoter sequence.
9. The method of claim 2 , wherein the detecting of step (c) comprises sequencing the plurality of amplification products.
10. The method of claim 9 , wherein the sequencing comprises sequencing with a plurality of dideoxy nucleotides.
11. The method of claim 9 , wherein the sequencing comprises massively parallel sequencing.
12. The method of claim 1 , wherein the plurality of RNA molecules comprise a small non-coding RNA or mRNA or polyA RNA.
13. The method of claim 1 , wherein the plurality of RNA molecules are fragmented RNA molecules.
14. The method of claim 13 , wherein the fragmented RNA molecules are generated by contacting an RNA sample with RNase III.
15. The method of claim 1 , wherein the RNA ligase comprises an Rnl2 family ligase.
16. The method of claim 15 , wherein the RNA ligase comprises bacteriophage T4 RNA ligase 2 (Rnl2).
17. The method of claim 1 , wherein the first strand of the first double-stranded adaptor and the first strand of the second double-stranded adaptor comprise different nucleotide sequences.
18. The method of claim 1 , wherein at least one of the first double-stranded nucleic acid adaptors of the plurality, or at least one of the second double-stranded nucleic acid adaptors of the plurality, comprises a unique identification sequence.
19. The method of claim 1 , wherein the first single-stranded portion of the first double-stranded adaptors of the plurality and the second single-stranded portion of the second double-stranded adaptors of the plurality, comprises adenosine, guanosine, cytidine, and thymidine.
20. The method of claim 1 , wherein the first single-stranded portions of the plurality of first double-stranded nucleic acid adaptors contain different degenerate sequences, and wherein the second single-stranded portions of the plurality of second double-stranded nucleic acid adaptors contain different degenerate sequences.