Modified stem-loop oligonucleotide mediated reverse transcription and base-spacing constrained quantitative PCR

1. A method for detecting a target RNA molecule in a sample, the method comprising:

reverse transcribing the target RNA contained in the sample using a reverse transcription (RT) oligonucleotide, the RT oligonucleotide comprising a stem-loop portion containing one or more nucleotides modifiable to block DNA polymerase extension and a target annealing portion that is complementary to a downstream portion of the target RNA, the target annealing portion located 3′ to the stem-loop portion, to produce a reverse transcription product that comprises the RT oligonucleotide and a 3′ extended region;

modifying the one or more modifiable nucleotides;

amplifying the reverse transcription product using (i) a first amplification primer that anneals to a downstream portion of the 3′ extended region of the reverse transcription product and (ii) a second amplification primer that anneals to an interface portion of a DNA strand complementary to the reverse transcription product, the interface portion comprising a region that is complementary to a 3′ portion of the RT oligonucleotide and a 5′ portion of the 3′ extended region in the reverse transcription product, to produce an amplification product; and

detecting the amplification product;

wherein the stem-loop portion adopts a stem-loop structure under conditions used for said reverse transcribing but does not adopt the stem-loop structure under conditions used for said amplifying and wherein the one or more nucleotides that are modifiable to block DNA polymerase extension comprise one or more ribonucleotides, and the modifying comprises treatment with an RNAse.

2. The method of claim 1 , wherein the target RNA is an miRNA.

3. The method of claim 2 , wherein the one or more nucleotides modifiable to block DNA polymerase extension is located within the loop of the stem-loop portion.

4. The method of claim 2 , wherein the stem-loop portion further comprises one or more nucleotides modified to block DNA polymerase extension.

5. The method of claim 4 , wherein the loop of the stem-loop portion comprises a nucleotide modified with an aliphatic carbon chain.

6. The method of claim 2 , wherein the second amplification primer has a nucleotide that displays thermal stability when hybridized to DNA as the 3′ terminal nucleotide.

7. The method of claim 6 , wherein the nucleotide that displays thermal stability when hybridized to DNA is locked in an N-type furanose conformation.

8. The method of claim 2 , wherein the distance in the sequence of the amplification product between the position of the 3′ end of the first amplification primer when annealed to the reverse transcription product and the position of the 3′ end of the second amplification primer when annealed to the DNA strand is from −4 to 5 nucleotides.

9. The method of claim 2 , wherein the target annealing portion of the RT oligonucleotide is 5 to 15 nucleotides in length.

10. The method of claim 2 , wherein the stem portion of the stem-loop is 4 to 6 nucleotides in length and the loop portion of the stem-loop is 4 to 12 nucleotides in length.

11. The method of claim 2 , wherein the second amplification primer anneals to a sequence complementary to 13 to 24 nucleotides of the stem-loop portion of the RT oligonucleotide, 5 to 15 nucleotides of the target annealing portion of the RT oligonucleotide and 1 to 5 nucleotides at the 5′ end of the 3′ extended region of the reverse transcription product.

12. The method of claim 2 , wherein the first amplification primer is 12 to 27 nucleotides in length.

13. The method of claim 2 , wherein said detecting comprises detecting with a fluorescent intercalating dye.

14. The method of claim 13 , wherein the fluorescent intercalating dye is SYBR GREEN™ (N′,N′-dimethyl-N-[4-[(E)-(3-methyl-1,3-benzothiazol-2-ylidene)methyl]-1-phenylquinolin-1-ium-2-yl]-N-propylpropane-1,3-diamine).

15. A method for detecting a target RNA molecule in a sample, the method comprising:

reverse transcribing the target RNA contained in the sample using an RT oligonucleotide, the RT oligonucleotide comprising a stem-loop portion containing at least one dU nucleotide or a ribonucleotide and a target annealing portion that is complementary to a downstream portion of the target RNA, the stem portion of the stem-loop being 4 to 6 nucleotides in length and the loop portion of the stem-loop being 4 to 12 nucleotides in length, and the target annealing portion located 3′ to the stem-loop portion and being 5 to 15 nucleotides in length, to produce a reverse transcription product that comprises the RT oligonucleotide and a 3′ extended region;

modifying the dU nucleotide by treatment with uracil-DNA glycosylase or the ribonucleotide by treatment with an RNAse;

amplifying the reverse transcription product using (i) a first amplification primer that anneals to a downstream portion of the 3′ extended region of the reverse transcription product and is 12 to 27 nucleotides in length, and (ii) a second amplification primer that anneals to an interface portion of a DNA strand complementary to the reverse transcription product, the interface portion comprising a region that is complementary to 13 to 24 nucleotides of the stem-loop portion of the RT oligonucleotide, 5 to 15 nucleotides of the target annealing portion of the RT oligonucleotide and 1 to 5 nucleotides at the 5′ end of the 3′ extended region of the reverse transcription product, to produce an amplification product in which the distance in the sequence of the amplification product between the position of the 3′ end of the first amplification primer when annealed to the reverse transcription product and the position of the 3′ end of the second amplification primer when annealed to the DNA strand is from −4 to 5 nucleotides; and

detecting the amplification product;

wherein the stem-loop portion adopts a stem-loop structure under conditions used for said reverse transcribing but does not adopt the stem-loop structure under conditions used for said amplifying.

16. The method of claim 15 , wherein the target RNA is an miRNA.

17. A method for detecting a target miRNA molecule in a sample, the method comprising:

reverse transcribing the target miRNA contained in the sample using an RT oligonucleotide, the RT oligonucleotide comprising a stem-loop portion containing a dU nucleotide and a target annealing portion that is complementary to a downstream portion of the target miRNA, the target annealing portion located 3′ to the stem-loop portion, the stem portion of the stem-loop being 5 to 6 nucleotides in length and the loop portion of the stem-loop being 11 nucleotides in length, and the target annealing portion located 3′ to the stem-loop portion and being 6 nucleotides in length, to produce a reverse transcription product that comprises the RT oligonucleotide and a 3′ extended region;

modifying the dU nucleotide by treatment with uracil-DNA glycosylase;

amplifying the reverse transcription product using (i) a first amplification primer that anneals to a downstream portion of the 3′ extended region of the reverse transcription product and is 21 nucleotides in length, and (ii) a second amplification primer that anneals to an interface portion of a DNA strand complementary to the reverse transcription product, the interface portion comprising a region that is complementary to 8 to 10 nucleotides of the stem-loop portion of the RT oligonucleotide, 6 nucleotides of the target annealing portion of the RT oligonucleotide and 3 to 5 nucleotides at the 5′ end of the 3′ extended region of the reverse transcription product, to produce an amplification product in which the distance in the sequence of the amplification product between the position of the 3′ end of the first amplification primer when annealed to the reverse transcription product and the position of the 3′ end of the second amplification primer when annealed to the DNA strand is from −2 to 2 nucleotides; and

detecting the amplification product;

wherein the stem-loop portion adopts a stem-loop structure under conditions used for said reverse transcribing but does not adopt the stem-loop structure under conditions used for said amplifying.

18. The method of claim 15 , wherein the stem-loop portion of the RT oligonucleotide contains dU nucleotide and modifying the du nucleotide by treatment with uracil-DNA glycosylase.

19. The method of claim 1 , wherein the distance in the sequence of the amplification product between the position of the 3′ end of the first amplification primer when annealed to the reverse transcription product and the position of the 3′ end of the second amplification primer when annealed to the DNA strand is from −4 to 5 nucleotides; the target annealing portion of the RT oligonucleotide is 5 to 15 nucleotides in length; the stem portion of the stem-loop is 4 to 6 nucleotides in length and the loop portion of the stem-loop is 4 to 12 nucleotides in length; the second amplification primer anneals to a sequence complementary to 13 to 24 nucleotides of the stem-loop portion of the RT oligonucleotide, 5 to 15 nucleotides of the target annealing portion of the RT oligonucleotide and 1 to 5 nucleotides at the 5′ end of the 3′ extended region of the reverse transcription product; and the first amplification primer is 12 to 27 nucleotides in length.