Methods and compositions for full-length cDNA Cloning using a template-switching oligonucleotide
First Claim
1. A method for preparing DNA that is complementary to an RNA molecule and a template switching oligonucleotide, said method comprising the steps of:
- annealing a cDNA synthesis primer to said RNA molecule and synthesizing a first cDNA strand to form an RNA-cDNA intermediate;
contacting said RNA-cDNA intermediate with a template switching oligonucleotide, wherein said template switching oligonucleotide has at it'"'"'s 3'"'"' end at least one nucleotide which forms a basepair(s) with a nucleotide(s) at a 3'"'"' end of said first cDNA strand of said RNA-cDNA intermediate, said template switching oligonucleotide serves as a template for extension of said 3'"'"' end of said first cDNA strand, and said template switching oligonucleotide has a pre-selected arbitrary nucleotide sequence at its 5'"'"' end and at least one ribonucleotide residue at its 3'"'"' end; and
extending said 3'"'"' end of said first cDNA strand to produce a DNA that is complementary to said RNA molecule and said template switching oligonucleotide.
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Abstract
The present invention pertains to methods for the synthesis and cloning of full-length cDNA, or cDNA fragments, that correspond to the complete sequence of 5'"'"'-ends of mRNA molecules. The method of the present invention comprises contacting RNA with a cDNA synthesis primer which can anneal to RNA, a suitable enzyme which possesses reverse transcriptase activity, and a template switching oligonucleotide under conditions sufficient to permit the template-dependent extension of the primer to generate an mRNA-cDNA hybrid. The template switching oligonucleotide hybridizes to the CAP site at the 5'"'"'-end of the RNA molecule and serves as a short, extended template for CAP-dependent extension of the 3'"'"'-end of the ss cDNA that is complementary to the template switching oligonucleotide. The resulting full-length ss cDNA includes the complete 5'"'"'-end of the RNA molecule as well as the sequence complementary to the template switching oligonucleotide, which can then serve as a universal priming site in subsequent amplification of the cDNA.
The subject invention also pertains to the template switching oligonucleotides that can be used according to the subject method. Kits containing the template switching oligonucleotide are also included within the scope of the present invention.
260 Citations
29 Claims
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1. A method for preparing DNA that is complementary to an RNA molecule and a template switching oligonucleotide, said method comprising the steps of:
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annealing a cDNA synthesis primer to said RNA molecule and synthesizing a first cDNA strand to form an RNA-cDNA intermediate; contacting said RNA-cDNA intermediate with a template switching oligonucleotide, wherein said template switching oligonucleotide has at it'"'"'s 3'"'"' end at least one nucleotide which forms a basepair(s) with a nucleotide(s) at a 3'"'"' end of said first cDNA strand of said RNA-cDNA intermediate, said template switching oligonucleotide serves as a template for extension of said 3'"'"' end of said first cDNA strand, and said template switching oligonucleotide has a pre-selected arbitrary nucleotide sequence at its 5'"'"' end and at least one ribonucleotide residue at its 3'"'"' end; and extending said 3'"'"' end of said first cDNA strand to produce a DNA that is complementary to said RNA molecule and said template switching oligonucleotide. - View Dependent Claims (2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19)
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- 20. A template switching oligonucleotide having at it'"'"'s 3'"'"' end at least one nucleotide which forms a basepair(s) with a nucleotide(s) at a 3'"'"' end of a first cDNA strand of an RNA-cDNA intermediate, wherein said template switching oligonucleotide is capable of serving as a template for extension of said 3'"'"' end of said first cDNA strand, and said template switching oligonucleotide has a pre-selected arbitrary nucleotide sequence at its 5'"'"' end and at least three ribonucleotide residues at its 3'"'"' end.
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28. A template switching oligonucleotide selected from the group consisting of SEQ ID Nos. 1-7, 9, 13, 18-66, 68, and 84-108.
Specification