Ligase activity
Compositions and methods are provided for ligating polynucleotides having a length that is greater than 8 nucleotides on an RNA splint. The ligation reaction provides consistent results in high or low ATP concentrations. The reaction can occur rapidly and is generally at least 10 fold more efficient than T4DNA ligase under optimal conditions for T4DNA ligase and the reaction time is less than 6 hours for example, less than 1 hour.
1. A method for detecting a polymorphism in an RNA, comprising:
(a) hybridizing at least two DNA polynucleotide sequences to a polymorphic sequence in an RNA;
(b) ligating the at least two DNA polynucleotide sequences to one another using a ligase that has an amino acid sequence that is at least 90% identical to the Chlorella virus PBCV-1 ligase of SEQ ID NO:1, to produce a ligation product, and
(c) detecting the ligation product of (b), thereby detecting the polymorphic sequence.
2. The method of claim 1 , wherein the RNA is of biological origin.
3. The method of claim 1 , wherein the RNA is the genome of an RNA virus.
4. The method of claim 1 , wherein the RNA is a cellular RNA.
5. The method of claim 4 , wherein the cellular RNA is a miRNA, long non-coding RNA, mRNA or tRNA.
6. The method of claim 1 , wherein the ligation of step (b) is a done in a buffer comprising 1 μM to 1.5 mM ATP.
7. The method of claim 1 , wherein the RNA has a length of at least 10 nucleotides.
8. The method of claim 1 , wherein the ligation product of step (b) is circular.
9. The method of claim 1 , wherein the ligation product of step (b) is linear.
10. The method of claim 1 , wherein the ligase is PBCV-1 ligase.
11. The method of claim 1 , wherein the detecting step (c) comprises amplifying the ligation product of step (b).
12. The method of claim 11 , wherein the amplifying is done by PCR.
13. The method of claim 11 , wherein the amplifying is done by rolling circle amplification.
14. The method of claim 1 , wherein the RNA is complementary to at least 8 nucleotides of each of the at least two DNA polynucleotide sequences.
15. The method of claim 1 , wherein the detecting is quantitative.
16. The method of claim 1 , wherein the ligase that has an amino acid sequence that is at least 95% identical to the Chlorella virus PBCV-1 ligase of SEQ ID NO:1.