Method for removing and/or detecting nucleic acids having mismatched nucleotides
Provided herein, among other things, are various in vitro methods that involve cleaving dsDNA molecules that comprise a mismatched nucleotide using EndoMS. In some embodiments, the method may comprise ligating a T-tailed double-stranded adapter to A-tailed double-stranded fragments of nucleic acid to produce ligation products that comprise adapter-ligated fragments and double-stranded adapter dimers that comprise a T:T mismatch at the ligation junction and cleaving both strands of the adapter dimers using EndoMS.
1. A method for cleaving adapter dimers produced in a ligation reaction, comprising:
(a) ligating a T-tailed double-stranded adapter to A-tailed double-stranded fragments of nucleic acid to produce ligation products that comprise: (i) adapter-ligated double-stranded nucleic acid fragments and (ii) double-stranded adapter dimers that comprise a T:T mismatch at the ligation junction; and
(b) cleaving both strands of the adapter dimers using EndoMS.
2. The method of claim 1 , further comprising (c) amplifying the adapter-ligated double-stranded nucleic acid fragments.
3. The method of claim 2 , wherein the amplifying is done using primers that hybridize to the ligated adapter, or complement thereof.
4. The method of claim 2 , wherein the method is done without enriching for the adapter-ligated double-stranded nucleic acid fragments by size.
5. The method of claim 1 , wherein the double-stranded nucleic acid fragments are genomic fragments.
6. The method of claim 1 , wherein the T-tailed double-stranded adapter is a Y adapter or a pair of Y adapters.
7. The method of claim 1 , wherein the T-tailed double-stranded adapter is a loop adapter.
8. The method of claim 1 , wherein the method comprises incubating a reaction mix comprising the T-tailed double-stranded adapter, the A-tailed double-stranded fragments of nucleic acid, a ligase, and the EndoMS, to produce the ligation products and cleave both strands of the adapter dimers.
9. The method of claim 1 , wherein the EndoMS is thermostable.