Enhanced adaptor ligation

1. A method of producing a processed substrate nucleic acid molecule, the method comprising:

(1) adding a first polynucleotide and a ligase to a sample comprising a substrate nucleic acid molecule, wherein the substrate nucleic acid molecule is at least partially double-stranded and has a phosphate at its 5′ ends, wherein the first polynucleotide comprises oligonucleotide A, oligonucleotide B, and a double-stranded portion, wherein the double-stranded portion comprises oligonucleotide A hybridized to oligonucleotide B, wherein oligonucleotide A lacks a 5′ phosphate and comprises a base that is susceptible to degradation;

(2) incubating the sample under conditions sufficient to ligate oligonucleotide B to the 5′ ends of the substrate nucleic acid molecule;

(3) adding to the sample a second polynucleotide, an enzyme capable of degrading oligonucleotide A, a DNA polymerase, deoxynucleotide triphosphates, wherein the second polynucleotide lacks a 5′ phosphate and is capable of annealing to a 3′ portion of oligonucleotide B, and wherein the DNA polymerase is capable of nick-translation DNA synthesis; and

(4) incubating the sample under conditions sufficient to (i) promote degradation of oligonucleotide A by the enzyme, (ii) promote annealing of the second polynucleotide to oligonucleotide B and (iii) allow the DNA polymerase and ligase to act on the substrate nucleic acid molecule in order to add the second polynucleotide to the 3′ ends of the substrate nucleic acid molecule thereby forming the processed substrate nucleic acid molecule.

2. The method of claim 1 , wherein the substrate nucleic acid molecule is genomic DNA.

3. The method of claim 2 , wherein the genomic DNA is eukaryotic or prokaryotic.

4. The method of any one of claims 1 - 3 , wherein the substrate nucleic acid molecule is synthetic and is selected from the group consisting of cDNA, DNA produced by whole genome amplification, primer extension products comprising at least one double-stranded terminus, and a PCR amplicon.

5. The method of any one of claims 1 - 4 , wherein the deoxynucleotide triphosphates comprise no more than three different types of deoxynucleotide triphosphates.

6. The method of claim 1 , further comprising a purification step after step (2), wherein the purification step removes any unused first polynucleotide.

7. The method of claim 6 , wherein step (3) further comprises adding ligase to the sample.