Low sequence bias single-stranded DNA ligation
The invention provides compositions and methods for ligating single stranded nucleic acids wherein the ligation is based on fast, efficient, and low-sequence bias hybridization of an acceptor molecule with a donor molecule. In one embodiment, the structure of the donor molecule comprises a stem-loop intramolecular nucleotide base pairing (i.e., hairpin) and a 3′-overhang region such that the overhang is able to hybridize to nucleotides present in the 3′ end of the acceptor molecule.
1. A method of producing a ligated single stranded nucleic acid molecule, the method comprising:
a) contacting a single-stranded acceptor nucleic acid molecule with a population of donor nucleic acid molecules, wherein each of the donor nucleic acid molecules comprises a stem region, and a single-stranded 3′ terminal overhang region, wherein the sequence of the donor nucleic acid is designed to contain at least one mismatch internally in the stem region, and wherein at least the four 5′ terminal nucleotides of the donor molecule form Watson-Crick base pairs as part of the stem region, and wherein the donor molecule comprises at least one randomized templating nucleotide in the 3′ terminal overhang region at the position nearest the stem loop, thereby allowing unbiased hybridization with a multiplicity of different acceptor molecules;
b) hybridizing the single stranded 3′ terminal overhang region of the donor nucleic acid molecule to the acceptor molecule under conditions where the stem structure is formed in the donor molecule, wherein the acceptor molecule may comprise any nucleotide sequence at the 3′ end, thereby forming an acceptor-donor hybrid molecule comprising a nick or gap between the acceptor nucleic acid and donor nucleic acid molecule; and
c) ligating the 5′ end of the donor nucleic acid molecule to the 3′ end of the acceptor nucleic acid molecule with a ligase that is active under conditions where the stem structure is formed in the donor nucleic acid molecule, thereby generating a ligated product, whereby the yield of ligated product is at least 65%.
2. The method of claim 1 , wherein the ligation in step c) is accomplished after the hybridization in step b), wherein the hybridization step positions the acceptor and donor molecule in a way that ligation occurs under conditions that allow for ligation between the 5′ end of the donor nucleic acid molecule and the 3′ end of the acceptor nucleic acid molecule.
3. The method of claim 1 , wherein the ligase comprises a DNA ligase.
4. The method of claim 3 , wherein the DNA ligase is T4 DNA ligase.
5. The method of claim 1 , wherein the 3′ terminal overhang region of donor molecule comprises at least 6 base(s).
6. The method of claim 1 , wherein the stem region of the donor molecule is double stranded and comprises at least 6 nucleotide pairs.
7. The method of claim 1 , wherein the donor molecule further comprises a loop structure, wherein the loop structure comprises at least 3 bases.
8. The method of claim 7 , wherein the loop structure comprises a portion of a primer binding site.
9. The method of claim 1 , wherein at least one donor molecule comprises a nucleotide sequence selected from the group consisting of SEQ ID NO: 11, SEQ ID NO: 12, SEQ ID NO: 13, SEQ ID NO: 16, SEQ ID NO: 17, SEQ ID NO: 18, SEQ ID NO: 19, SEQ ID NO: 20, SEQ ID NO: 21, SEQ ID NO: 22, SEQ ID NO: 28 and SEQ ID NO: 29, and wherein the ligation is performed using T4 DNA ligase.
10. The method of claim 1 , wherein the stem of at least one donor molecule comprises a restriction enzyme cleavage site.
11. The method of claim 1 , wherein at least one donor molecule comprises at least six randomized templating nucleotides in the 3′ overhang, and wherein the yield is at least 90%.
12. The method of claim 11 , wherein at least one donor molecule comprises the nucleotide sequence as set forth in SEQ ID NO: 29.