Methods for nucleic acid manipulation
A method for replicating and amplifying a target nucleic acid sequence is described. A method of the invention involves the formation of a recombination intermediate without the prior denaturing of a nucleic acid duplex through the use of a recombination factor. The recombination intermediate is treated with a high fidelity polymerase to permit the replication and amplification of the target nucleic acid sequence. In preferred embodiments, the polymerase comprises a polymerase holoenzyme. In further preferred embodiments, the recombination factor is bacteriophage T4 UvsX protein or homologs from other species, and the polymerase holoenzyme comprises a polymerase enzyme, a clamp protein and a clamp loader protein, derived from viral, bacteriophage, prokaryotic, archaebacterial, or eukaryotic systems.
1. A composition for amplifying a target DNA sequence comprising bacteriophage UvsX protein, two primers that anneal to the flanking ends of said target DNA sequence, and a DNA polymerase.
2. The composition of claim 1 , wherein said polymerase is a prokaryotic polymerase.
3. The composition of claim 1 , wherein said primers are present in a molar excess relative to said target nucleic acid sequence.
4. The composition of claim 1 , further comprising an ATP regeneration system.
5. The composition of claim 1 , further comprising a single stranded nucleic acid binding protein.
6. The composition of claim 1 , further comprising bacteriophage UvsY protein.
7. The composition of claim 1 , further comprising nucleotides in an amount sufficient to support amplification of said target DNA sequence.
8. A composition for amplifying a target DNA sequence comprising bacteriophage UvsX protein, two primers that anneal to the flanking ends of said target DNA sequence, and a DNA polymerase having proofreading activity.
9. The composition of claim 8 , wherein said polymerase is a prokaryotic polymerase.
10. The composition of claim 8 , wherein said primers are present in a molar excess relative to said target nucleic acid sequence.
11. The composition of claim 8 , further comprising an ATP regeneration system.
12. The composition of claim 8 , further comprising a single stranded nucleic acid binding protein.
13. The composition of claim 8 , further comprising bacteriophage UvsY protein.
14. The composition of claim 8 , further comprising nucleotides in an amount sufficient to support amplification of said target DNA sequence.