Abstract: In one aspect the invention provides methods for cloning polymerase chain reaction (PCR) products without the need for restriction enzymes, ligation enzymes, or DNA purification steps. According to these methods, a PCR product is transferred into a vector in vivo using a site-specific recombination system. In some embodiments, the methods include the steps of (1) providing a PCR product flanked by a first site-specific recombination site and a second site-specific recombination site; and (2) transferring the PCR product into a cell comprising a target sequence flanked by a first recombination site partner and a second recombination site partner, and at least one recombination protein that mediates recombination between the first site-specific recombination site and the first recombination site partner, and between the second site-specific recombination site and the second recombination site partner.

Abstract: In one aspect the invention provides methods for moving an insert nucleic acid molecule between vectors using site-specific recombination in vivo. In another aspect, the invention provides methods for the functional analysis of a genome using site-specific recombination in vivo. Another aspect of the invention provides methods for deleting a target genomic region by intra-molecular site-specific recombination. Further aspects provide vectors and kits for use in the methods of the invention.