A method of stimulating homologous recombination by creating at least one nick in a targeted polynucleotide sequence. Wherein nonhomologous recombination is suppressed resulting in increasing the ratio of targeted to nontargeted events. A method of increasing double strand break-initiated gene targeting by inducing a nick in a targeted polynucleotide sequence, wherein overall recombination levels are increased. A method of increasing homologous recombination employing a recombinase that releases the ends in living cells by stimulating homolgous recombination to higher levels than those attainable with standard nucleases. A composition for stimulating homologous recombination including a nicking mechanism for creating nicks in a polynucleotide, wherein the nicking mechanism stimulates homologous recombination. A composition for stimulating homologous recombination including a nicking endonucleases. Various kits for stimulating homologous recombination. A method for modulating and channeling site-specific DNA stand breaks by shepherding the DNA strand breaks to particular recombination pathways.