The FLP recombinase is encoded by the yeast plasmid 2 microns circle and catalyses a site-specific recombination reaction that results in inversion of a segment of the 2 micron plasmid. We describe a method for the isolation of inactivating mutations in the FLP gene. The analysis of the recombination and binding activity of defective FLP proteins in vitro resulted in the identification of two classes of mutations: those that completely abolish FLP function by interfering with DNA binding and others that block recombination after the binding step. We have shown that FLP-mediated recombination is accompanied by bending of the DNA target and that mutations in the FLP recombinase that block bending also eliminate recombination.