Synaptic intermediates promoted by the FLP recombinase.

We have devised a novel assay to trap nucleoprotein synaptic intermediates of the FLP recombination reaction. DNase I footprinting analysis of these intermediates indicates that synapsis is mediated by protein-protein interactions between FLP molecules bound to each FLP recombination target (FRT) site. Under certain conditions we have observed a synaptic structure in which the FRT sites have come together in an aberrant arrangement. Although our analysis shows that homology between the core sequences of the sites is not a prerequisite for synapsis, the data suggest that homology between cores dictates the directionality of the reaction. Many of the intermediates contain a Holliday junction indicating that the FLP protein has catalysed strand exchanges between the FRT sites. The general scheme of the assay should prove useful to analyse nucleoprotein intermediates in other site-specific recombination systems, and to investigate protein-protein and protein-DNA interactions in intermediates important for DNA replication and transcription.