DIRECTED PROTEIN REPLACEMENT IN RECOMBINATION FULL SITES REVEALS TRANS-HORIZONTAL DNA CLEAVAGE BY FLP RECOMBINASE

One round of site-specific recombination between two DNA partners medi ated by the Flp recombinase requires the breakage and reformation of f our phosphodiester bonds. The reaction is accomplished by the combined action of four Flp monomers. Within the recombination complex, what i s the relative disposition of a Flp monomer with respect to the target diester that it cleaves? To address this question, we have devised a strategy for the targeted orientation of Flp monomers within full-site recombination substrates. Our experimental design is not dependent on 'altered binding specificity' of the recombinase. Analysis of the pat tern of DNA cleavage by this method reveals no evidence for DNA cleava ge in cis. A Flp monomer bound to its recognition element within the f ull site does not cleave the scissile phosphodiester bond adjacent to it. Our results are most consistent with 'trans-horizontal cleavage'. cleavage by Flp occurs at the scissile phosphodiester distal to it, bu t within the same full site. The general experimental design employed here will be of widespread utility in mechanistic analyses of nucleic acid transactions involving multimeric DNA-protein assemblies.