Analysis of higher order intermediates and synapsis in the bent-L pathway of bacteriophage lambda site-specific recombination.

The integrase protein of bacteriophage lambda mediates recombination via four distinct pathways. The recent in vitro reconstitution of the efficient bidirectional reaction between two attLtenP'1 target sites now allows comparisons of this pathway, known as the bent-L pathway, with the inefficient bidirectional straight-L pathway and with the efficient but unidirectional pathways of integration and excision. To this end, a series of higher order intermediates of the bent-L pathway was characterized using gel mobility shift assays, two-dimensional gel analysis, and footprinting. The analysis spans the initial binding of proteins to individual DNA target sites, synapsis of two partner DNA targets, and strand exchange. This study identifies a presynaptic "checkpoint" of recombination. It shows that synapsis is a slow step in the recombination reaction, while subsequent strand exchange is comparatively fast. Synaptic complexes contain a preponderance of recombinant products, suggesting that an energetically favorable but somewhat subtle conformational change drives strand exchange. In addition, comparison of wild-type integrase with a catalytically defective mutant of integrase, IntF, showed that, in addition to the catalysis defect, this mutant has different DNA-binding properties than the wild-type protein.