Dynamics of long-range interactions on DNA: the speed of synapsis during site-specific recombination by resolvase

A noninvasive method for monitoring communications on DNA was developed from the specificity of resolvase for the arrangement of its recombinational sites. Constraints in DNA structure, caused by interactions between distant sites, can be detected by resolvase as they arise. The method was used to follow the formation and decay of synaptic intermediates during site-specific recombination by resolvase. Synaptic complexes were formed very rapidly, at a rate limited by the initial association of the protein with DNA rather than the physical motion of DNA segments. The recombinational sites seem to encounter each other by an ordered motion, perhaps dictated by DNA supercoiling instead of random collisions, so that the first encounter produces the active complex.