STRUCTURAL ALTERATIONS AND CONFORMATIONAL DYNAMICS IN HOLLIDAY JUNCTIONS INDUCED BY BINDING OF A SITE-SPECIFIC RECOMBINASE

Binding of a cleavage-incompetent mutant of the Flp recombinase induce s a roughly square-planar geometry in synthetic immobile Holliday junc tions. The branch points, which are rigidly fixed in these junctions i n their free forms, tend to be more flexible in their protein-bound fo rms. Our results (1) suggest a plausible mechanism for the switching o f the recombination complex from the Holliday-forming mode to the Holl iday-resolving mode, (2) provide a rationale for previous observations that Flp resolves preformed immobile Holliday structures in the paren tal or in the recombinant mode in a relatively unbiased manner, and (3 ) accommodate two modes of DNA cleavage by Flp (transhorizontal or tra nsdiagonal) in Holliday substrates.