We have characterized complexes between the
gamma delta resolvase and its recombination site, res, using both a gel retardation assay and
DNase I cleavage. The mobility of
resolvase-res complexes in
polyacrylamide gels is sensitive to the location of res within the
DNA fragment and is at a minimum when res is at its center. This behavior is characteristic of a
protein-dependent bend. By the same assay we have found that
bends are induced upon the binding of
resolvase to each of the three individual binding sites that constitute res. In the wild-type res, the centers of binding sites I and II are 53 bp apart and the central section of the intersite
DNA is sensitive to
DNase I cleavage. We find that insertions of 10 or 21 bp (one or two turns of the
DNA helix) have no discernible effect on the ability of res to recombine or to form complexes with
resolvase. However, insertions of short segment (e.g. 6 or 17 bp) equivalent to nonintegral numbers of helical turns, inhibit recombination and prevent the formation of the normally compact
resolvase-res complex. Complexes of
resolvase with res containing 10 or 21 bp insertions exhibit a pattern of enhanced and suppressed
DNase I cleavages that suggest that the intersite segment is curved. This curvature requires both that site I and II are appropriately spaced, and that site III is also present and occupied.