THE BINDING OF UVRAB PROTEINS TO BUBBLE AND LOOP REGIONS IN DUPLEX DNA

Based on the binding of the UvrAB complex to a promoter region in tran scription open complexes (Ahn, B., and Grossman, L, (1996) J. Biol. Ch em. 271, 21453-21461) and the requirement of a single-stranded region for UVrAB helicase activity, we examined the binding of UvrAB proteins to synthetic bubble or loop regions in duplex DNA and the role of the se regions in translocation of the UvrAB complex as well as incision o f DNA damage. We found that the UvrAB complex was able to bind to bubb le and loop regions with an affinity similar to that for damaged DNA i n the absence of RNAP. The preferential recognition and incision of da maged sites by the UvAB complex was observed downstream of the bubble or loop region in the strand complementary to the strand along which t he UVrAB complex translocates. These results imply that the bubble reg ion generated in duplex DNA by RNAP serves as a preferred entry site f or the translocation of the UvrAB complex, and that preferential bindi ng and unidirectional translocation of the UvrAB complex predetermine where incision is to occur.