The binding motif recognized by HU on both nicked and cruciform DNA

The heterodimeric HU protein, highly conserved in bacteria and involved in transposition, recombination, DNA repair, etc., shares similarity with hist ones and HMGs. HU, which binds DNA with lon affinity and without sequence s pecificity, binds strongly and specifically to DNA junctions and DNA contai ning single-strand breaks. The fine structure of these specific complexes w as studied by footprinting and HU chemically converted into nucleases, The positioning of HU alpha P on nicked DNA is asymmetrical and specifically or iented: the p-arm binds the area surrounding the break whereas the a-arm li es on the 3' DNA branch. This positioning necessitates a pronounced bend in the DNA at the discontinuous point, which was estimated by circular permut ation assay to be 65 degrees, At junctions, HU is similarly asymmetrically positioned in an identical orientation: the junction point plays the role o f the discontinuous point in the nicked DNA. The HU binding motif present i n both structures is a pair of inclined DNA helices.