DNA bending by Cro protein in specific and nonspecific complexes: implications for protein site recognition and specificity.

Scanning force microscopy was used to resolve lambda Cro protein when bound as a single dimer or multiple dimers to its three operator (OR) sites. The bend angles induced by binding of Cro to specific and nonspecific sites were determined and are 69 degrees +/- 11 degrees for specific and 62 degrees +/- 23 degrees for nonspecific complexes. Bending of the nonspecific sites is advantageous for a protein such as Cro that bends its specific site, because it increases the binding specificity of the protein and it can be used by the protein to sample contacts required for the recognition of its target sequence. It is proposed here that bending of nonspecific DNA may be a general property among DNA binding proteins that bend their specific sites.