The interaction of Escherichia coli replication factor Y with complementary strand origins of DNA replication. Contact points revealed by DNase footprinting and protection from methylation.

A defined region of the viral (+) strand of phi X174 and of each strand of pBR322 DNA serves as an effector for the ATPase activity of replication factor Y from Escherichia coli. These loci can also function as complementary strand origins of DNA replication in a single-stranded circular leads to replicative form pathway whose protein requirements are characteristic of phi X174 DNA. Despite this functional similarity, these three sites possess no extensive sequence homology. To uncover a possible common structural determinant, factor Y recognition sequences were treated with pancreatic DNase or dimethyl sulfate in the presence and absence of this replication protein. When factor Y was present, the action of the nuclease was altered in a similar manner on each of the three templates, indicating that factor Y was bound to the entire length of its effector site. Factor Y-mediated modification of the dimethyl sulfate methylation patterns gave evidence of specific, tight protein-DNA contacts. Protection maps, devised by plotting the results of the methylation and footprinting experiments on duplex structures, suggest that tertiary interactions are either involved in the formation of a factor Y effector site or are induced by the binding of the protein.