A Shared, Non-canonical DNA Conformation Detected at DNA/Protein Contact Sites and Bent DNA in the Absence of Supercoiling or Cognate Protein Binding

A hybrid protein (H144), consisting of Lac repressor and T7 endonuclease I, binds at the lac operator and cleaves relaxed double stranded DNA at distal but distinct sites. These sites are shown here to coincide with a bacterial promoter, a phage T7 promoter, a site for gyrase and intrinsically bent DNA. The targets do not seem to share a particular DNA sequence, and in bent DNA, cleavage occurs at the physical center rather than at the common A-tracts. These results indicate that protein contact sites and intrinsic bends assume a non-canonical conformation in the absence of supercoiling or cognate protein binding. This feature may serve as a recognition signal or facilitate protein binding to initiate transcription and recombination.