Adjacent cooperation of proteins on DNA are not representative of long-distance interactions

The cI repressor of bacteriophage lambda is better-fitted to the proximal interactions in which it naturally takes part than to the long-distance cooperative interactions on DNA for which it has become representative. The first observation in support of this statement is the ambiguity of an untypical DNAase I footprint which has become a diagnostic for DNA circularisation (and thus for the capacity of the protein to control expression at a distance). However, it was also observed without effective DNA looping when lac repressor binds to nearly contiguous sites. Additionally, the surface of interaction between the two dimers seems to be more important than the one commonly admitted (via some contacts between the flexible arms), the biological function of the repressor is lost when the sites are separated and loops have not been observed for large separation of the sites. In fact, naturally distant interactions can conform to shorter distances, as an intrinsic property of DNA looping. On the contrary, interactions which are naturally optimised for contiguity are generally constrained to proximity. Alternative protein-protein contacts are generally responsible for this situation (cf. CRP versus NRI in Escherichia coli).