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

The cl repressor of bacteriophage lambda is better-fitted to the proximal i nteractions in which it naturally takes part than to the long-distance coop erative interactions on DNA for which it has become representative. The fir st observation in support of this statement is the ambiguity of an untypica l DNAase I footprint which has become a diagnostic for DNA circularisation land thus for the capacity of the protein to control expression at a distan ce). However, it was also observed without effective DNA looping when lac r epressor binds to nearly contiguous sites. Additionally, the surface of int eraction between the two dimers seems to be more important than the one com monly admitted (via some contacts between the flexible arms), the biologica l 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, naturall y distant interactions can conform to shorter distances, as an intrinsic pr operty of DNA looping. On the contrary, interactions which are naturally op timised for contiguity are generally constrained to proximity. Alternative protein-protein contacts are generally responsible for this situation (cf. CRP versus NRI in Escherichia coin. ((C) Academie des sciences / Elsevier, Paris.)