Multiple repressor binding at the operators in bacteriophage lambda.

Short DNA duplexes are protected when lambda DNA is digested with nuclease in the presence of lambda repressor. As the ratio of repressor to operator is increased, six successively larger fragments are recovered, ranging in size from 35 to 100 base pairs, each of which binds repressor. Study of these fragments indicates that, at each of the two lambda operators (o(L) and o(R)), repressor first binds to a unique site (not necessarily terminal), and that five additional sites are then filled in linear right-ward or left-ward order. The nucleotide sequences and affinities for repressor of o(L) and o(R) are not identical, although six fragments of similar size are protected at each operator. Evidence is presented arguing against the existence of hairpin-like structures in the operator fragments, and, moreover, it is shown that the operator duplex does not unwind when repressor binds to it.