A new DNA binding mode for CAP

In the absence of cyclic AMP, the Escherichia coli cyclic AMP receptor protein (CAP) binds without detectable sequence specificity to restriction fragments containing lac and crp promoter sequences. Under standard conditions (10 mM Tris, 1 mM EDTA, pH 8.0), our estimates of the equilibrium constant and cooper-ativity parameter for complex formation are 114,000 ± 1400 M^-1 and 1.3 ± 0.8, respectively. Thus, this interaction lacks the substantial cooperativity previously reported for CAP binding to genomic DNAs. Using the electrophoresis mobility shift assay, we find that complexes of increasing CAP content differ by a highly uniform mobility decrement. This result is most consistent with a binding mode in which little or no DNA bending occurs. The ability of CAP to distinguish between restriction fragments and genomic DNA, shown by the difference in binding cooperativity, suggests the existence of previously unsuspected DNA sequences or structures that modulate its binding cooperativity.