DNA bending and twisting properties of integration host factor determined by DNA cyclization

The binding of many proteins to DNA is profoundly affected by DNA bending, twisting, and supercoiling. When protein binding alters DNA conformation, i nteraction between inherent and induced DNA conformation can affect protein binding affinity and specificity. Integration host factor (IHF), a sequenc e-specific, DNA-binding protein of Escherichia coli, strongly bends the DNA upon binding. To assess the influence of inherent DNA bending on IHF bindi ng, we took advantage of the high degree of natural static curvature associ ated with an IHF site on a 163-bp minicircle and measured the binding affin ity of MF for its recognition site contained on this DNA in both circular a nd linear form. IHF showed a higher affinity for the circular form of the D NA when compared to the linear form. In addition, the presence of MF during DNA cyclization changed the topology of cyclization products and their abi lity to bind IHF, consistent with IHF untwisting DNA. These results show th at inherent DNA conformation anisotropy is an important determinant of IHF binding affinity and suggests a mechanism for modulation of IHF activity by local DNA conformation. (C) 2000 Academic Press.