STRUCTURAL DISTORTIONS INDUCED BY INTEGRATION HOST FACTOR (IHF) AT THE H' SITE OF PHAGE-LAMBDA PROBED BY (-CC-1065, PLURAMYCIN, AND KMNO4 AND BY DNA CYCLIZATION STUDIES())

Integration Host Factor (IHF) is a sequence-specific DNA-bending prote in that is proposed to interact with DNA primarily through the minor g roove. We have used various chemical probes [(+)-CC-1065, a minor-groo ve-specific agent that alkylates N3 of adenine and traps bends into th e minor groove; pluramycin, a minor-major-groove threading intercalato r that alkylates N7 of guanine; KMnO4, which reacts more strongly with bases in denatured DNA] to gain more information on the interaction o f IHF with the H' site of phage lambda. In addition to the 13-bp core consensus recognition element present at all IHF binding sites, the H' site also has an upstream AT-rich element that increases the affinity of IHF for this site. Our results reveal new details of IHF-DNA inter action at this site. Results with (+)-CC-1065 modification suggest tha t IHF interacts with the adenines on the 3'-side of the AT-rich elemen t and likely induces a minor-groove bend in its vicinity, which in tur n stabilizes the interaction. Pluramycin modification experiments sugg est the presence of both short- and long-range structural perturbation s (possible DNA unwinding events) on either side of the IHF contact re gion. Although IHF is known to induce a large bend in DNA at the H' si te, no separation of base pairs was detected when the bent DNA was pro bed with KMnO4. DNA cyclization studies indicate a large magnitude (ap proximately 180 degrees) for the IHF-induced bend at the H' site, cons istent with >140 degrees bend estimated by gel electrophoresis methods . These studies suggest that IHF-induced DNA bending is accompanied by the introduction of a DNA node, DNA unwinding, and/or by some other D NA distortion. An enhanced binding and stability of IHF was observed o n small circular DNA.