Interaction of calicheamicin gamma(I)(1) and its related carbohydrates with DNA-protein complexes

We report studies of the contribution of DNA structure, holding the sequenc e constant, to the affinity of calicheamicin gamma(1)(I) and its aryltetras accharide moiety for DNA. We used polynucleotide chains as models of known protein-binding sequences [the catabolite activator protein (CAP) consensus sequence, AP-1 and cAMP response element (CRE) sites] in their free and pr otein-bound forms. The proteins were selected to provide examples in which the minor-groove binding site for the carbohydrate is (CAP) or is not (GCN4 ) covered by the protein. Additionally, peptides related to the GCN4 and CR EB families, which have different bending effects on their DNA-binding site s, were used. We observe that proteins of the CREB class, which induce a te ndency to bend toward the minor groove at the center of the site, inhibit d rug-cleavage sites located at the center of the free AP-1 or CRE DNA sites. In the case of GCN4, which does not induce DNA bending, there is no effect on calicheamicin cleavage of the CRE site, but we observe a GCN4-induced r earrangement of the cutting pattern in the AP-1 site. This effect may arise from either a subtle local conformational rearrangement not accompanied by bending or a localized reduction in DNA flexibility. Whereas GCN4 binding is not inhibited by the calicheamicin aryltetrasaccharide, binding of CAP t o its DNA target is significantly inhibited, and calicheamicin cutting of D NA at the center of the CAP-DNA complex site is strongly reduced by protein binding. This result probably reflects steric inhibition of drug binding b y the protein.