| Abstract
| - Calicheamicin is a hydrophobic enediyne antibiotic that binds noncovalently to DNA andcauses sequence-selective oxidation of deoxyribose. While the drug makes several base contacts alongthe minor groove, the diversity of binding-site sequences and the effects of DNA conformation oncalicheamicin-induced DNA cleavage suggest that sequence recognition per se is not the primarydeterminant of target selection. We now present evidence that calicheamicin bends its DNA targets. Usinga gel mobility assay, we observed that polymers of oligonucleotide constructs containing AGGA andACAA binding sites for calicheamicin did not possess intrinsic curvature. Binding of calicheamicin ε, thearomatized form of the parent calicheamicin γ1I, to oligonucleotide constructs containing binding sites inphase with the helical repeat caused a shift to smaller circle sizes in T4 ligase-mediated circle formationassays, with a much smaller shift observed with constructs containing out-of-phase binding sites. It wasalso observed that binding of calicheamicin ε to a 273 bp construct with phased binding sites caused anincrease in the molar cyclization factor, J, from 8 × 10-8 to 9 × 10-6 M. These results are consistentwith DNA bending as part of an induced-fit mechanism of DNA target recognition and with the hypothesisthat the preferred targets of calicheamicin, the 3‘ ends of oligopurine tracts, are characterized by uniqueconformational properties.
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