Site-specific topoisomerase I-mediated DNA cleavage induced by nogalamycin: A potential role of ligand-induced DNA bending at a distal site

Many DNA binding Ligands (e.g., nogalamycin, actinomycin D, terbenzimidazol es, indolo-carbazoles, nitidine, and coralyne) and various types of DNA les ions (e.g., UV dimers, DNA mismatches, and abasic sites) are known to stimu late topoisomerase I-mediated DNA cleavage. However, the mechanism(s) by wh ich these covalent and noncovalent DNA interactions stimulate topoisomerase I-mediated DNA cleavage remains unclear. Using nogalamycin as a model, we have studied the mechanism of ligand-induced topoisomerase I-mediated DNA c leavage. We show by both mutational and DNA footprinting analyses that the binding of nogalamycin to an upstream site (from position -6 to -3) can ind uce highly specific topoisomerase I-mediated DNA cleavage. Substitution of this nogalamycin binding site with a DNA bending sequence (A(5)) stimulated topoisomerase I-mediated DNA at the same site in the absence of nogalamyci n. Replacement of the A(5) sequence with a disrupted DNA bending sequence ( A(2)-TA(2)) significantly reduced the level of topoisomerase I-mediated DNA cleavage. These results? together with the known DNA bending property of n ogalamycin, suggest that the nogalamycin-DNA complex may provide a DNA stru ctural bend to stimulate topoisomerase I-mediated DNA cleavage.