STRUCTURAL BASIS FOR THE SEQUENCE-SPECIFIC DNA STRAND CLEAVAGE BY THEENEDIYNE NEOCARZINOSTATIN CHROMOPHORE - STRUCTURE OF THE POST-ACTIVATED CHROMOPHORE DNA COMPLEX

Neocarzinostatin chromophore (NCS chrom) belongs to a family of highly potent enediyne antitumor antibiotics which bind to specific DNA sequ ences and cause single- and/or double-strand lesions. NCS chrom-DNA co mplexes have eluded structural studies since the native form of the dr ug is extremely labile in aqueous conditions. We report the three-dime nsional structure of the stable glutathione post-activated NCS chrom ( NCSi-glu)-DNA complex [NCSi-glu-d(GGAGCGC).d(GCGCTCC)] using NMR and d istance geometry-molecular dynamics simulation methods, NCSi-glu inter acts with the GCTC tetranucleotide on one strand and with the AGC trin ucleotide on the other strand through the unique intercalation at the 5'-CT/5'-AG step and minor groove binding. The DNA-drug complex exhibi ts an extended, unwound V-shaped intercalation site and wider and shal lower grooves than the free DNA duplex. The structure of the complex m anifests specific van der Waals interactions and H-bond formation betw een the carbohydrate moiety and a specific DNA sugar/phosphate. Promin ent among those are the contacts of the NCSi-glu residues with the fun ctional groups in the minor groove that are characteristic of individu al DNA bases. These results provide a structural model for understandi ng the sequence specificity of the single- and double-strand cleavage at the AGC and related sites by the enediyne NCS chrom.