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Research demonstrates that the two ring systems of neocarzinostatin chromophore mimics are arranged closer to each other in the DNA bulge binding pocket and this arrangement has mechanistic implications for the bulge-specific cleavage reaction.

The base-catalyzed thiol-independent cleavage reaction of neocarzinostin chromophore (NCS) has been characterized using circular ss phage DNAs and long fragment of ss DNA as substrates. The results showed that compared to DNAs, RNAs with the same sequences and sites were undamaged by the NCS chrom under the same reaction conditions. The nonreactivity of RNA is found to be related to a much lower binding affinity of the cleaving species for RNA sites.

Examination of the efficiency of three drug products, derived from the enediyne anticancer antibiotic neocarzinostatin chromophore, to bind with oligonucleotides containing a bulge reveals that one of the three drug products, which significantly resembles the biradical intermediate in the cleavage reaction, generates a stable complex with the bulged DNA. Cleavage reaction is competitively inhibited by this complexation. The influence of pH on the binding reveals that cleavage reaction is not influenced by the charge on the amino group of the sugar.

NMR and distance geometry-molecular dynamics simulation studies of the three-dimensional structure of the stable glutathione post-activated neocarzinostatin chromophore (NCS chrom) (NCSi-glu)-DNA complex provide structural basis for the sequence-specific DNA strand cleavage by NCS chrom. An intercalation at the 5'-CT 5'-AG step and minor groove binding are involved in the interaction of NCSi-glu with the GCTC tetranucleotide on one strand and with the AGC trinucleotide on the other strand. The DNA-drug complex has an extended, unwound intercalation site and wide grooves and also exhibits van der Waals interactions and H-bond formation between the carbohydrate and a specific DNA sugar phosphate.

Binding stoichiometries found in biochemical systems are obtained by a new method, which incorporates the affinity capillary electrophoresis (ACE). The conditions for a ligand to bind to the receptor protein are determined from the inverted peak in the electropherogram. The inverted peak occurs due to the free ligand when the same concentration of liquid is used in the electrophoresis buffer. The new method is a fast, easy and sensitive technique for determining the ligand to protein binding stoichiometries.

The reactivity properties of [Fesub2sup2+(H2Hbamb)2(N-MeIm)2] and its mixed-valence [Fe2+,Fe3+] unit were analyzed to characterize its catalytic efficiency. The competent binuclear non-heme oxo Fe complexes were capable of catalyzing the oxidation of alkanes, alkenes and sulfides via OIPh. The simple binuclear non-heme iron complex also contained one ferrous center that acted as an efficient oxygen-atom transfer catalyst to the donor molecule.

Examines the role of postactivated neocarzinostatin chromophore (NCS-chrom) in the formation of DNA bulge structure. Identification on the DNA chain cleavage properties of NCS-chrom; Occurrence of bulge-DNA sequences; Mechanisms involved in the formation of binding and cleaving species.