The design, construction, and characterization of a site-directed CC-1065-N3-adenine adduct in a 117 base pair segment of M13mpI DNA are described. CC-1065 is an extremely potent antitumor antibiotic produced by Streptomyces zelensis. Previous studies have demonstrated that the cyclopropyl ring of CC-1065 reacts quite specifically with N3 of adenine in double-stranded DNA to form a CC-1065-DNA adduct. Following alkylation, the drug molecule lies snugly within the minor groove of DNA, overlapping with five base pairs for which a marked sequence preference exists [Hurley, L. H., Reynolds, V. R., Swenson, D. H., Petzold, G. L., & Scahill, T. A. (1984) Science (Washington, D.C.) 226, 843–844]. On the basis of the unique characteristics of the reaction of CC-1065 with DNA and the structure of the resulting DNA adduct, we have designed a general strategy to construct a site-directed CC-1065-DNA adduct in a restriction fragment. The presence of unique Alul and HaeIII restriction enzymes sites on each side of a high-affinity CC-1065 binding sequence (5'-GATTA) permitted the preparation of a partial duplex DNA molecule containing the CC-1065 binding sequence in the duplex DNA region. Since CC-1065 only binds to duplex DNA, potential CC-1065 binding sequences in the long single-stranded regions were protected from drug binding during the construction process. After purification of the CC-1065 partial duplex DNA adduct by differential melting of the modified and unmodified partial duplex DNA, DNA polymerase I was used to generate the full duplex DNA molecule, which contained a single site-directed CC-1065-N3-adenine adduct at adenine 6229 of the 117 base pair MspI-BstNI DNA restriction fragment of the Escherichia coli lac insert of M13mpl DNA. A CC-1065 thermal strand scission assay was used to confirm the unique binding site on the covalently modified strand. Methidiumpropyl-EDTA-iron(II) [MPE-Fe(II)] digestions were used to locate the binding site and the orientation of CC-1065 in the minor groove of DNA. MPE-Fe(II) footprinting revealed a slight enhancement of digestion on both DNA strands, but just to one side of the CC-1065-DNA adduct.
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