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Nucleic Acids Research, 1989, Vol. 17, No. 14 5809
© 1989

CHEMISTRY

DNA microstructural requirements for neocarzinostatin chromophore-induced direct strand cleavage

Seock Ho Lee, Jeanne O. Thivierge and Irving H. Goldberg

Department of Biological Chemistry and Molecular Pharmacology, harvard medical School Boston, MA 02115, USA

Received February 16, 1988. Revised June 22, 1989. Accepted June 22, 1989.

The microstructural requirements for optimal interaction of neocarzinostatin chromophore (NCS–C) with DNA have been investigated using a series of hexadeoxyribonucleotides with modified bases such as O6–methyl G(MeG), I, 5–methyl C (MeC), U, or 5–Bromo U (BrU) at specific sites in its preferred trinucleotide 5‘GNaNb3‘:5‘Na‘Nb‘C3‘(Na = A, C, or T).Results show that MeG:C and G:MeG in place of G:C improve direct strand cleavage at the target Nb (Nb = T > A ≥ C > G), whereas MeC:G and C:MeG in place of Na:Na‘ hinder cleavage. The optimal base target at Nb appears to be determined by its ability to form T:A type base pairing instead of C:G type. The observed differences in DNA strand cleavage patterns can be rationalized by induced changes in target site structure and are compatible with a model for NCS–C:DNA interaction in which the naphthoate moiety intercalates between 5‘G N a3‘, and the activated tetrahydro–s–indacene, lying in the minor groove, abstracts a hydrogen atom from C–5‘ of Nb.


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