A NONCOVALENT BINDING-TRANSLOCATION MECHANISM FOR SITE-SPECIFIC CC-1065-DNA RECOGNITION

The molecular strategy by which small organic compounds recognise spec ific DNA sequences is of primary importance for rational drug design. CC-1065 is a potent alkylating agent that binds covalently to N3 of ad enine and lies in the minor groove of double-stranded DNA. Its reactio n with DNA occurs in a site-specific manner, with a preference for A . T-rich nucleotide sequences. In the present study, we developed a dru g translocation assay to investigate the mechanism underlying this seq uence selectivity. After exposure of plasmid DNA to saturating amounts of CC-1065, we observed that nearly 70% of plasmid-bound CC-1065 mole cules formed stable, but noncovalent, complexes with DNA. These noncov alently bound drug molecules resisted purification by ethanol precipit ation, dialysis, and sucrose gradient centrifugation, but retained the ability to translocate to DNA fragments containing a single high-affi nity site for alkylation. This combination of noncovalent binding inte ractions and drug translocation provides a mechanism by which CC-1065 may locate specific alkylation sites in DNA.