A noncovalent binding-translocation mechanism for site-specific CC-1065-DNA recognition

The molecular strategy by which small organic compounds recognise specific DNA sequences is of primary importance for rational drug design. CC-1065 is a potent alkylating agent that binds covalently to N3 of adenine and lies in the minor groove of double-stranded DNA. Its reaction with DNA occurs in a site-specific manner, with a preference for A. T-rich nucleotide sequences. In the present study, we developed a drug translocation assay to investigate the mechanism underlying this sequence selectivity. After exposure of plasmid DNA to saturating amounts of CC-1065, we observed that nearly 70% of plasmid-bound CC-1065 molecules formed stable, but noncovalent, complexes with DNA. These noncovalently bound drug molecules resisted purification by ethanol precipitation, dialysis, and sucrose gradient centrifugation, but retained the ability to translocate to DNA fragments containing a single high-affinity site for alkylation. This combination of non-covalent binding interactions and drug translocation provides a mechanism by which CC-1065 may locate specific alkylation sites in DNA.