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Nucleic Acids Research, 1989, Vol. 17, No. 14 5447-5460
© 1989

MOLECULAR BIOLOGY

High resolution hydroxyi radical footprinting of the binding of mithramydn and related antibiotics to DNA

Benjamin M.G. Cons and Keith R. Fox

Department of Physiology and Pharmacology, University of Southampton, Bassett Crescent East Southampton SO9 3TU, UK

To whom correspondence should be addressed

Received May 19, 1989. Accepted June 19, 1989.

The preferred binding sites for mithramycin on three different DNA fragments have been determined by hydroxyi radical footprinting. Sequences which appear as one long protected region using DNAase I as a footprinting probe are resolved into several discrete binding domains. Each drug molecule protects three bases from radical attack, though adjacent regions show attenuated cleavage. Mithramycin and the other related compounds induce similar footprinting patterns and appear to recognise GC rich regions with a preference for those containing the dinucleotide step GpG. The ability of each such site to bind the drug depends on the sequence environment in which it is located. The data are consistent with mithramycin binding to the DNA minor groove.


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