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Nucleic Acids Research, 1990, Vol. 18, No. 8 1957-1963
© 1990

CHEMISTRY

Echinomycin binding to the sequence CG(AT)nCG alters the structure of the central AT region

Keith R. Fox* and Edwina Kentebe

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

* To whom correspondence should be addressed

Received February 12, 1990. Revised March 20, 1990. Accepted March 20, 1990.

DNA fragments containing the sequence CG(AT)nCG have been used in footprinting experiments to assess the effect of echinomycin, which binds to the CG steps, on the structure of the central AT region. DNAase I normally cuts ApT much better than TpA; in the presence of the drug this preference is retained but cleavage at TpA is enhanced. Changes in cleavage by micrococcal nuclease have also been observed. Echinomycin renders alternate adenines hyperreactive to diethylpyrocarbonate. The results suggest that echinomycin induces structural changes in regions surrounding its binding site and that these can be cooperatively propagated over several turns of the DNA helix.


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