Chromomycin A3 (CHR) binding to the duplex d(CAAGTCTGGCCATCAGTC). d(GACTGATGGCCAGACTTG) has been studied using quantitative footprinting methods. Previous NMR studies indicated CHR binds as a dimer in the minor groove. Analysis of autoradiographic spot intensities derived from DNase I cleavage of the 18-mer in the presence of various amounts of CHR revealed that the drug binds as a dimer to the sequence 5ʹ-TGGCCA-3ʹ,3ʹ-ACCGGT-5'in the 18-mer with a binding constant of (2.7 ± 1.4) X 107 M−1. Footprinting and fluorescence data indicate that the dimerization constant for the drug in solution is ~ 105 M−1. Since it has been suggested that CHR binding alters DNA to the A configuration, quantitative footprinting studies using dimethyl sulfate, which alkylates at N-7 of guanine in the major groove, were also carried out. Apparently, any drug-induced alteration in DNA structure does not affect cleavage by DMS enough to be observed by these experiments.
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