Quantitative footprinting analysis of the chromomycin A3-DNA interaction

Allison Stankus, Jerry Goodisman, James C. Dabrowiak

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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 5′-TGGCCA-3′, 3′-ACCGGT-5′ in the 18-mer with a binding constant of (2.7 ± 1.4) × 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.

Original languageEnglish (US)
Pages (from-to)9310-9318
Number of pages9
Issue number38
StatePublished - 1992


ASJC Scopus subject areas

  • Biochemistry

Cite this

Stankus, A., Goodisman, J., & Dabrowiak, J. C. (1992). Quantitative footprinting analysis of the chromomycin A3-DNA interaction. Biochemistry, 31(38), 9310-9318.