Quantitative footprinting analysis of the chromomycin A3--DNA interaction.
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) x 10(7) M-1. Footprinting and fluorescence data indicate that the dimerization constant for the drug in solution is approximately 10(5) 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.
Stankus
A
A
Department of Chemistry, Syracuse University, New York 13244-4100.
Goodisman
J
J
Dabrowiak
J C
JC
D001482:Base Composition; D001483:Base Sequence; D001665:Binding Sites; D014128:Chromomycin A3 / Q000737:chemistry*; D004247:DNA / Q000737:chemistry*; D007202:Indicators and Reagents; D007700:Kinetics; D008433:Mathematics; D008969:Molecular Sequence Data; D009838:Oligodeoxyribonucleotides / Q000737:chemistry*
D007202:Indicators and Reagents; D009838:Oligodeoxyribonucleotides; D004247:DNA; D014128:Chromomycin A3