Evidence of different binding sites for nogalamycin in DNA revealed by association kinetics.

The kinetics of association between nogalamycin and DNA have been measured by stopped-flow spectrometry. With a naturally occurring DNA (calf thymus) the reaction profile requires not less than three exponentials for its complete description. By contrast, binding to poly(dA-dT) is fully described by two exponentials which correspond to the two faster components seen with the natural DNA, whereas binding to poly(dG-dC) is a single exponential process whose time constant is about the same as the slowest component measured with calf thymus DNA. In all cases the amplitude of each component in the decay varies considerably with polynucleotide concentration. The results are consistent with a model in which the antibiotic is only able to bind directly to regions of the DNA which are transiently perturbed, probably non-basepaired. As a result, the antibiotic interacts much faster with AT-rich rather than GC-rich DNA sequences, which may provide a basis for its apparent sequence selectivity.