Binding of daunomycin to calf thymus nucleosomes

Abstract

We report equilibrium, hydrodynamic, and electric dichroism studies of the complex of daunomycin with H1-depleted 175 base pair nucleosomes, along with some comparative data for ethidium. In contrast to ethidium, daunomycin binding to nucleosomes is strongly reduced relative to the affinity for free DNA. The salt concentration dependence of the binding constant indicates that approximately one Na+ ion is released from both nucleosomes and free DNA upon daunomycin binding. The early melting transition of nucleosomes is preferentially stabilized by low levels of both drugs, but more markedly by ethidium. Ethidium also stabilizes the second nucleosome melting transition, but daunomycin barely does so. Dichroism and rotational relaxation time measurements indicate that daunomycin unfolds nucleosomes in a manner analogous to the influence of ethidium, although about twice as much daunomycin as ethidium is required complete the unfolding process. The data support an unfold structure in which the nucleosome elongates along the DNA superhelical axis. Levels of daunomycin greater than about 0.15 per DNA base pair promote nucleosome aggregation. To relate our results to the activity of daunomycin as an antitumor agent, we propose that the drug, because of its special intercalation geometry, strongly prefers free DNA regions over the bent helices found in nucleosomes and chromatin. The result of this preference should be an increased local concentration of the drug in the genetically active regions of nuclear DNA in which nucleosomal structure is less prevalent. Presumably the abundance of such regions in tumor cells makes them especially sensitive to daunomycin.