Binding of daunomycin to calf thymus nucleosomes

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Abstract
Equilibrium, hydrodynamic and electric dichroism studies of the complex of daunomycin with H1-depleted 175 base pair nucleosomes are reported, 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 .apprx. 1 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 2nd 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 to complete the unfolding process. The data support an unfolded structure in which the nucleosome elongates along the DNA superhelical axis. Levels of daunomycin > .apprx. 0.15/DNA base pair promote nucleosome aggregation. To relate these results to the activity of daunomycin as an antitumor agent, it is proposed that the drug, because of its special intercalation geometry, strongly prefers free DNA regions over the bent helices found in nucleosomes and chromatin. This preference should result in 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 [vertebrate] tumor cells makes them especially sensitive to daunomycin.