An interpretation of the binding of ethidium bromide to the core nucleosome, based on Monte Carlo calculations

We propose a model of ethidium binding to the nucleosome core particle. Ligand molecules are assumed to intercalate between the base pairs of the DNA core particle. The DNA is assumed to be divided into a finite number of segments. In the native core particle, one segment only is accessible to ethidium. The other DNA segments become progressively accessible when the binding ratio is increased. The binding isotherm resulting from such a model has been determined by a Monte Carlo method. The computed Scatchard plot exhibits the shape characteristic of a cooperative process. By fitting this curve with the experimental data of Erard et al. [1] one finds that 130 over the 140 DNA base pairs are accessible to the ethidium binding. The full accessibility of these sites is obtained when 8 or 9 ethidium at least are already bound to the core particle.