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

Analysis of protein binding to receptor-doped lipid monolayers by Monte Carlo simulation

This paper presents a Monte Carlo simulation (MCS) method for estimating the parameters that characterize ligand-receptor binding directly from experimentally derived binding isotherms. Binding parameters are estimated by incorporating an MCS algorithm for ligand binding to a two-dimensional receptor array into a nonlinear regression program. The MCS method was tested by analyzing experimental isotherms of avidin binding to biotinylated lipid in Langmuir-Blodgett (LB) monolayers. The MCS-derived cooperativity coefficients and intrinsic association constants for avidin-biotin binding to LB films are correlated strongly (R2 > 0.93) with the binding parameters determined from the same experimental data by a thermodynamic equilibrium binding model (Zhao et al. 1993. Langmuir. 9:3166-3173). This result shows MCS to be an accurate and potentially more versatile method for characterizing biomolecular interactions at surfaces.

Fluorescence anisotropy decay of ethidium bromide bound to nucleosomal core particles

We have measured the fluorescence anisotropy decay of ethidium bromide bound to nucleosomal core particles (145 DNA base pairs) for very small values of the binding ratio (0.0005 less than or equal to r less than or equal to 0.01). For r = 0.0005 the anisotropy decay could be described by a sum of two exponential functions. The two correlation times theta 1 and theta 2 increase with r until r congruent to 0.0025 and then decrease while the apparent fundamental anisotropy A'0 decreases until r congruent to 0.0025 and then remains constant. The anisotropy decay parameters of the first ethidium molecule bound to a core particle have been obtained by extrapolating theta 1, theta 2 and A'0 to r = 0. We propose the following interpretation of these results. The first bound ethidium molecule is located on a DNA segment linked by its two ends to the histone core. This ethidium molecule follows the torsional motion of the DNA segment. The length of this segment (15 base pairs) was determined by fitting a mathematical expression, derived from the torsional dynamics of DNA, to the extrapolated anisotropy decay. The second ethidium molecule binds to the same DNA segment which explains the decrease of A'0 by fast excitation energy transfer. At the same time theta 1 and theta 2 increase. On binding, a third ethidium molecule breaks the links between the DNA segment and the histone core. This entails the decrease of theta 1 and theta 2.