Calorimetric investigation of ethidium and netropsin binding to chicken erythrocyte chromatin

We have investigated the thermodynamic aspects of the ligand binding to chromatin, using isothermal titration calorimetry. Two classical DNA ligands were used: an intercalator, ethidium bromide, and a minor groove binder, netropsin. Stoichiometry, affinity constant, and thermodynamic parameters were determined at various salt concentrations and different temperatures. The effect of ionic strength was analyzed according to the Record theory applied to chromatin. We also compared the binding parameters on naked DNA, H1/H5-depleted chromatin, and chromatin. We demonstrated that the presence of histones on DNA still allows the ligand binding that takes place according to a simple one single-site model. For both ligand types, the thermodynamic driving force is enthalpic and the association is characterized by a somewhat weaker affinity and more scattered ligand distribution than on naked DNA. The ligand affinity is weakly altered by the salt-induced compaction of the chromatin and the binding is accompanied by a release of one counterion per ligand molecule. The temperature-dependent studies revealed the existence of a small heat capacity change associated with ligand binding to chromatin, together with an enthalpy-entropy compensation that maintains the free energy constant over the investigated temperature range.