Polyelectrolyte theory of charged-ligand binding to nucleic acids

The Poisson-Boltzmann framework provides simple and sound formulae for evaluation of the interactions of polynucleotides with charged ligands. The theory is based on the observation that shape-dependent effects are small. Hence the results for the charged plane may be used as a first approximation for polyelectrolytes. The counterion distribution and the extent of counterion or ligand binding is derived on the basis of a sum-rule for counterion concentrations, combined with the mass-action law. Calculations require no more than a pocket calculator even in the case of mixed-salt solutions. Significant qualitative results are given, and applied to the problems of site-binding and of repressor-DNA interaction.