Ions as regulators of protein-nucleic acid interactions in vitro and in vivo

The key feature of the kinetics and equilibria of both specific and non-specific noncovalent interactions of proteins with nucleic acids is their sensitivity to the details of the ionic environment. Investigation of the effects of ion concentrations provides detailed and otherwise unobtainable information about the thermodynamics and mechanisms of these interactions. We discuss the molecular and thermodynamic basis of the contribution to these ion effects from electrolyte-nucleic acid interactions, and demonstrate that a simple ion exchange formalism, involving the stoichiometric participation of individual ions, is the appropriate basis for interpreting these profound effects at a thermodynamic level. Since the in vivo ionic environment is both complex and variable, we propose that variations in intracellular concentrations of individual ions play both global and specific roles in the control of the protein-nucleic acid interactions responsible for nucleoprotein structure and gene expression.