Direct measurement of sodium ion release from DNA on binding of cationic ligands

Abstract

This chapter reviews that DNA is a polyelectrolyte with a high charge density along the duplex chain, there are important thermodynamic issues associated with long-range electrostatic interactions between associated counterions or cationic ligands and the DNA. The overall conformation and binding characteristics are thus linked to counterion association, and thus binding equilibria, particularly with cationic ligands, is dependent on counterion-exchange processes. Information about the exchange of sodium ion as interaction with other cationic ligands occurs is thus a vital link to understanding some of the thermodynamic consequences of the long-range interactions between the polyelectrolyte and ligand. The chapter presents the results that the potentiometric determination of sodium ion can provide useful information about the nature of cationic ligand binding to DNA. The counterion-exchange process can be quantified and the simple ion-exchange equilibrium model is confirmed for cases for which there is little or no hydrophobic interaction. The approach to studying ion release from DNA has potential for providing information about the linkage between sodium ion binding and the binding of other cationic ligands, including proteins, cationic peptides, or positively charged drugs. The method could also be of value in examining the role of ion condensation in the stability of various conformational forms of DNA, including triple helical complexes.