A variation of affinity capillary electrophoresis, called the Replacement Ion (RI) method, has been developed to measure the binding of monovalent cations to random sequence, double-stranded (ds) DNA. In this method, the ionic strength is kept constant by gradually replacing a non-binding ion in the solution with a binding ion, and measuring the mobility of binding and non-binding analytes as a function of binding ion concentration. The binding of monovalent cations to DNA and other polynucleotides has been studied for many years. Early free boundary electrophoresis and conductivity studies (1-3) showed that the affinity of cations for calf thymus DNA decreases in the order Li + > Na + > K + ≫ tetramethylammonium (TMA + ). Competitive dialysis measurements (4) showed that Li + , Na + , K + , Cs + and tetrabutylammonium (TBA + ) ions bind to double-stranded (ds) DNA in a sequence-independent manner, while TMA + and tetraethylammonium (TEA + ) ions are