Differential electrophoretic mobility of synthetic DNA motifs and duplex DNA in various counter ions

Abstract

In this work, we analyzed the electrophoretic behavior of a double crossover (DX) DNA motif in various counter ions. The influence of the type and concentration of counter ions on electrophoretic behavior is different for the DX motif compared to a duplex of the same molecular weight. Higher concentrations of divalent ions Mg²⁺ and Ca²⁺ in the gel and running buffer reduce the electrophoretic migration of the DX motif. This effect is less pronounced in the monovalent ion Na⁺ while K⁺ ion did not have any significant effect on the electrophoretic behavior.