Ion Binding and Electrostatics in Condensed DNA Arrays Probed by Ion Counting Techniques

Abstract

Despite decades of theoretical and experimental research, the mechanism of DNA condensation remains elusive. Numerous models successfully describe this condendsation, including those invoking dynamic counterion fluctuations, salt bridges, static counterion lattices, and models that invoke the underlying DNA geometry, all while presenting vastly different models for ion binding. Here we present new experimental data that quantifies the ions bound to condensed DNA arrays. By measuring the competition between condensing ions and various non-condensing ions we quantify the electrostatic interactions between the DNA and ions. Furthermore, by varying the inter-axial spacing of condensed DNA utilizing crowding agents, we report on the interplay between the packing force of DNA and competitive ion binding. Finally, we present a simple new Ion Binding Model (IBM) that captures much of the observed binding. These data should prove vital in determining the underlying electrostatic mechanisms that drive DNA condensation.