Quantifying the Ion Atmosphere of Unfolded, Single-Stranded Nucleic Acids

Abstract

Secondary structure formation in nucleic acids (NAs) is strongly dependent on the local ion atmosphere, which screens the negative charge of the NA and reduces self-repulsion. Consideration of such interactions must include both the folded and unfolded states, as both contribute to the free energy of folding. The interaction of ions with folded, double-helical NAs has been studied with a variety of experimental techniques and, at the level of monovalent ions, is well captured by solutions to the Poisson-Boltzmann equation. However, comparatively little is known, experimentally or theoretically, about ion interactions with the unfolded, random-coil state.Here, we report on the ion atmosphere of unfolded, single-stranded DNA and RNA by measuring the ion excess: the number of cations surrounding the negatively charged macromolecule above the number due to the bulk salt concentration. We used two independent approaches to make these measurements. In one, we took advantage of the existing results for folded NAs and used a single-molecule differential ion counting approach to connect those results to the unfolded state. In the other, we directly measured the ion excess of the unfolded state through equilibrium dialysis read out by atomic emission spectroscopy. The two methods are complementary and give consistent results, which we interpret in light of recent findings on the conformation of flexible polyelectrolytes.