Quantitative and Comprehensive Decomposition of the Ion Atmosphere around Nucleic Acids

Abstract

The ion atmosphere around nucleic acids critically affects biological and physical processes such as chromosome packing, RNA folding, and molecular recognition. However, the dynamic nature of the ion atmosphere renders it difficult to characterize. The basic thermodynamic description of this atmosphere, a full accounting of the type and number of associated ions, has remained elusive. Here we provide the first complete accounting of the ion atmosphere, using buffer equilibration and atomic emission spectroscopy (BE-AES) to accurately quantitate the cation association and anion depletion. We have examined the influence of ion size and charge on ion occupancy around simple, well-defined DNA molecules. The relative affinity of monovalent and divalent cations correlates inversely with their size. Divalent cations associate preferentially over monovalent cations; e.g., with Na + in four-fold excess of Mg 2+ (20 vs. 5 mM), the ion atmosphere nevertheless has three-fold more Mg 2+ than Na + . Further, the dicationic polyamine putrescine 2+ does not compete effectively for association relative to divalent metal ions, presumably because of its lower charge density. These and other BE-AES results can be used to evaluate and guide the improvement of electrostatic treatments. As a first step, we compare the BE-AES results to predictions from the widely-used nonlinear Poisson Boltzmann (NLPB) theory and assess the applicability and precision of this theory. In the future, BE-AES in conjunction with improved theoretical models, can be applied to complex binding and folding equilibria of nucleic acids and their complexes, to parse the electrostatic contribution from the overall thermodynamics of important biological processes.

Accurate small and wide angle x-ray scattering profiles from atomic models of proteins and nucleic acids

“…DNA. 30,31 Popular theoretical models include counterion condensation 32,33 or Poisson-Boltzmann (PB) theories, 34,35 although PB results for duplex DNA are in poor agreement with results from dialysis-type experiments. 26 MD simulation can also provide atomic details and in principle can describe the ionic atmosphere with great accuracy.…”

Unwinding RNA's secrets: advances in the biology, physics, and modeling of complex RNAs

“…Further, the contents of the atmosphere have recently been quantitatively dissected, by essentially counting the ions associated with a nucleic acid under a variety of ionic conditions. This technique allows RNA systems to be characterized stoichiometrically in terms of the number of each cation and anion species present in the ion atmosphere [58].…”

“…However, the opposite conclusion has been drawn from fitting RNA folding transitions to PB predictions [70][71][72][73][74]. Ion-counting and SAXS experiments have provided a simple test for these effects and have revealed effects of ion size and valence that are not accounted for by PB theory, with deviations up to an order of magnitude in the systems investigated [58,75]. Advances in theory and simulation are required to account for these discrepancies and obtain accurate electrostatic energies for use in dissecting RNA folding and RNA/protein energetics [76,77].…”

Extracting water and ion distributions from solution x-ray scattering experiments

“…Ion counting via dialysis can provide a quantitative measure of the ionic atmosphere around the solute, but it provides only a total (excess) number, and not any information the shape of the ion cloud. 11,12 The q = 0 limit of small-angle X-ray scattering (SAXS) can provide similar excess counts for both water and ions. 13 Anomalous small angle X-ray scattering (ASAXS) data in principle yield additional information about the extent of perturbations of the ion/water environment, [14][15][16][17] but the ASAXS signal is known to be intertwined with all components in the system, complicating the analysis.…”