Does Cation Size Affect Occupancy and Electrostatic Screening of the Nucleic Acid Ion Atmosphere?

Abstract

Electrostatics are central to all aspects of nucleic acid behavior, including their folding, condensation, and binding to other molecules, and the energetics of these processes are profoundly influenced by the ion atmosphere that surrounds nucleic acids. Given the highly complex and dynamic nature of the ion atmosphere, understanding its properties and effects will require synergy between computational modeling and experiment. Prior computational models and experiments suggest that cation occupancy in the ion atmosphere depends on the size of the cation. However, the computational models have not been independently tested, and the experimentally observed effects were small. Here, we evaluate a computational model of ion size effects by experimentally testing a blind prediction made from that model, and we present additional experimental results that extend our understanding of the ion atmosphere. Giambasu et al. developed and implemented a three-dimensional reference interaction site (3D-RISM) model for monovalent cations surrounding DNA and RNA helices, and this model predicts that Na+ would outcompete Cs+ by 1.8–2.1-fold; i.e., with Cs+ in 2-fold excess of Na+ the ion atmosphere would contain an equal number of each cation (Nucleic Acids Res.2015, 43, 8405). However, our ion counting experiments indicate that there is no significant preference for Na+ over Cs+. There is an ∼25% preferential occupancy of Li+ over larger cations in the ion atmosphere but, counter to general expectations from existing models, no size dependence for the other alkali metal ions. Further, we followed the folding of the P4–P6 RNA and showed that differences in folding with different alkali metal ions observed at high concentration arise from cation–anion interactions and not cation size effects. Overall, our results provide a critical test of a computational prediction, fundamental information about ion atmosphere properties, and parameters that will aid in the development of next-generation nucleic acid computational models.

Determination of Ion Atmosphere Effects on the Nucleic Acid Electrostatic Potential and Ligand Association Using AH+·C Wobble Formation in Double-Stranded DNA

“…64 We tested this expectation with Li + and Cs + for the K + effect and with Ba 2+ for the Mg 2+ effect and observed consistent effects for cations of the same valence (Figure S7). These results support that proton association with 24bp AC is minimally influenced by specific metal ion binding and that this system is suitable for testing ion atmosphere effects.…”

Quantitative tests of a reconstitution model for RNA folding thermodynamics and kinetics

“…2B). Prior work demonstrated equivalent P4-P6 folding in Mg 2+ and Ba 2+ upon ablation of the MC, and independent studies demonstrated equal ion atmosphere occupancy for Mg 2+ and Ba 2+ surrounding a nucleic acid (21,45). Thus, we could change the electrostatic environment without complications from site-specific metal ion binding and formation of an additional tertiary contact ( (21) concentrations (Fig.…”

Predicting Ion Effects in an RNA Conformational Equilibrium

“…In order to make direct comparisons between the two models, we also show the prediction data in Table 1 for a 24-bp B-DNA, for which the experimental data is available. 100 Indeed, the relative error Δ E (see table 1) shows that the PCTBI is (slightly) better than MCTBI. Third, f K + of RNA-protein complex predicted by the PCTBI model is lower than that predicted by the original MCTBI model [see Fig.…”

“…31, 100 The fluorescence titration measurements take advantage of a fluorescent dye for an ion species such as Mg 2+ to count the bound ions. Therefore, the method focuses on single ion species in each measurement.…”

“…100. ** The relative error Δ E = |( f pre − f exp ) /f exp |, where f pre and f exp are the prediction and experiment data. …”