Quantitative studies of an RNA duplex electrostatics by ion counting

Abstract

Ribonucleic acids are one of the most charged polyelectrolytes in nature, and understanding of their electrostatics is fundamental to their structure and biological functions. An effective way to characterize the electrostatic field generated by nucleic acids is to quantify interactions between nucleic acids and ions that surround the molecules. These ions form a loosely associated cloud referred as an ion atmosphere. While theoretical and computational studies can describe the ion atmosphere around RNAs, benchmarks are needed to guide the development of these approaches and experiments to-date that read out RNA-ion interaction are limited. Here we present ion counting studies to quantify the number of ions surrounding well-defined model systems of 24-bp RNA and DNA duplexes. We observe that the RNA duplex attracts more cations and expels fewer anions compared to the DNA duplex and the RNA duplex interacts significantly more strongly with the divalent cation Mg 2+ . These experimental results strongly suggest that the RNA duplex generates a stronger electrostatic field than DNA, as is predicted based on the structural differences between their helices. Theoretical calculations using non-linear Poisson-Boltzmann equation give excellent agreement with experiment for monovalent ions but underestimate Mg 2+ -DNA and Mg 2+ -RNA interactions by 20%. These studies provide needed stringent benchmarks to use against other all-atom theoretical models of RNA-ion interactions, interactions that likely must be well accounted for structurally, dynamically, and energetically to confidently model RNA structure, interactions, and function.

Quantifying and visualizing weak interactions between anions and proteins

“…Compared to nucleic acids, the proteins appear to have a weaker ability to accumulate counterions per charge. Whereas ΔN ia (cations)/|n| is 0.80-0.90 for DNA and RNA duplexes at ionic strength < 100 mM (8,12), our NMR data show that ΔN ia (anions)/|n| is 0.56 for the Antp homeodomain and 0.68 for BPTI. The weaker ability to attract counterions is presumably due to the smaller charge density on the molecular surfaces.…”

“…For nucleic acids, ΔN ia (anions) and ΔN ia (cations) have been well studied. Herschlag and coworkers studied the ion atmosphere around various DNA and RNA molecules using ion-counting methods (7,8,12). They showed that the experimental ΔN ia (anions) and ΔN ia (cations) data agreed well with those predicted by the Poisson-Boltzmann equation-based theory.…”

Exploring the role of polymer hydrophobicity in polymer–metal binding thermodynamics

“…We chose the AMOEBA force field because it accounts for electrostatic anisotropy and electronic polarizability effects, [43][44][45] which is key to describing the ion-polymer interaction in solution. [46][47][48][49][50][51] Further, AMOEBA parameters for solvated Eu 3+ have already been developed and validated. 46,52 The simulation data showed greater metal desolvation with increasing polymer hydrophobicity, consistent with our interpretation of ITC data, and previous studies.…”

Dynamics of Ionic Interactions at Protein–Nucleic Acid Interfaces

“…In the 21st century, the physical presence of the ion atmosphere around DNA was confirmed with anomalous small-angle X-ray scattering (ASAXS) using heavy alkali metal ions such as Rb + . 23 − 25 More recently, so-called “ion counting” methods that utilize atomic emission spectroscopy or mass spectrometry were developed for quantitative analysis of the ion atmosphere around DNA, 26 , 27 RNA, 27 − 29 and nucleosomes. 30 The ion-counting methods can provide information about how many cations are condensed in the ion atmosphere and how many anions are excluded from the ion atmosphere.…”

“…Perhaps most importantly, the experiments confirmed that despite lacking solution correlations, the Poisson–Boltzmann approximation can account for the number of condensed cations around DNA or RNA with certain assumptions. 26 , 29 Theoretical predications from 3D RISM were also validated. 27 The ion-counting data also illuminated some theoretical limitations.…”