Quantitative studies of an RNA duplex electrostatics by ion counting

Abstract

ABSTRACTRibonucleic 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 Mg2+. 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 Mg2+-DNA and Mg2+-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.