Dynamic effects of the spine of hydrated magnesium on viral RNA pseudoknot structure

In the cellular environment, a viral RNA Pseudoknot (PK) structure is responsive to its prevailing ion atmosphere created by a mixture of monovalent and divalent cations. We investigate the influence of such a mixed-salt environment on RNA-PK structure at an atomic resolution through three sets of 1.5 μs explicit solvent molecular dynamics (MD) simulations and also by building a dynamic counterion-condensation (DCC) model at varying divalent Mg 2+ concentrations. The DCC model includes explicit interaction of the ligand and adjacent chelated Mg 2+ by extending the recently developed generalized Manning condensation model. Its implementation within an all-atom structure-based molecular dynamics framework bolsters its opportunity to explore large-length scale and long-timescale phenomena associated with complex RNA systems immersed in its dynamic ion environment. In the present case of RNA-PK, both explicit MD and DCC simulations reveal a spine of hydrated-Mg 2+ to induce stem-I and stem-II closure where the minor groove between these stems is akin to breathing. Mg 2+ mediated minor-groove narrowing is coupled with local base-flipping dynamics of a base triple and quadruple, changing the stem structure of such RNA. Contrary to the conversational view of the indispensable need for Mg 2+ for the tertiary structure of RNA, the study warns about the plausible detrimental effect of specific Mg 2+ -phosphate interactions on the RNA-PK structure beyond a certain concentration of Mg 2+ . Minor groove narrowing in a viral RNA pseudoknot is induced by a spine of hydrated-Mg 2+ at high Mg 2+ concentration.