We examined** the interactions between RNA and its ion atmosphere at atomic resolution by carrying out ten 2  explicit solvent molecular dynamics simulationsof the SAM-I aptamer. A notable result is that the population of Mg2+ ions around the RNA exhibits several classes: chelated, outer-sphere, diffuse, and free. We have explicitly determined the excess number of ions around a nucleic acid as a function of varying ion concentrations. This quantity, which is experimentally measurable, is called the preferential interaction coefficient. We show that over eighty percent of the excess Mg2+ ions that contribute to preferential interaction coefficient reside in the outer-sphere layer. As the outer-sphere accounts for most of Mg2+ it changes the paradigm of the characteristics of RNA-Mg2+ interactions. ** in collaboration with R. Hayes, J. Noel, P. Whitford, S. Hennelly, J. M. Onuchic, and K. Y. Sanbonmatsu. UM acknowledges a John Simon Guggenheim Memorial fellowship.

Magnesium fluctuations modulate RNA dynamics in riboswitch

245th National Meeting (2013)

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