RNA is highly sensitive to the ionic environment due to its negative charge, and typically requires Mg2+ to form compact structures. Consequently, Mg2+ is crucial for the structure and function of RNA systems, and has a profound effect on their stability and kinetics. This thesis describes the development of simplified models incorporating ionic and electrostatic effects that can provide detailed insight into the functional dynamics of RNA.
In the first part, we characterize Mg2+-RNA interactions in long explicit solvent simulations of the SAM-I riboswitch. We find the majority of associated Mg2+ ions are coordinated with the RNA via outer sphere contacts, challenging the previous paradigm of a few chelated ions surrounded by a continuum of diffuse ions. The coupling to RNA dynamics, slowed diffusion, and distributions of the outer-sphere layer of Mg2+ are explored.
In the second part, we design models of the Mg2+ dependence of the RNA free energy landscape informed by the explicit solvent results. Two electrostatic models are added to a structure-based model of RNA, which captures the energetic drive toward a native structure that many RNA systems possess. The models are tested against experimental measurements of the excess Mg2+ associated with the RNA, Γ2+, because Γ2+ is directly related to the Mg2+-RNA interaction free energy. The first model assumes every Mg2+ ion drives off two condensed K+ ions, and rescales the RNA charge by the remaining amount of condensed KCl. The model shows good agreement with experimental measurements of Γ2+ for the adenine riboswitch, but contains one system specific fitting parameter and thus is not transferable. The second model extends Manning condensation to deal with arbitrary RNA conformations, non-limiting KCl concentrations, and the ion inaccessible volume of RNA. The excellent agreement with experiment for several systems and a wide range of ionic concentrations demonstrates the model captures the ionic dependence of the
RNA free energy landscape.