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87 Recent progress in determining RNA 3D structure and dynamics using all-atom molecular dynamics simulations

RNA’s biochemical versatility arises from its ability to form tertiary structures, which are governed by the intrinsic flexibility of single-stranded loops, weak stacking interactions, and non-canonical hydrogen bonding patterns. However, capturing the correct balance between these disparate driving forces with molecular mechanics force-fields has proved to be extremely challenging. In prior work (Chen & Garcia, 2013), we demonstrated that an improved RNA force-field extensively calibrated against experimentally measured properties of mono and di-nucleotides in solution enabled the reversible, de novo folding of three hyperstable RNA tetraloop motifs from the unfolded state. Building upon this initial success, we have further improved the interaction model to better reflect the temperature dependence of base-pair formation. This innovation has enabled us to use all-atom simulations to investigate a diverse array of RNA systems that were previously stymied by forcefield inaccuracies. An overview of work in-progress across a variety of systems will be presented, including aptamer– ligand interactions, chemically modified nucleotides, and RNA-graphene biosensors.