(346aa) Transition Path Sampling Simulations of Base Flipping in RNA

Base flipping is a key biophysical event involved in recognition of various ligands by nucleic acids. Therefore, the dynamics of spontaneous flipping in/out of a mismatched base in nucleic acids has a significant implication in modifications in DNA/RNA by enzymes. While the mechanisms of base flipping in nucleic acids have been probed using experimental and computational techniques previously, our understanding of molecular scale details of this biophysical event remains limited. Specifically, it remains unclear how neighboring nucleobases, solvent molecules, and ions reorganize to trigger a base flipping event. In this work, we applied transition path sampling methods to overcome limitations of classical molecular dynamics (MD) simulations for studying rare biophysical events and obtained 1000 transition trajectories to describe the base flipping process in a double-stranded ribonucleic acid (RNA) molecule. These trajectories facilitated the selection of key collective variables (CVs) that can distinguish between the inward/outward configurations and provide an optimal reaction coordinate when combined, as tested by applying the likelihood maximization and Bayesian information criterion. The free energy surface and the transition dynamics were then projected along the optimal reaction coordinate, and the rate constant for the base-flipping event was determined.