National Academy of Sciences, Proceedings of the National Academy of Sciences, 24(113), p. 6665-6670, 2016
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Significance We report a multistate folding free-energy landscape for a hyperstable RNA tetraloop obtained from high-performance molecular dynamic simulations under multiple temperature and pressure conditions. These studies advance previous successes of de novo folding of RNA tetraloops and our understanding of the folded landscape of basic RNA motifs. In addition to the canonical A-RNA conformation, our analysis describes de novo folding of a left-handed Z-RNA conformation and the formation of a purine Triplet, each showing differential stabilization as a function of temperature and pressure. These results provide important insights into the ability of all-atom RNA force fields to describe the conformational heterogeneity of the most basic RNA secondary structures and represent a significant advancement in the utility of RNA molecular dynamics for describing RNA thermodynamics.