RNA tertiary structure energetics predicted by an ensemble model of the RNA double helix

Over 50% of residues within functional structured RNAs are base-paired in Watson-Crick helices, but it is not fully understood how these helices geometric preferences and flexibility might influence RNA tertiary structure. Here, we show experimentally and computationally that the ensemble fluctuations of RNA helices substantially impact RNA tertiary structure stability. We updated a model for the conformational ensemble of the RNA helix using crystallographic structures of Watson-Crick base pair steps. To test this model, we made blind predictions of the thermodynamic stability of >1500 tertiary assemblies with differing helical sequences and compared calculations to independent measurements from a high-throughput experimental platform. The blind predictions accounted for thermodynamic effects from changing helix sequence and length with unexpectedly tight accuracies (RMSD of 0.34 and 0.77 kcal/mol, respectively). These comparisons lead to a detailed picture of how RNA base pair steps fluctuate within complex assemblies and suggest a new route toward predicting RNA tertiary structure formation and energetics.