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

Joseph D. Yesselman, Sarah K. Denny, Namita Bisaria, Daniel Herschlag, William J. Greenleaf, Rhiju Das
doi: https://doi.org/10.1101/341107
Joseph D. Yesselman
1Department of Biochemistry, Stanford University, Stanford, CA 94305, United States
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Sarah K. Denny
2Program in Biophysics, Stanford University, Stanford, CA 94305, United States
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Namita Bisaria
1Department of Biochemistry, Stanford University, Stanford, CA 94305, United States
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Daniel Herschlag
1Department of Biochemistry, Stanford University, Stanford, CA 94305, United States
5Department of Chemistry, Stanford University, Stanford, CA 94305, United States
6Stanford ChEM-H (Chemistry, Engineering, and Medicine for Human Health), Stanford University, Stanford, California 94305, USA
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  • For correspondence: herschla@stanford.edu wjg@stanford.edu rhiju@stanford.edu
William J. Greenleaf
2Program in Biophysics, Stanford University, Stanford, CA 94305, United States
3Department of Genetics, Stanford University, Stanford, CA 94305, United States
4Department of Applied Physics, Stanford University, Stanford, CA 94305, United States
5Department of Chemistry, Stanford University, Stanford, CA 94305, United States
7Chan Zuckerberg Biohub, San Francisco, CA, United States
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  • For correspondence: herschla@stanford.edu wjg@stanford.edu rhiju@stanford.edu
Rhiju Das
1Department of Biochemistry, Stanford University, Stanford, CA 94305, United States
8Department of Physics, Stanford University, Stanford, CA 94305, United States
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  • For correspondence: herschla@stanford.edu wjg@stanford.edu rhiju@stanford.edu
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ABSTRACT

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.

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Posted June 06, 2018.
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RNA tertiary structure energetics predicted by an ensemble model of the RNA double helix
Joseph D. Yesselman, Sarah K. Denny, Namita Bisaria, Daniel Herschlag, William J. Greenleaf, Rhiju Das
bioRxiv 341107; doi: https://doi.org/10.1101/341107
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RNA tertiary structure energetics predicted by an ensemble model of the RNA double helix
Joseph D. Yesselman, Sarah K. Denny, Namita Bisaria, Daniel Herschlag, William J. Greenleaf, Rhiju Das
bioRxiv 341107; doi: https://doi.org/10.1101/341107

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