High-Throughput Investigation of Diverse Junction Elements in RNA Tertiary Folding

Sarah Knight Denny; Namita Bisaria; Joseph David Yesselman; Rhiju Das; Daniel Herschlag; William James Greenleaf

doi:10.1016/j.cell.2018.05.038

High-Throughput Investigation of Diverse Junction Elements in RNA Tertiary Folding

Cell. 2018 Jul 12;174(2):377-390.e20. doi: 10.1016/j.cell.2018.05.038. Epub 2018 Jun 28.

Authors

Sarah Knight Denny¹, Namita Bisaria², Joseph David Yesselman², Rhiju Das³, Daniel Herschlag⁴, William James Greenleaf⁵

Affiliations

¹ Program in Biophysics, Stanford University, Stanford, CA 94305, USA.
² Department of Biochemistry, Stanford University School of Medicine, Stanford, CA 94305, USA.
³ Department of Biochemistry, Stanford University School of Medicine, Stanford, CA 94305, USA; Department of Applied Physics, Stanford University, Stanford, CA 94305, USA.
⁴ Department of Biochemistry, Stanford University School of Medicine, Stanford, CA 94305, USA; Department of Chemistry, Stanford University, Stanford, CA 94305, USA; Department of Chemical Engineering, Stanford University, Stanford, CA 94305, USA; ChEM-H Institute, Stanford University, Stanford, CA 94305, USA. Electronic address: herschla@stanford.edu.
⁵ Program in Biophysics, Stanford University, Stanford, CA 94305, USA; Department of Applied Physics, Stanford University, Stanford, CA 94305, USA; Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA; Chan Zuckerberg Biohub, San Francisco, CA 94158, USA. Electronic address: wjg@stanford.edu.

Abstract

RNAs fold into defined tertiary structures to function in critical biological processes. While quantitative models can predict RNA secondary structure stability, we are still unable to predict the thermodynamic stability of RNA tertiary structure. Here, we probe conformational preferences of diverse RNA two-way junctions to develop a predictive model for the formation of RNA tertiary structure. We quantitatively measured tertiary assembly energetics of >1,000 of RNA junctions inserted in multiple structural scaffolds to generate a "thermodynamic fingerprint" for each junction. Thermodynamic fingerprints enabled comparison of junction conformational preferences, revealing principles for how sequence influences 3-dimensional conformations. Utilizing fingerprints of junctions with known crystal structures, we generated ensembles for related junctions that predicted their thermodynamic effects on assembly formation. This work reveals sequence-structure-energetic relationships in RNA, demonstrates the capacity for diverse compensation strategies within tertiary structures, and provides a path to quantitative modeling of RNA folding energetics based on "ensemble modularity."

Keywords: High-throughput biophysics; RNA folding; RNA structure; RNA tertiary structure; nucleic acid thermodynamics.

Publication types

Research Support, N.I.H., Extramural
Research Support, Non-U.S. Gov't
Research Support, U.S. Gov't, Non-P.H.S.

MeSH terms

Base Pair Mismatch
Gene Library
Nucleic Acid Conformation
Photobleaching
RNA / chemistry
RNA / metabolism*
RNA Folding
RNA Stability
Thermodynamics

Substances

RNA

Abstract

Publication types

MeSH terms

Substances

Grants and funding