Predicting 3D Structure, Flexibility, and Stability of RNA Hairpins in Monovalent and Divalent Ion Solutions

Shi, Ya-Zhou
Jin, Lei
Wang, Feng-Hua
Zhu, Xiao-Long
Tan, Zhi-Jie

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Publication date

December 2015

DOI

10.1016/j.bpj.2015.11.006

Publisher

Biophysical Society. Published by Elsevier Inc.

Abstract

AbstractA full understanding of RNA-mediated biology would require the knowledge of three-dimensional (3D) structures, structural flexibility, and stability of RNAs. To predict RNA 3D structures and stability, we have previously proposed a three-bead coarse-grained predictive model with implicit salt/solvent potentials. In this study, we further develop the model by improving the implicit-salt electrostatic potential and including a sequence-dependent coaxial stacking potential to enable the model to simulate RNA 3D structure folding in divalent/monovalent ion solutions. The model presented here can predict 3D structures of RNA hairpins with bulges/internal loops (<77 nucleotides) from their sequences at the corresponding experimental ion c...