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

A 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/solven...

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Bibliographic Details
Published in:Biophysical journal 2015-12, Vol.109 (12), p.2654-2665
Main Authors: Shi, Ya-Zhou, Jin, Lei, Wang, Feng-Hua, Zhu, Xiao-Long, Tan, Zhi-Jie
Format: Article
Language:English
Subjects:
Base Sequence
Biophysics
Cations, Divalent - chemistry
Cations, Divalent - pharmacology
Electrostatics
Inverted Repeat Sequences - drug effects
Ions
Models, Molecular
Nucleic Acid Conformation - drug effects
Proteins and Nucleic Acids
Ribonucleic acid
RNA
RNA - chemistry
RNA - genetics
RNA Folding - drug effects
RNA Stability - drug effects
Sodium Chloride - chemistry
Sodium Chloride - pharmacology
Solutions
Static Electricity
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Summary:A 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 (
ISSN:0006-3495
1542-0086
DOI:10.1016/j.bpj.2015.11.006