title: Predicting 3D Structure, Flexibility, and Stability of RNA Hairpins in Monovalent and Divalent Ion Solutions.
abstract: 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 (<77 nucleotides) from their sequences at the corresponding experimental ion conditions with an overall improved accuracy compared to the experimental data; the model also makes reliable predictions for the flexibility of RNA hairpins with bulge loops of different lengths at several divalent/monovalent ion conditions. In addition, the model successfully predicts the stability of RNA hairpins with various loops/stems in divalent/monovalent ion solutions.
authors.affiliation: Department of Physics and Key Laboratory of Artificial Micro- and Nano-structures of the Ministry of Education, School of Physics and Technology, Wuhan University, Wuhan, China.
authors.forename: Ya-Zhou
authors.initials: YZ
authors.lastname: Shi
authors.affiliation: Department of Physics and Key Laboratory of Artificial Micro- and Nano-structures of the Ministry of Education, School of Physics and Technology, Wuhan University, Wuhan, China.
authors.forename: Lei
authors.initials: L
authors.lastname: Jin
authors.affiliation: Engineering Training Center, Jianghan University, Wuhan, China.
authors.forename: Feng-Hua
authors.initials: FH
authors.lastname: Wang
authors.affiliation: Department of Physics, School of Physics and Information Engineering, Jianghan University, Wuhan, China.
authors.forename: Xiao-Long
authors.initials: XL
authors.lastname: Zhu
authors.affiliation: Department of Physics and Key Laboratory of Artificial Micro- and Nano-structures of the Ministry of Education, School of Physics and Technology, Wuhan University, Wuhan, China. Electronic address: zjtan@whu.edu.cn.
authors.forename: Zhi-Jie
authors.initials: ZJ
authors.lastname: Tan
mesh_terms: D001483:Base Sequence; D002413:Cations, Divalent / Q000737:chemistry* / Q000494:pharmacology*; D055029:Inverted Repeat Sequences / Q000187:drug effects; D008958:Models, Molecular; D009690:Nucleic Acid Conformation / Q000187:drug effects*; D012313:RNA / Q000737:chemistry* / Q000235:genetics; D059370:RNA Folding / Q000187:drug effects; D020871:RNA Stability / Q000187:drug effects*; D012965:Sodium Chloride / Q000737:chemistry / Q000494:pharmacology; D012996:Solutions; D055672:Static Electricity
chemical_list: D002413:Cations, Divalent; D012996:Solutions; D012965:Sodium Chloride; D012313:RNA