title: Theory and Modeling of RNA Structure and Interactions with Metal Ions and Small Molecules.
abstract: In addition to continuous rapid progress in RNA structure determination, probing, and biophysical studies, the past decade has seen remarkable advances in the development of a new generation of RNA folding theories and models. In this article, we review RNA structure prediction models and models for ion-RNA and ligand-RNA interactions. These new models are becoming increasingly important for a mechanistic understanding of RNA function and quantitative design of RNA nanotechnology. We focus on new methods for physics-based, knowledge-based, and experimental data-directed modeling for RNA structures and explore the new theories for the predictions of metal ion and ligand binding sites and metal ion-dependent RNA stabilities. The integration of these new methods with theories about the cellular environment effects in RNA folding, such as molecular crowding and cotranscriptional kinetic effects, may ultimately lead to an all-encompassing RNA folding model.
authors.affiliation: Department of Physics, Department of Biochemistry, and MU Informatics Institute, University of Missouri, Columbia, Missouri 65211; email: chenshi@missouri.edu.
authors.forename: Li-Zhen
authors.initials: LZ
authors.lastname: Sun
authors.affiliation: Department of Physics, Department of Biochemistry, and MU Informatics Institute, University of Missouri, Columbia, Missouri 65211; email: chenshi@missouri.edu.
authors.forename: Dong
authors.initials: D
authors.lastname: Zhang
authors.affiliation: Department of Physics, Department of Biochemistry, and MU Informatics Institute, University of Missouri, Columbia, Missouri 65211; email: chenshi@missouri.edu.
authors.forename: Shi-Jie
authors.initials: SJ
authors.lastname: Chen
mesh_terms: D002412:Cations; D030561:Databases, Nucleic Acid; D007700:Kinetics; D008024:Ligands; D008274:Magnesium / Q000737:chemistry; D008670:Metals / Q000737:chemistry*; D008958:Models, Molecular; D009690:Nucleic Acid Conformation; D011188:Potassium / Q000737:chemistry; D012313:RNA / Q000737:chemistry*; D012964:Sodium / Q000737:chemistry; D013816:Thermodynamics
chemical_list: D002412:Cations; D008024:Ligands; D008670:Metals; D012313:RNA; D012964:Sodium; D008274:Magnesium; D011188:Potassium
keywords: knowledge-based approach; nonspecific ion binding; physics-based modeling; specific ion binding; three-dimensional structure prediction