title: Ion-mediated RNA structural collapse: effect of spatial confinement.
abstract: RNAs are negatively charged molecules that reside in cellular environments with macromolecular crowding. Macromolecular confinement can influence the ion effects in RNA folding. In this work, using the recently developed tightly bound ion model for ion fluctuation and correlation, we investigate the effect of confinement on ion-mediated RNA structural collapse for a simple model system. We find that for both Na(+) and Mg(2+), the ion efficiencies in mediating structural collapse/folding are significantly enhanced by the structural confinement. This enhancement of ion efficiency is attributed to the decreased electrostatic free-energy difference between the compact conformation ensemble and the (restricted) extended conformation ensemble due to the spatial restriction.
authors.affiliation: Department of Physics and Key Laboratory of Artificial Micro- and Nano-Structures of Ministry of Education, School of Physics and Technology, Wuhan University, Wuhan, People's Republic of China. zjtan@whu.edu.cn
authors.forename: Zhi-Jie
authors.initials: ZJ
authors.lastname: Tan
authors.forename: Shi-Jie
authors.initials: SJ
authors.lastname: Chen
mesh_terms: D008274:Magnesium / Q000378:metabolism / Q000494:pharmacology*; D008958:Models, Molecular; D009690:Nucleic Acid Conformation / Q000187:drug effects*; D012313:RNA / Q000737:chemistry* / Q000378:metabolism; D012399:Rotation; D012964:Sodium / Q000378:metabolism / Q000494:pharmacology*; D012996:Solutions; D055672:Static Electricity; D013816:Thermodynamics
chemical_list: D012996:Solutions; D012313:RNA; D012964:Sodium; D008274:Magnesium