title: Generalized Manning Condensation Model Captures the RNA Ion Atmosphere.
abstract: RNA is highly sensitive to the ionic environment and typically requires Mg(2+) to form compact structures. There is a need for models capable of describing the ion atmosphere surrounding RNA with quantitative accuracy. We present a model of RNA electrostatics and apply it within coarse-grained molecular dynamics simulation. The model treats Mg(2+) ions explicitly to account for ion-ion correlations neglected by mean-field theories. Since mean-field theories capture KCl well, it is treated implicitly by a generalized Manning counterion condensation model. The model extends Manning condensation to deal with arbitrary RNA conformations, nonlimiting KCl concentrations, and the ion inaccessible volume of RNA. The model is tested against experimental measurements of the excess Mg(2+) associated with the RNA, Γ(2+), because Γ(2+) is directly related to the Mg(2+)-RNA interaction free energy. The excellent agreement with experiment demonstrates that the model captures the ionic dependence of the RNA free energy landscape.
authors.affiliation: Center for Theoretical Biological Physics and Department of Physics and Astronomy, Rice University, Houston, Texas 77030, USA.
authors.forename: Ryan L
authors.initials: RL
authors.lastname: Hayes
authors.affiliation: Center for Theoretical Biological Physics and Department of Physics and Astronomy, Rice University, Houston, Texas 77030, USA.
authors.forename: Jeffrey K
authors.initials: JK
authors.lastname: Noel
authors.affiliation: Department of Biomedical Engineering, University of Houston, Houston, Texas 77004, USA.
authors.forename: Ana
authors.initials: A
authors.lastname: Mandic
authors.affiliation: Department of Physics, Northeastern University, Boston, Massachusetts 02115, USA.
authors.forename: Paul C
authors.initials: PC
authors.lastname: Whitford
authors.affiliation: Theoretic Biology and Biophysics, Theoretic Division, Los Alamos National Labs, Los Alamos, New Mexico 87545, USA.
authors.forename: Karissa Y
authors.initials: KY
authors.lastname: Sanbonmatsu
authors.affiliation: Department of Chemistry, Boston College, Chestnut Hill, Massachusetts 02467, USA.
authors.forename: Udayan
authors.initials: U
authors.lastname: Mohanty
authors.affiliation: Center for Theoretical Biological Physics and Department of Physics and Astronomy, Rice University, Houston, Texas 77030, USA.
authors.forename: José N
authors.initials: JN
authors.lastname: Onuchic
mesh_terms: D002414:Cations, Monovalent / Q000737:chemistry; D008274:Magnesium / Q000737:chemistry*; D008956:Models, Chemical; D009690:Nucleic Acid Conformation; D012313:RNA / Q000737:chemistry*; D055672:Static Electricity
chemical_list: D002414:Cations, Monovalent; D012313:RNA; D008274:Magnesium