title: Ion atmosphere of three-way junction nucleic acid.
abstract: The ion atmosphere of three-armed symmetric Y-shaped and asymmetric y-shaped A-RNA junctions in aqueous solution containing multivalent ions is described within the framework of a polyelectrolyte model. The fraction of "screening counterions" per polyion charge that shield the residual unneutralized charges from interacting with one another and the condensed counterions per polyion charge as a function of sodium and magnesium ion concentrations are determined. The predictions for the slope of log(k(o)/k(f)) as a function of Na+ and Mg2+ concentration, where k(o) and k(f) are the opening and folding rates of the three-helix junction molecule, respectively, are compared with experimental data (Kim et al. Proc. Nat. Acad. Sci. U.S.A. 2002, 96, 9077-9082).
authors.affiliation: Department of Chemistry, Boston College, Chestnut Hill, Massachusetts 02467, USA.
authors.forename: Udayan
authors.initials: U
authors.lastname: Mohanty
authors.forename: Alexander
authors.initials: A
authors.lastname: Spasic
authors.forename: Harold D
authors.initials: HD
authors.lastname: Kim
authors.forename: Steven
authors.initials: S
authors.lastname: Chu
mesh_terms: D007477:Ions / Q000737:chemistry*; D007700:Kinetics; D008274:Magnesium / Q000494:pharmacology; D009690:Nucleic Acid Conformation / Q000187:drug effects; D009696:Nucleic Acids / Q000737:chemistry*; D012313:RNA / Q000737:chemistry*; D012964:Sodium / Q000494:pharmacology
chemical_list: D007477:Ions; D009696:Nucleic Acids; D012313:RNA; D012964:Sodium; D008274:Magnesium