Ion atmosphere of three-way junction nucleic acid.
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).
Mohanty
Udayan
U
Department of Chemistry, Boston College, Chestnut Hill, Massachusetts 02467, USA.
Spasic
Alexander
A
Kim
Harold D
HD
Chu
Steven
S
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
D007477:Ions; D009696:Nucleic Acids; D012313:RNA; D012964:Sodium; D008274:Magnesium