title: Competition between Na⁺ and Rb⁺ in the minor groove of DNA.
abstract: The competition between Na⁺ and Rb⁺ ions in the minor groove of a synthetic B-DNA dodecamer d (CGCGAATTCGCG) is studied using molecular dynamics simulations as the ratio of these two ions changing from 9:1 to 1:9 with the DNA merged into the solvent of water molecule at 298 K. When the concentration of Rb⁺ ions increases, from minority to majority, Na⁺ ions are gradually released from the A tract, and the binding sites in the minor groove are occupied by Rb⁺ ions, extending from the A tract to the whole minor groove. Comparing Na⁺ with Rb⁺ ions, the conformation of the minor groove is influenced strongly by Na⁺ ions.
authors.affiliation: Key Laboratory of Beam Technology and Material Modification of Ministry of Education, College of Nuclear Science and Technology, Beijing Normal University, Beijing 100875, China.
authors.forename: X
authors.initials: X
authors.lastname: Shen
authors.forename: N A
authors.initials: NA
authors.lastname: Atamas
authors.forename: F S
authors.initials: FS
authors.lastname: Zhang
mesh_terms: D001483:Base Sequence; D001667:Binding, Competitive; D059371:DNA, B-Form / Q000737:chemistry* / Q000235:genetics / Q000378:metabolism*; D056004:Molecular Dynamics Simulation; D009690:Nucleic Acid Conformation; D012413:Rubidium / Q000378:metabolism*; D012964:Sodium / Q000378:metabolism*; D013696:Temperature; D014867:Water / Q000737:chemistry
chemical_list: D059371:DNA, B-Form; D014867:Water; D012964:Sodium; D012413:Rubidium