title: Multivalent ion-mediated nucleic acid helix-helix interactions: RNA versus DNA.
abstract: Ion-mediated interaction is critical to the structure and stability of nucleic acids. Recent experiments suggest that the multivalent ion-induced aggregation of double-stranded (ds) RNAs and DNAs may strongly depend on the topological nature of helices, while there is still lack of an understanding on the relevant ion-mediated interactions at atomistic level. In this work, we have directly calculated the potentials of mean force (PMF) between two dsRNAs and between two dsDNAs in Co(NH3)6 (3+) (Co-Hex) solutions by the atomistic molecular dynamics simulations. Our calculations show that at low [Co-Hex], the PMFs between B-DNAs and between A-RNAs are both (strongly) repulsive. However, at high [Co-Hex], the PMF between B-DNAs is strongly attractive, while those between A-RNAs and between A-DNAs are still (weakly) repulsive. The microscopic analyses show that for A-form helices, Co-Hex would become 'internal binding' into the deep major groove and consequently cannot form the evident ion-bridge between adjacent helices, while for B-form helices without deep grooves, Co-Hex would exhibit 'external binding' to strongly bridge adjacent helices. In addition, our further calculations show that, the PMF between A-RNAs could become strongly attractive either at very high [Co-Hex] or when the bottom of deep major groove is fixed with a layer of water.
authors.affiliation: Department of Physics and Key Laboratory of Artificial Micro & Nano-structures of Ministry of Education, School of Physics and Technology, Wuhan University, Wuhan 430072, China.
authors.forename: Yuan-Yan
authors.initials: YY
authors.lastname: Wu
authors.affiliation: Department of Physics and Key Laboratory of Artificial Micro & Nano-structures of Ministry of Education, School of Physics and Technology, Wuhan University, Wuhan 430072, China.
authors.forename: Zhong-Liang
authors.initials: ZL
authors.lastname: Zhang
authors.affiliation: Department of Physics and Key Laboratory of Artificial Micro & Nano-structures of Ministry of Education, School of Physics and Technology, Wuhan University, Wuhan 430072, China.
authors.forename: Jin-Si
authors.initials: JS
authors.lastname: Zhang
authors.affiliation: Department of Physics, School of Physics & Information Engineering, Jianghan University, Wuhan 430056, China.
authors.forename: Xiao-Long
authors.initials: XL
authors.lastname: Zhu
authors.affiliation: Department of Physics and Key Laboratory of Artificial Micro & Nano-structures of Ministry of Education, School of Physics and Technology, Wuhan University, Wuhan 430072, China zjtan@whu.edu.cn.
authors.forename: Zhi-Jie
authors.initials: ZJ
authors.lastname: Tan
mesh_terms: D002413:Cations, Divalent / Q000737:chemistry; D059371:DNA, B-Form / Q000737:chemistry*; D056004:Molecular Dynamics Simulation; D009690:Nucleic Acid Conformation; D012330:RNA, Double-Stranded / Q000737:chemistry*
chemical_list: D002413:Cations, Divalent; D059371:DNA, B-Form; D012330:RNA, Double-Stranded