Molecular dynamics simulations of A-DNA in bivalent metal ions salt solution  

作　　者：Jingjing Xue Xinpeng Li Rongri Tan Wenjun Zong 薛晶晶;李新朋;谈荣日;宗文君(Department of Physics,Jiangxi Science and Technology Normal University,Nanchang 330013,China)

机构地区：[1]Department of Physics,Jiangxi Science and Technology Normal University,Nanchang 330013,China

出　　处：《Chinese Physics B》2022年第4期733-741,共9页中国物理B（英文版）

基　　金：supported by the National Natural Science Foundation of China(Grant No.11564015);the Foundation of Educational Committee of Jiangxi Province,China(Grant No.GJJ211112);the Fund for Distinguished Young Scholars of Jiangxi Science&Technology Normal University(Grant No.2015QN-BJRC002)。

摘　　要：A-form DNA is one of the biologically active double helical structure.The study of A-DNA structure has an extensive application for developing the field of DNA packaging in biotechnology.In aqueous solution,the A-DNA structure will have a free transformation,the A-DNA structure will be translated into B-form structure with the evolution of time,and eventually stabilized in the B-DNA structure.To explore the stability function of the bivalent metal ions on the A-DNA structure,a series of molecular dynamics simulations have been performed on the A-DNA of sequence(CCCGGCCGGG).The results show that bivalent metal ions(Mg^(2+),Zn^(2+),Ca^(2+))generate a great effect on the structural stability of A-DNA in the environment of high concentration.As the interaction between metal ions and electronegative DNA chains,the stability of A-DNA in solution is gradually improved with the increasing solution concentration of ions.In metal salt solution with high concentration,metal ions can be easily distributed in the solvation shells around the phosphate groups and further lead to the formation of shorter and more compact DNA structure.Also,under the condition of the same concentration and valency of the metal ions,the stability of A-DNA structure is different.The calculations indicate that the structure of A-DNA in CaCl_(2)solution is less stable than in MgCl_(2)and ZnCl_(2)solution.

关 键 词：transition of DNA structure bivalent metal ions molecular dynamics simulations effect of concentration 

分 类 号：Q523[生物学—生物化学]