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

doi:10.1088/1674-1056/ac3caa

中国物理B ›› 2022, Vol. 31 ›› Issue (4): 48702-048702.doi: 10.1088/1674-1056/ac3caa

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

Jingjing Xue(薛晶晶), Xinpeng Li(李新朋), Rongri Tan(谈荣日)^†, and Wenjun Zong(宗文军)^‡

Department of Physics, Jiangxi Science and Technology Normal University, Nanchang 330013, China

收稿日期:2021-08-04 修回日期:2021-10-06 接受日期:2021-11-24 出版日期:2022-03-16 发布日期:2022-03-16
通讯作者: Rongri Tan, Wenjun Zong E-mail:rogertanr@hotmail.com;13807065116@163.com
基金资助:
This work was supported by the National Natural Science Foundation of China (Grant No. 11564015), the Foundation of Educational Committee of Jiangxi Province, China (Grant No. GJJ211112), and the Fund for Distinguished Young Scholars of Jiangxi Science & Technology Normal University (Grant No. 2015QN-BJRC002).

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

Jingjing Xue(薛晶晶), Xinpeng Li(李新朋), Rongri Tan(谈荣日)^†, and Wenjun Zong(宗文军)^‡

Department of Physics, Jiangxi Science and Technology Normal University, Nanchang 330013, China

Received:2021-08-04 Revised:2021-10-06 Accepted:2021-11-24 Online:2022-03-16 Published:2022-03-16
Contact: Rongri Tan, Wenjun Zong E-mail:rogertanr@hotmail.com;13807065116@163.com
Supported by:
This work was supported by the National Natural Science Foundation of China (Grant No. 11564015), the Foundation of Educational Committee of Jiangxi Province, China (Grant No. GJJ211112), and the Fund for Distinguished Young Scholars of Jiangxi Science & Technology Normal University (Grant No. 2015QN-BJRC002).

摘要/Abstract

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 (Mg²⁺, Zn²⁺, Ca²⁺) 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 CaCl₂ solution is less stable than in MgCl₂ and ZnCl₂ solution.

关键词: transition of DNA structure, bivalent metal ions, molecular dynamics simulations, effect of concentration

Abstract: 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 (Mg²⁺, Zn²⁺, Ca²⁺) 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 CaCl₂ solution is less stable than in MgCl₂ and ZnCl₂ solution.

Key words: transition of DNA structure, bivalent metal ions, molecular dynamics simulations, effect of concentration

中图分类号: (DNA)

87.14.gk

87.15.ap (Molecular dynamics simulation) 87.15.-v (Biomolecules: structure and physical properties) 87.15.hp (Conformational changes)

Jingjing Xue(薛晶晶), Xinpeng Li(李新朋), Rongri Tan(谈荣日), and Wenjun Zong(宗文军). Molecular dynamics simulations of A-DNA in bivalent metal ions salt solution[J]. 中国物理B, 2022, 31(4): 48702-048702.

Jingjing Xue(薛晶晶), Xinpeng Li(李新朋), Rongri Tan(谈荣日), and Wenjun Zong(宗文军). Molecular dynamics simulations of A-DNA in bivalent metal ions salt solution[J]. Chin. Phys. B, 2022, 31(4): 48702-048702.

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

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

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