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

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.