Transformation characteristics of A-DNA in salt solution revealed through molecular dynamics simulations

The structure of A-DNA with biological activity is double helix. Researches of A-DNA structure have wide application on the development of DNA drug. In aqueous solution, the structure of A-DNA will have a free transformation over time and be finally stabilized in the B-form. In this work, molecular dynamics simulations have been performed on the A-DNA with sequence of CCCGGCCGGG, to elucidate the influence of ionic valence and temperature on the structural stability of A-DNA in salt solution. The results show that the structure of A-DNA is more stable in AlCl₃ solution compared with MgCl₂ and NaCl solution. To further discuss the influence of ionic valency, two kinds of virtual ions (monovalent X⁺ and trivalent Z³⁺) are created based on the properties of magnesium ions. From the simulations, the stability of A-DNA structure is better in high valent cationic salt solution. This has something to do with electrostatic interaction between metal ions and DNA chains. The electrostatic interaction force is gradually improved with the increasing of ionic valency, which is conducive to the formation of more compact DNA structure. Also, in the condition of same concentration and ionc valency, low temperature has a contribution to the stability of A-DNA structure.