The effect of ethanol on B-DNA in salt solution through Molecular Dynamics Simulations

Abstract

DNA is an important biomacromolecule in biological cell. The researches of DNA have a significant meaning in the fields of DNA drugs and DNA nanotechnology. The differences of solution environment will have great effect on the DNA. In pure water, B-DNA is the stable structure of DNA. To explore the effect of ethanol on B-DNA in salt solution, a series of molecular dynamics simulations have been performed on 171D DNA with the sequence of (CGCGAATTCGCG). The results show that ethanol molecules have a great effect on the DNA structural stability in the MgCl2 salt solution. The stability of DNA structure is gradually declined with the increasing of the concentration of ethanol. The DNA structural changes always occur at the both ends of DNA chain, rather than the central part. In high concentration of ethanol, the combination between metal ions and phosphate groups is great stronger which affect the interaction between electropositive metal ions and the electronegative phosphate groups of DNA. For multiple DNA chains in salt solution, the presence of ethanol makes a contribution to the aggregation of DNA chains in solution.