Reconfiguration of B-DNA structure induced by ethanol

Abstract Solution environment can influence the flexible structure of DNA under specific conditions, thereby affecting the stability of nucleic acids and ultimately impacting critical biological processes such as replication and transcription. Intracellular solution environment is variable, and previous studies have demonstrated that it can enhance the stability of DNA structures under certain circumstances. In this work, molecular dynamics simulations were conducted on B-DNA (1ZEW, with a nucleotide sequence of CCTCTAGAGG) derived from human breast cancer cells (MDA-MB231) to explore the effects of ethanol solution on DNA configuration transformation at different temperature and concentration. The calculated results indicated that ethanol facilitates the transition of 1ZEW from B-DNA to A-DNA at lower temperature. Furthermore, it is observed that temperature affects DNA structure to some extent, thereby modifying the trend in DNA configuration transformation. At low temperatures, the ethanol can promote the transformation of B-DNA into A-DNA at higher concentrations. While at higher temperatures, the DNA could be in a state of thermal melting. These conclusions presented here can give valuable insights into ethanol affects B-DNA configuration transformations.