Simulating the Helicase Enzymatic Action on ds-DNA: A First-Principles Molecular Dynamics Study

Understanding DNA replication is fundamental for advancements in fields such as genetics, molecular biology, and medical research. In this study, we investigate the mechanical characteristics of three distinct double-stranded DNA molecules (ds-DNA) as each of them is unwound into two individual single strands. To simulate the helicase action, the double strands are subjected to Langevin forces. By use of sequential and helical steering harmonic forces that simulate the enzymatic action of a helicase, each strand of ds-DNA is opened. The research focuses on determining thermal fluctuations, energy changes, charge variations, and individual forces associated with the separation of each base pair in the examined sequences. The findings emphasize the importance of combining quantum mechanical techniques with an implicit force model. This integrative approach is versatile and provides valuable insights into the essential processes governing DNA mechanisms, particularly in relation to cellular functioning, thereby enhancing our understanding of biological molecules.