Stability and structural evolution of double-stranded DNA molecules under high pressures: A molecular dynamics study

• DOI: 10.3389/fphy.2023.1076787
• Publication Date: 2023-02-06T05:14:41Z
• Authors: Salvador Herrera-...; José Ramón Villan...; Paola Mendoza-Esp...; Ramón Castañeda-P...
• Keywords: Hydrostatic pressure; Denaturation (fissile materials); Structural Stability

Conformational changes and stability of interacting double-stranded DNA chains under high hydrostatic pressure in biological systems are striking topics importance to study several biomolecular phenomena. For example, unravel the physiological conditions at which life might occur ensure right functionality biochemical processes into cell extreme thermodynamic conditions. Furthermore, such could shed light on physicochemical properties confinement how, through different mechanisms, a virus releases its genome order infect and, therefore, promote process viral replication. To achieve few steps toward this direction, we propose an all-atomistic molecular dynamics approach NPT isothermal-isobaric ensemble account for how interplay DNA—DNA interaction, hydrogen bonding, modifies both conformational degrees freedom spatial organization available volume. We consider two immersed explicit aqueous solution, i.e., water ions. Our preliminary results highlight role bonding electrostatic interactions between strands avoid denaturation provide mechanical molecules. However, structural evolution, whose kinetics depends relaxation stresses induced by pressure, indicates that almost all conditions, equilibrium configuration corresponds alignment molecules along their main axis symmetry; rearrangement approaching dodecamers does not always correspond complementary base pairs becomes function