Speaker
Description
Quantifying how temperature and ionic strength jointly determine the elastic properties of double-stranded DNA remains a central challenge in molecular biophysics. Although individual temperature or salt dependent trends have been measured, a unified, mechanistic map across high-salt and elevated-temperature regimes is still lacking. Here, we use the oxDNA2 coarse-grained model to compute a 3×9 thermodynamic ionic grid spanning 300 –373 K and 0.5 – 1.5 M monovalent salt, enabling controlled evaluation of elastic properties and structural observables under conditions where electrostatic screening is extremely strong. Simulations were performed on long 500-bp duplexes with full ensemble averaging over independent replicate trajectories at each condition. Across all salt concentrations, DNA softens as temperature increases, but the degree of softening depends on ionic strength. At 0.5 M, the bending persistence length drops from about 43 nm at 300 K to 32 nm at 373 K. At 1.5 M, the decrease is far smaller (46 → 39 nm), showing that high salt reduces thermal sensitivity by roughly 40–50%. Torsional stiffness shows the same pattern (110 → 92 units at 0.5 M vs. 118 → 105 units at 1.5 M), as does twist–stretch coupling, which changes by 0.7 units at low salt but only 0.4 units at high salt. Helical twist decreases by roughly 1.1–1.3° per kbp per 10 K at 0.5 M, with a visibly weaker dependence at 1.5 M. While both bending and torsional rigidities soften with temperature, torsional elasticity remains closer to harmonic behavior than bending, with anharmonic deviations staying below ~10% even at the highest temperatures. Structural measures, including base-pair occupancy and stacking energies, show that the duplex remains intact up to about 95 –100 °C, with only limited end fraying. Beyond quantifying these trends, the present work introduces a unified thermodynamic interpretation of DNA elasticity. The simulations demonstrate that the weakening of base-stacking interactions precedes significant hydrogen-bond disruption and acts as the primary microscopic driver of thermoelastic softening. This perspective provides a compact statistical-mechanical description of DNA thermoelasticity and helps reconcile observations from coarse-grained simulations, atomistic molecular dynamics, and single-molecule experiments.
