Kinetic and thermodynamic DNA elasticity at micro- and mesoscopic scales

Recent theoretical and experimental studies have suggested that the elastic behavior of the small-length double-helical DNA does not correspond to the simple harmonic model. This article presents a thorough comparison of classical atom-level molecular dynamics (MD) and coarse-grained harmonic approximations. It is shown that the previously predicted duration of MD trajectories necessary for accurate assessment of DNA elasticity was significantly overestimated and that reliable estimates of elastic parameters can be obtained after a few tens of nanoseconds. The all-atom and coarse-grained ensembles were compared head-to-head, including the amplitudes and relaxation rates of internal fluctuations as well as translational diffusion. The computed diffusion rates were found to be similar, with good correspondence to experimental data. The torsional persistence length (PL) in MD agrees reasonably well with experiment, with the relaxation rate of twisting fluctuations corresponding well to the harmonic model. The bending PL also agrees reasonably well with experiment, but the corresponding relaxation rate is much higher than the harmonic approximation. For a tetradecamer DNA, the difference reaches 1 order of magnitude, with the bending dynamics faster than the twisting dynamics, in qualitative contrast to the coarse-grained model. The possible mechanisms of this anomalous behavior are discussed.