Large-amplitude fast motions in double-stranded DNA driven by solvent thermal fluctuations

The nature of the internal dynamics of double-stranded DNA in aqueous environment remains to be established. We consider the motions to stem from thermal fluctuations/dissipations of the harmonic modes of beads (bases and sugars) in a cylindrical geometry that are tracked through the stochastic Langevin trajectories; these are characterized by parameters obtained from published data. The present approach has allowed a comparative study of the dynamics for DNA lengths in the range of 20-600 base pairs. For this range, we find that rotational motions about directions parallel to the helix axis (opening, twist) and perpendicular to it (propeller-twist, roll) contribute significantly to the dynamics. For a 20-mer at a solvent viscosity of 1 cP, the calculated fluorescence anisotropy profile exhibits a fast decay in the subnanosecond range due to large-amplitude fluctuations at the mesoscopic level. This feature reproduces the experimental behavior well, and suggests a possible way for the initiation of biological processes: they may be suddenly triggered on this scale through the occurrence of favorable thermal fluctuations. This analysis also reveals that, as is the case for a 20-mer, the dynamics of longer N-mers are dominated by internal motions, and are modulated by the viscosity of the solvent, in agreement with our previous experimental observations. Moreover, the model indicates that occurrence of partially concerted rotations of the bases due to thermal fluctuations can possibly be sustained over a DNA length of the order of 100 A at 1 ns, suggesting a possible mechanism for action-at-a-distance in transcription.