Dynamics of a DNA minicircle: Poloidal rotation and in-plane circular vibration

We investigated the dynamics of a 90-base pair-long DNA minicircle with the sequence of (AT)(45)/(AT)(45) using the all-atom molecular dynamics (MD) simulation. The simulation was run for a duration of 5 mu s and the internal dynamics was analyzed in terms of the poloidal rotation and the in-plane circular vibration. The poloidal rotation was defined by the directional variation of each base pair relative to the plane of the DNA minicircle, and its correlation time was estimated to be 61 ns. The in-plane circular vibration was measured as the radial distance variation of each base pair from the center-of-mass of the DNA, and the correlation time was 6.3 ns. The characteristic time scales determined for the poloidal rotation and the radial fluctuation suggest that the internal motion of a small DNA minicircle is highly dynamic. This work provides a new set of dynamic information for small DNA minicircles, available for future applications.