Simulation of the conformation and dynamics of a double-helical model for DNA

We propose a partially flexible, double-helical model for describing the conformational and dynamic properties of DNA. In this model, each nucleotide is represented by one element (bead), and the known geometrical features of the double helix are incorporated in the equilibrium conformation. Each bead is connected to a few neighbor beads in both strands by means of stiff springs that maintain the connectivity but still allow for some extent of flexibility and internal motion. We have used Brownian dynamics simulation to sample the conformational space and monitor the overall and internal dynamics of short DNA pieces, with up to 20 basepairs. From Brownian trajectories, we calculate the dimensions of the helix and estimate its persistence length. We obtain translational diffusion coefficient and various rotational relaxation times, including both overall rotation and internal motion. Although we have not carried out a detailed parameterization of the model, the calculated properties agree rather well with experimental data available for those oligomers.