The Worm-Like Chain Theory And Bending Of Short DNA

The probability distributions for bending angles in double helical DNA obtained in all-atom molecular dynamics simulations are compared with theoretical predictions. For double helices of one helical turn and longer the computed distributions remarkably agree with the worm-like chain theory and qualitatively differ from predictions of the semi-elastic chain model. The computed data exhibit only small anomalies in the apparent flexibility of short DNA and cannot account for the recently reported AFM data (Wiggins et al, Nature nanotechnology 1, 137 (2006)). It is possible that the current atomistic DNA models miss some essential mechanisms of DNA bending on intermediate length scales. Analysis of bent DNA structures reveals, however, that the bending motion is structurally heterogeneous and directionally anisotropic on the intermediate length scales where the experimental anomalies were detected. These effects are essential for interpretation of the experimental data and they also can be responsible for the apparent discrepancy.