Brownian dynamics simulations of supercoiled DNA with bent sequences.

The recently presented Brownian dynamics model for superhelical DNA is extended to include local curvature of the DNA helix axis. Here we analyze the effect of a permanent bend on the structure and dynamics of an 1870-bp superhelix with delta Lk = -10. Furthermore, we define quantitative expressions for computing structural parameters such as loop positions, superhelix diameter, and plectonemic content for trajectories of superhelical DNA, and assess the convergence toward global equilibrium. The structural fluctuations in an interwound superhelix, as reflected in the change in end loop positions, seem to occur by destruction/creation of loops rather than by a sliding motion of the DNA around its contour. Their time scale is on the order of 30-100 microseconds. A permanent bend changes the structure and the internal motions of the DNA drastically. The position of the end loop is fixed at the permanent bend, and the local motions of the chain are enhanced near the loops. A displacement of the bend from the end loop to a position inside the plectonemic part of the superhelix results in the formation of a new loop and the disappearance of the old one; we estimate the time involved in this process to be about 0.5 ms.