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 an alyze the effect of a permanent bend on the structure and dynamics of an 1870-bp superhelix with Delta Lk = -10. Furthermore, we define quan titative expressions for computing structural parameters such as loop positions, superhelix diameter, and plectonemic content for trajectori es of superhelical DNA, and assess the convergence toward global equil ibrium, The structural fluctuations in an interwound superhelix, as re flected in the change in end loop positions, seem to occur by destruct ion/creation of loops rather than by a sliding motion of the DNA aroun d its contour, Their time scale is on the order of 30-100 mu s, A perm anent bend changes the structure and the internal motions of the DNA d rastically, The position of the end loop is fixed at the permanent ben d, and the local motions of the chain are enhanced near the loops, A d isplacement of the bend from the end loop to a position inside the ple ctonemic part of the superhelix results in the formation of a new loop and the disappearance of the old one; we estimate the time involved i n this process to be about 0.5 ms.