Study of flexible joints and permanent bends in DNA fragments by brownian dynamics simulations

The use of Brownian dynamics simulations to investigate the presence of str uctural (kinks) and dynamic (bulges) anomalies in short DNA stretches is an alyzed in connection with a string-of-beads model, A settling method to cho ose the hydrodynamic translational and rotational parameters of the beads i s proposed and tested on straight, kinked and bulged DNA fragments 17 nm lo ng. The model reproduces the rigid-body rotational diffusion for the straig ht DNA and for the fluorescence polarization anisotropy decay of the kinked and bulged DNAs the model predicts a different behavior which is found exp erimentally.