Folding path in a semiflexible homopolymer chain: A Brownian dynamics simulation

We studied the kinetics of the folding transition of a semiflexible homopolymer chain, such as DNA, using a Brownian dynamics simulation. The folding product of a semiflexible chain exhibits a toroidal morphology. We show that semiflexible chains fold through various paths from coiled states to toroidal states stochastically. Some chains fold directly by winding around a ring along a chain. Others fold through rod states, which are kinetically trapped metastable states. Both in toroids and rods, sliding motions are noticeable. Large toroids are generated as the intermediate conformation first, and then they become smaller through the sliding motion. (C) 2000 American Institute of Physics. [S0021-9606(00)50926-X].