Kinetics of single DNA compaction by hexaammine cobalt chloride

Abstract

Stepwise folding and unfolding dynamics of compaction of single DNAs by multivalent cations has been observed in recent single-molecule experiments. The causes of the stepwise signals, however, have not been carefully investigated. Using stochastic dynamical simulation algorism, we predict the time courses of changes in the extension of a single DNA subject to various tensions based on a spool model proposed recently. Compared with single-molecule experiments performed using a magnetic tweezer at the same forces, we find that the spool model is in reasonable agreement with the folding dynamics, but not in agreement with the unfolding dynamics. The disagreement of the unfolding dynamics can be remedied if some rare, long waiting time events are removed from the unfolding time courses. The implications of the experiments are discussed. Copyright © 2010 American Scientific Publishers. All right reserved.