title: Surface-induced DNA superhelicity.
abstract: Certain biopolymers, such as DNA, have a double-stranded twisted structure and frequently exhibit a supercoiled conformation. Over the past decade, extensive conformational analyses of different biopolymers have been performed using atomic force microscopy. In this technique, a necessary step in sample preparation is the adsorption of molecules on the surface, which could affect the chain conformation. Using a Monte Carlo simulation, we studied the adsorption process of circular semiflexible twisted double-stranded polymer chains on a solid surface with an emphasis on the conformational properties. We found that the conformation of an adsorbed chain strongly depends on the number of double-helical turns of the chain. Chains with weak twisting adsorbed on the surface assumes higher superhelical twisting, whereas the coiled state is seen in the bulk solution. After the adsorption, double-helical turns are accumulated in the adsorbed ("train") sections giving more conformational freedom to the nonadsorbed ("loop") sections. Chains with strong twisting show small conformational changes with adsorption. In both cases, superhelicity shows the opposite sign of writhing.
authors.affiliation: Graduate School of Human Informatics, Nagoya University, Nagoya 464-8601, Japan.
authors.forename: Y S
authors.initials: YS
authors.lastname: Velichko
authors.forename: K
authors.initials: K
authors.lastname: Yoshikawa
authors.forename: A R
authors.initials: AR
authors.lastname: Khokhlov
mesh_terms: D000465:Algorithms; D004278:DNA, Superhelical / Q000737:chemistry*; D008958:Models, Molecular; D009010:Monte Carlo Method; D013499:Surface Properties
chemical_list: D004278:DNA, Superhelical