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BY-NC-ND 3.0 license Open Access Published by De Gruyter Open Access September 5, 2010

Simulation of dissociation of DNA duplexes attached to the surface

Vladimir Zhdanov, Anders Gunnarsson and Fredrik Höök
From the journal Open Physics

Abstract

We present Monte Carlo simulations of dissociation of duplexes formed of complementary single-stranded DNAs with one of the strands attached to the surface. To describe the transition from the bound state to the unbound state of two strands located nearby, we use a lattice model taking DNA base-pair interactions and comformational changes into account. The results obtained are employed as a basis for a more coarse-grained model including strand backward association and diffusion resulting in complete dissociation. The distribution of the dissociation time is found to be exponential. This finding indicates that the non-exponential kinetic features observed in the corresponding experiments seem to be related to extrinsic factors, e.g., to the surface heterogeneity.

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Published Online: 2010-9-5
Published in Print: 2010-12-1

© 2010 Versita Warsaw

This work is licensed under the Creative Commons Attribution-NonCommercial-NoDerivatives 3.0 License.

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