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Simulation of dissociation of DNA duplexes attached to the surface

Vladimir P. Zhdanov (Institutionen för teknisk fysik, Kemisk fysik) ; Anders Gunnarsson (Institutionen för teknisk fysik, Biologisk fysik) ; Fredrik Höök (Institutionen för teknisk fysik, Biologisk fysik)
Central European Journal of Physics (1895-1082). Vol. 8 (2010), 6, p. 883-892.
[Artikel, övrig vetenskaplig]

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.

Nyckelord: DNA dissociation, non-exponential kinetic, lattice models, Monte Carlo, simulations, helix-coil transition, single-molecule, mismatch discrimination, polyamino acids, hybridization, denaturation, kinetics, binding, models, arrays

Denna post skapades 2010-10-28. Senast ändrad 2012-02-22.
CPL Pubid: 128287


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Institutioner (Chalmers)

Institutionen för teknisk fysik, Kemisk fysik (1900-2015)
Institutionen för teknisk fysik, Biologisk fysik (2007-2015)



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