Simulation of dissociation of DNA duplexes attached to the surface
Magazine article, 2010
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.
Monte Carlo
single-molecule
arrays
lattice models
models
denaturation
polyamino acids
DNA dissociation
hybridization
simulations
mismatch discrimination
kinetics
helix-coil transition
non-exponential kinetic
binding
Author
Vladimir Zhdanov
Chalmers, Applied Physics, Chemical Physics
Anders Gunnarsson
Chalmers, Applied Physics, Biological Physics
Fredrik Höök
Chalmers, Applied Physics, Biological Physics
Central European Journal of Physics
1895-1082 (ISSN) 1644-3608 (eISSN)
Vol. 8 6 883-892Subject Categories
Chemical Sciences
DOI
10.2478/s11534-010-0012-1