Simulation of dissociation of DNA duplexes attached to the surface
Artikel i övriga tidskrifter, 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

Författare

Vladimir Zhdanov

Chalmers, Teknisk fysik, Kemisk fysik

Anders Gunnarsson

Chalmers, Teknisk fysik, Biologisk fysik

Fredrik Höök

Chalmers, Teknisk fysik, Biologisk fysik

Central European Journal of Physics

1895-1082 (ISSN) 1644-3608 (eISSN)

Vol. 8 6 883-892

Ämneskategorier

Kemi

DOI

10.2478/s11534-010-0012-1

Mer information

Skapat

2017-10-07