Nonlinear breathing modes at a defect site in DNA.
Molecular-dynamics simulations of a normal DNA duplex show that breathing events typically occur on the microsecond time scale. This paper analyzes a 12 base pairs DNA duplex containing the "rogue" base difluorotoluene (F) in place of a thymine base (T), for which the breathing events occur on the nanosecond time scale. Starting from a nonlinear Klein-Gordon lattice model and adding noise and damping, we obtain a mesoscopic model of the DNA duplex close to that observed in experiments and all-atom molecular dynamics simulations. The mesoscopic model is calibrated to data from the all-atom molecular dynamics package AMBER for a variety of twist angles of the DNA duplex. Defects are considered in the interchain interactions as well as in the along-chain interactions. This paper also discusses the role of the fluctuation-dissipation relations in the derivation of reduced (mesoscopic) models, the differences between the potential of mean force and the potential energies used in Klein-Gordon lattices, and how breathing can be viewed as competition between the along-chain elastic energy and the interchain binding energy.
Duduială
Ciprian-Ionuţ
CI
School of Mathematical Sciences, University of Nottingham, Nottingham NG7 2RD, United Kingdom.
Wattis
Jonathan A D
JA
Dryden
Ian L
IL
Laughton
Charles A
CA
D020137:Base Pair Mismatch; D003198:Computer Simulation; D004247:DNA / Q000737:chemistry* / Q000648:ultrastructure*; D008956:Models, Chemical; D008958:Models, Molecular; D017711:Nonlinear Dynamics
D004247:DNA