Nonlinear breathing modes due to a defect in a DNA chain.
Recent molecular-dynamics simulations of a DNA duplex containing the 'rogue' base difluorotoluene (F) in place of a thymine (T) base show that breathing events can occur on the nanosecond time-scale, whereas breathing events in a normal DNA duplex take place on the microsecond time-scale. The main aim of this paper is to analyse a nonlinear Klein-Gordon lattice model of the DNA duplex, including both nonlinear interactions between opposing bases and a defect in the interaction at one lattice site, each of which can cause localization of energy. Solutions for a breather mode either side of the defect are derived using multiple-scales asymptotics and are pieced together across the defect to form a solution which includes the effects of the nonlinearity and the defect. We consider defects in the inter-chain interactions and in the along-chain interactions. In most cases we find in-phase breather modes and/or out-of-phase breather modes, with one case displaying a shifted mode.
Theoretical Mechanics, School of Mathematical Sciences, University Park, University of Nottingham, Nottingham NG7 2RD, UK. jonathan.watts@nottingham.ac.uk
Jonathan A D
JA
Wattis
D020137:Base Pair Mismatch; D001483:Base Sequence; D003198:Computer Simulation; D004247:DNA / Q000737:chemistry* / Q000648:ultrastructure*; D004249:DNA Damage; D004548:Elasticity; D008958:Models, Molecular; D008969:Molecular Sequence Data; D009038:Motion; D017711:Nonlinear Dynamics; D009690:Nucleic Acid Conformation; D009691:Nucleic Acid Denaturation; D009692:Nucleic Acid Heteroduplexes / Q000737:chemistry*; D013314:Stress, Mechanical; D013329:Structure-Activity Relationship; D019415:Torque
D009692:Nucleic Acid Heteroduplexes; D004247:DNA