Despite a large number of publications devoted to nonlinear DNA dynamics, and, in particular, to the study of the features of the movement of kinks in inhomogeneous sequences, many problems in this area remain unresolved. The problem of kinks movement in the sequence of the circular DNA - plasmid pBR322, is among them. In this paper, the problem is considered by the methods of mathematical modeling. To simulate the movement of kinks, the McLaughlin-Scott equation is used, and the solution of this equation is found by the block method. The results of the calculations are presented in the form of trajectories in 3D space.
pBR322, nonlinear dynamics of inhomogeneous DNA, McLaughlin-Scott equation, kinks, block method, 3D trajectories, plasmid pBR322
1. Aleynikova T.L. Biohimiya. M.: GEOTAR-MED, red. E.S. Severin, 2003, 779 s. [Aleynikova T.L. Biochemistry. Moscow: GEOTAR-MED, ed. E.S. Severin, 2003, 779 p. (In Russ.)]
2. GenBank: URL: ncbi.nlm.nih.gov/nuccore/J01749.1
3. Watson N.A new revision of the sequence of plasmid pBR322. Gene, 1988, vol. 70, pp. 399-403.
4. McLaughlin D.W., Scott A.C. Perturbation analysis of fuxon dynamics. Phys. Rev. A, 1978, vol. 18, p. 1652.
5. Grinevich A.A., Ryasik A.A., Yakushevich L.V. Trajectories of DNA bubbles. Chaos, Solitons & Fractals, 2015, vol. 75, pp. 62-75.
6. Yakushevich L.V., Krasnobaeva L.A. Effects of dissipation and external fields on the dynamics of conformational distortions in DNA. Biophysics, 2007, vol. 52, pp. 237-243.
7. Yakushevich L.V., Grinevich A.A., Ryasik A.A. Simulation of a kink movement in homogeneous and heterogeneous DNA. RJNAMM, 2014, vol. 29, pp.197-204.
