Nonlinear dynamics of DNA bubble induced by site specific DNA-protein interaction

Conference on Theoretical Physics and Nonlinear Phenomena 2016

Dwiputra, Donny^1 ; Hidayat, Wahyu^1,2 ; Zen, Freddy P.^1,2

Theoretical Physics Laboratory, Faculty of Mathematics and Natural Sciences, Institut Teknologi Bandung, Jl. Ganesha no. 10, Bandung

40132, Indonesia^1

Indonesian Center of Theoretical and Mathematical Physics (ICTMP), Jl. Ganesha no. 10, Bandung

40132, Indonesia^2

关键词: Biological information;    Construct models;    Coupling dynamics;    DNA-protein interaction;    Genetic information;    Hybridization process;    Site-specificity;    Soliton formation;   

Others  :  https://iopscience.iop.org/article/10.1088/1742-6596/856/1/012005/pdf
DOI  :  10.1088/1742-6596/856/1/012005

来源: IOP

【 摘 要 】

We propose a dynamical model describing interactions between DNA and a specific binding protein involving long-range transmission of biological information. The model couples the hydrogen bonds between the one connecting DNA and protein side chain and the one connecting DNA base pairs since they account for site specificity of the binding. We adopt Morse potentials with coupling terms to construct model of coupled hydrogen bonds. We show that the model gives rise to a breather soliton formation, corresponding to the DNA bubbles, which propagates through DNA chain as the carrier of genetic information. We investigate various kinds of possible coupling dynamics and suggest the model realism in depicting the renaturation or hybridization processes.