Long-range interactions between adjacent and distant bases in a DNA and their impact on the ribonucleic acid polymerase-DNA dynamics

When an inhomogeneous RNA-polymerase (RNAP) binds to an inhomogeneous DNA at the physiological temperature, we propose a spin-like model of DNA nonlinear dynamics with long-range interactions (LRI) between adjacent and distant base pairs to study RNAP-DNA dynamics. Using Holstein-Primakoff's representation and Glauber's coherent state representation, we show that the model equation is a completely integrable nonlinear Schrodinger equation whose dispersive coefficient depends on LRI's parameter. Inhomogeneities have introduced perturbation terms in the equation of motion of RNAP-DNA dynamics. Considering the homogeneous part of that equation, a detailed study of the solution shows that the number of base pairs which form the bubble, the height, and the width of that bubble depend on the long-range parameter. The results of the perturbation analysis show that the inhomogeneities due to the DNA and RNAP structures do not alter the velocity and amplitude of the soliton, but introduce some fluctuations in the localized region of the soliton. The events that happen in the present study may represent binding of an RNAP to a promoter site in the DNA during the transcription process. (C) 2012 American Institute of Physics. [doi:10.1063/1.3683430]