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arXiv · 0812.4538

Base pair opening and bubble transport in a DNA double helix induced by a protein molecule in a viscous medium

V. Vasumathi·M. Daniel
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Abstract

We study the nonlinear dynamics of a protein-DNA molecular system by treating DNA as a set of two coupled linear chains and protein in the form of a single linear chain sliding along the DNA at the physiological temperature in a viscous medium. The nonlinear dynamics of the above molecular system in general is governed by a perturbed nonlinear Schr\"{o}dinger equation. In the non-viscous limit, the equation reduces to the completely integrable nonlinear Schr\"{o}dinger (NLS) equation which admits N-soliton solutions. The soliton excitations of the DNA bases make localized base pair opening and travel along the DNA chain in the form of a bubble. This may represent the bubble generated during the transcription process when an RNA-polymerase binds to a promoter site in the DNA double helical chain. The perturbed NLS equation is solved using a perturbation theory by treating the viscous effect due to surrounding as a weak perturbation and the results show that the viscosity of the solvent in the surrounding damps out the amplitude of the soliton.

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V. Vasumathi, M. Daniel. 2008-12-24. Base pair opening and bubble transport in a DNA double helix induced by a protein molecule in a viscous medium. https://doi.org/10.1103/physreve.80.061904

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