title: Base-pair opening and bubble transport in a DNA double helix induced by a protein molecule in a viscous medium.
abstract: The protein-DNA interaction dynamics is studied by modeling the DNA bases as classical spins in a coupled spin system, which are bosonized and coupled to thermal phonons and longitudinal motion of the protein molecule in the nonviscous limit. The nonlinear dynamics of this protein-DNA complex molecular system is governed by the completely integrable nonlinear Schrödinger (NLS) equation which admits N -soliton solutions. The soliton excitations of the DNA bases in the two strands make localized base-pair opening and travel along the DNA chain in the form of a bubble. This may characterize the bubble generated during the transcription process, when an RNA polymerase binds to a promoter site in the DNA double helical chain. When the protein-DNA molecular system interacts with the surrounding viscous solvating water medium, the dynamics is governed by a perturbed NLS equation. This equation is solved using a multiple scale perturbation analysis, by treating the viscous effect as a weak perturbation, and the results show that the viscosity of the solvent medium damps out the soliton as time progresses.
authors.affiliation: Centre for Nonlinear Dynamics, School of Physics, Bharathidasan University, Tiruchirappalli 620 024, India. vasu@cnld.bdu.ac.in
authors.forename: V
authors.initials: V
authors.lastname: Vasumathi
authors.forename: M
authors.initials: M
authors.lastname: Daniel
mesh_terms: D020029:Base Pairing; D001826:Body Fluids / Q000737:chemistry*; D003198:Computer Simulation; D004247:DNA / Q000737:chemistry* / Q000648:ultrastructure; D004268:DNA-Binding Proteins / Q000737:chemistry*; D005740:Gases / Q000737:chemistry; D008956:Models, Chemical; D014783:Viscosity
chemical_list: D004268:DNA-Binding Proteins; D005740:Gases; D004247:DNA