Formation and propagation of oscillating bubbles in DNA initiated by structural distortions

Abstract

The initiation of the transcription process in DNA is linked with the dynamics originating from structural distortions of the double helix. It was proposed that such deformations might be caused by a ‘hit and run’ mechanism which is associated with the temporary attachment of some proteins, constituting activator factors, to regions of the DNA leaving it in deformed shape. In a nonlinear model approach we demonstrate that there exist such structural distortions of the double helix that appropriately serve to activate the formation of open regions in the form of oscillating bubble. The structure of the double helix form of DNA is modeled by a oscillator network model. We show that the underlying nonlinear dynamics supports localized solutions in the form of radial breathers and kink-shaped angular patterns. It is demonstrated that the radial breathers, which are attributed to localized H-bond deformations of the DNA molecule, move coherently along the double chain. We further illustrate that the breathers sustain the impact of heterogeneity due to the genetic code inscribed in DNA. Moreover, mobility of the breathers is also preserved when, the positions of the nucleotides are (randomly) modulated through fluctuational modes of the chemical environment, and energy dissipation due to non-elasticity damping of the motion of the nucleotides is incorporated. The amplitudes, oscillation periods and spatial extensions of the radial breathers resembles those found for the oscillating bubbles in real DNA molecules.