Nonlinear waves in double-stranded DNA

TL;DR

This paper introduces a nonlinear model for DNA bubble dynamics incorporating a novel curvature dissipation term, enabling analysis of stable localized structures relevant to biological processes like transcription and repair.

Contribution

The paper develops a first-principles nonlinear model with a new dissipative term, providing insights into stable bubble formations in DNA.

Findings

Stable pinned localized kinks can form in the model

Energy thresholds for bubble motion are identified

Model aligns with DNA dynamic properties

Abstract

We propose a nonlinear model derived from first principles, to describe bubble dynamics of DNA. Our model equations include a term derived from the dissipative effect of intermolecular vibrational modes. Such modes are excited by the propagating bubble, and we term it "curvature dissipation". The equations we derive allow for stable pinned localized kinks which form the bubble. We perform the stability analysis and specify the energy requirements for the motion of the localized solutions. Our findings are consistent with properties of DNA dynamics, and can be used in models for denaturation bubbles, RNA and DNA transcription, nucleotide excision repair and meiotic recombination.