Bubble dynamics in double stranded DNA : A Rouse chain based approach

TL;DR

This paper introduces a Rouse chain-based model for DNA bubble dynamics that captures local denaturation fluctuations and aligns with experimental autocorrelation data, emphasizing the collective chain behavior.

Contribution

The model incorporates chain dynamics and normal mode relaxation times, providing a more comprehensive description of DNA bubble fluctuations beyond single reaction coordinate approaches.

Findings

Reproduces experimental autocorrelation functions.

Highlights the importance of chain normal modes.

Shows sensitivity of dynamics to relaxation times.

Abstract

We propose a model for the fluctuation dynamics of the local denaturation zones (bubbles) in double-stranded DNA. In our formulation, the DNA strand is model as a one dimensional Rouse chain confined at both the ends. The bubble is formed when the transverse displacement of the chain attains a critical value. This simple model effectively reproduces the autocorrelation function for the tagged base pair in the DNA strand as measured in the seminal single molecule experiment by Altan-Bonnet et. al (Phys. Rev. Lett. 90, 138101 (2003)). Although our model is mathematically similar to the one proposed by Chatterjee et al. (J. Chem. Phys. 127, 155104 (2007)) it goes beyond a single reaction coordinate description by incorporating the chain dynamics through a confined Rouse chain and thus considers the collective nature of the dynamics. Our model also shows that the autocorrelation function is very sensitive to the relaxation times of the normal modes of the chain, which is obvious since the fluctuation dynamics of the bubble has the contribution from the different normal modes of the chain.