Bubble relaxation dynamics in homopolymer DNA sequences

TL;DR

This study uses a coarse-grained DNA model to analyze the relaxation times of large bubbles in homopolymer DNA, revealing sequence-dependent dynamics that impact long-term molecular behavior.

Contribution

The paper introduces a detailed simulation analysis of bubble relaxation times in homopolymer DNA, highlighting sequence-specific differences and their implications.

Findings

Relaxation times increase with bubble size and amplitude.

GC sequences have relaxation times two orders of magnitude longer than AT sequences.

Large bubbles significantly influence DNA dynamics over hundreds of nanoseconds.

Abstract

Understanding the inherent timescales of large bubbles in DNA is critical to a thorough comprehension of its physicochemical characteristics, as well as their potential role on helix opening and biological function. In this work we employ the coarse-grained Peyrard-Bishop-Dauxois model of DNA to study relaxation dynamics of large bubbles in homopolymer DNA, using simulations up to the microsecond time scale. By studying energy autocorrelation functions of relatively large bubbles inserted into thermalised DNA molecules, we extract characteristic relaxation times from the equilibration process for both adenine-thymine (AT) and guanine-cytosine (GC) homopolymers. Bubbles of different amplitudes and widths are investigated through extensive statistics and appropriate fittings of their relaxation. Characteristic relaxation times increase with bubble height and width. We show that, within the model, relaxation times are two orders of magnitude longer in GC sequences than in AT sequences. Overall, our results confirm that large bubbles leave a lasting impact on the molecule's dynamics, for times between 0.4-200ns depending on the homopolymer type and bubble shape, thus clearly affecting long-time evolutions of the molecule.