How dsDNA breathing enhances its flexibility and instability on short length scales

TL;DR

This paper investigates how local denaturation events, or breathing, in short double-stranded DNA increase its flexibility and instability, using Langevin dynamics simulations to explain experimental observations.

Contribution

The study introduces a Breathing DNA model and demonstrates how local denaturation bubbles and forks significantly reduce DNA stiffness at short lengths.

Findings

Local denaturation bubbles form independently of DNA length

Breathing events drastically lower persistence length in short DNA

Simulation results align with experimental data on DNA flexibility

Abstract

We study the unexpected high flexibility of short dsDNA which recently has been reported by a number of experiments. Via the Langevin dynamics simulation of our Breathing DNA model, first we observe the formation of bubbles within the duplex and also forks at the ends, with the size distributions independent of the contour length. We find that these local denaturations at a physiological temperature, despite their rare and transient presence, can lower the persistence length drastically for a short DNA segment in agreement with experiment.