Slow closure of denaturation bubbles in DNA: twist matters

TL;DR

This study uses Brownian dynamics simulations to investigate the slow closure of DNA denaturation bubbles, revealing the importance of twist and torsional energy barriers in the process.

Contribution

It introduces a mesoscopic model that quantitatively explains the slow bubble closure times observed experimentally, emphasizing the role of twist and torsional barriers.

Findings

Closure times range from 0.1 to 100 microseconds.

Closure mechanisms depend on torsional modulus and DNA length.

Temperature-activated Kramers process explains slow closure in long or clamped DNA.

Abstract

The closure of long equilibrated denaturation bubbles in DNA is studied using Brownian dynamics simulations. A minimal mesoscopic model is used where the double-helix is made of two interacting bead-spring freely rotating strands, with a non-zero torsional modulus in the duplex state, $\kappa_\phi=$200 to 300 kT. For DNAs of lengths N=40 to 100 base-pairs (bps) with a large initial bubble in their middle, long closure times of 0.1 to 100 microseconds are found. The bubble starts winding from both ends until it reaches a 10 bp metastable state. The final closure is limited by three competing mechanisms depending on $\kappa_\phi$ and N: arms diffusion until their alignment, bubble diffusion along the DNA until one end is reached, or local Kramers process (crossing over a torsional energy barrier). For clamped ends or long DNAs, the closure occurs via this latter temperature activated mechanism, yielding for the first time a good quantitative agreement with experiments.