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 nonzero torsional modulus in the duplex state, ${\kappa }_{\varphi }=200$ to $300k_{\mathrm{B}}T$. 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 $100\mu$s are found. The bubble starts winding from both ends until it reaches a $\approx 10$ bp metastable state due to the large elastic energy stored in the bubble. The final closure is limited by three competing mechanisms depending on ${\kappa }_{\varphi }$ 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 last temperature-activated mechanism, yielding a good quantitative agreement with the experiments.

• Received 7 February 2013

DOI:https://doi.org/10.1103/PhysRevE.87.052703