Anil Kumar Dasanna, Nicolas Destainville, John Palmeri, Manoel Manghi
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 $300\,k_{\rm B}T$. 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. 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.
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http://arxiv.org/abs/1302.1673
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