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arXiv · 1302.1673

Slow closure of denaturation bubbles in DNA: twist matters

Anil Kumar Dasanna·Nicolas Destainville·John Palmeri·Manoel Manghi
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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, $κ_ϕ=$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 $κ_ϕ$ 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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Anil Kumar Dasanna, Nicolas Destainville, John Palmeri, Manoel Manghi. 2013-04-24. Slow closure of denaturation bubbles in DNA: twist matters. https://doi.org/10.1103/physreve.87.052703

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