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arXiv · 1405.3867

DNA denaturation bubbles: free-energy landscape and nucleation/closure rates

François Sicard·Nicolas Destainville·Manoel Manghi
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Abstract

The issue of the nucleation and slow closure mechanisms of non superhelical stress-induced denaturation bubbles in DNA is tackled using coarse-grained MetaDynamics and Brownian simulations. A minimal mesoscopic model is used where the double helix is made of two interacting bead-spring rotating strands with a prescribed torsional modulus in the duplex state. We demonstrate that timescales for the nucleation (resp. closure) of an approximately 10 base-pair bubble, in agreement with experiments, are associated with the crossing of a free-energy barrier of $22~k_{\rm B}T$ (resp. $13~k_{\rm B}T$) at room temperature $T$. MetaDynamics allows us to reconstruct accurately the free-energy landscape, to show that the free-energy barriers come from the difference in torsional energy between the bubble and duplex states, and thus to highlight the limiting step, a collective twisting, that controls the nucleation/closure mechanism, and to access opening time scales on the millisecond range. Contrary to small breathing bubbles, these more than 4~base-pair bubbles are of biological relevance, for example when a preexisting state of denaturation is required by specific DNA-binding proteins.

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François Sicard, Nicolas Destainville, Manoel Manghi. 2015-01-12. DNA denaturation bubbles: free-energy landscape and nucleation/closure rates. https://doi.org/10.1063/1.4905668

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