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The issue of the nucleation and slow closure mechanisms of non superhelicalstress-induced denaturation bubbles in DNA is tackled using coarse-grainedMetaDynamics and Brownian simulations. A minimal mesoscopic model is used wherethe double helix is made of two interacting bead-spring rotating strands with aprescribed torsional modulus in the duplex state. We demonstrate thattimescales for the nucleation (resp. closure) of an approximately 10 base-pairbubble, in agreement with experiments, are associated with the crossing of afree-energy barrier of $22~k_{\rm B}T$ (resp. $13~k_{\rm B}T$) at roomtemperature $T$. MetaDynamics allows us to reconstruct accurately thefree-energy landscape, to show that the free-energy barriers come from thedifference in torsional energy between the bubble and duplex states, and thusto highlight the limiting step, a collective twisting, that controls thenucleation/closure mechanism, and to access opening time scales on themillisecond range. Contrary to small breathing bubbles, these more than4~base-pair bubbles are of biological relevance, for example when a preexistingstate of denaturation is required by specific DNA-binding proteins.

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