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

  title={DNA denaturation bubbles: free-energy landscape and nucleation/closure rates.},
  author={François Sicard and N. Destainville and M. Manghi},
  journal={The Journal of chemical physics},
  volume={142 3},
  • François Sicard, N. Destainville, M. Manghi
  • Published 2015
  • Materials Science, Medicine, Physics, Biology, Chemistry
  • The Journal of chemical physics
  • 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 (respectively, closure) of an approximately 10 base-pair bubble, in agreement with… CONTINUE READING
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