2014/05/31 by François Sicard, Nicolas Destainville, Manoel Manghi · 3 citations
Biochemistry, Genetics and Molecular Biology · Engineering · Physics and Astronomy · #Arrhenius equation #Bubble #DNA and Nucleic Acid Chemistry #Denaturation (fissile materials) #Energy landscape #Helix (gastropod) #Limiting #Mesoscopic physics #Metadynamics #Nanopore and Nanochannel Transport Studies #Nucleation #Protein Structure and Dynamics #Temperature jump #cond-mat.soft #physics.bio-ph #q-bio.BM
paper · pdf · doi:10.1063/1.4905668
published as J. Chem. Phys. 142, 034903 (2015) · 11 pages (5 pages and Appendix), 13 figures, published in Journal of Chemical Physics
arxiv created 2015/01/12 · openalex publication_date 2015/01/16 · arxiv updated 2015/04/13 · openalex created_date 2016/06/24 · openalex updated_date 2026/08/06
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 experiments, are associated with the crossing of a free-energy barrier of 22 kBT (respectively, 13 kBT) 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, those more than 4 base-pair bubbles are of biological relevance, for example, when a pre-existing state of denaturation is required by specific DNA-binding proteins.