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[hal-02468189] Dynamical control of denaturation bubble nucleation in supercoiled DNA minicircles  (02/06/2020)   Moins
We examine the behavior of supercoiled DNA minicircles containing between 200 and 400 base-pairs, also named microDNA, in which supercoiling favors thermally assisted DNA denaturation bubbles of nanometer size and controls their lifetime. Mesoscopic modeling and accelerated dynamics simulations allow us to overcome the limitations of atomistic simulations encountered in such systems, and offer detailed insight into the thermodynamic and dynamical properties associated with the nucleation and closure mechanisms of long-lived thermally assisted denaturation bubbles which do not stem from bending-or torque-driven stress. Suitable tuning of the degree of supercoiling and size of specifically designed microDNA is observed to lead to the control of opening characteristic times in the millisecond range, and closure characteristic times ranging over well distinct timescales, from microseconds to several minutes. We discuss how our results can be seen as a dynamical bandwidth which might enhance selectivity for specific DNA binding proteins.

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Transition vitreuse Glass transition Wisdom of crowds Phase separation Phase transition Violent relaxation Random tilings Random process Adsorption Mouvement brownien Ions close to interfaces Dark matter halo 9862Gq 9535+d Gravitation Black hole Processus stochastique 9536+x Chemotaxie Entropy DNA Dark matter Statistical Mechanics AQUEOUS-SOLUTIONS Brownian motion AIR/WATER INTERFACE Structure Automatic Keywords Gravitation collapse Collapse Potential quantum Smoluchowski-Poisson Effondrement gravitationnel Nonrelativistic Competition Bose–Einstein condensates 9880Jk Scalar field theory Thermodynamics Statistical mechanics Stability Théorème du viriel Fokker-Planck Self-gravitating systems Physique statistique Fermi gas Euler-Maclaurin Diffusion 9880-k Quasicrystals Cosmology Asymptotic expansion Suppression Long-range interactions Bethe ansatz Computational modeling Interacting agents Generalized thermodynamics Metastable states Aboav law Formation Condensation Bose-Einstein Scalar field Axion star Denaturation Quantum mechanics Absorption ADN Self-organization Catastrophe theory Keller-Segel Smoluchowski equation Apprentissage par Projet General relativity Turbulence Perturbation theory TASEP Random walker Quantum chromodynamics axion Field theory scalar Gravitational collapse AQUEOUS-SOLUTION Evaporation Collisionless stellar-systems Membrane transport 0440-b Angle-action variables Polytrope Marcheur aléatoire Wave function Energy high Nanofiltration Game theory Astrophysics and astroparticle physics Persistence Virial theorem Critical phenomena Hydrodynamics Chemotaxis 9530Sf