%0 Journal Article
%T Slow closure of denaturation bubbles in DNA: twist matters
%+ Physique Statistique des Systèmes Complexes (LPT) (PhyStat)
%+ Laboratoire de Physique Théorique (LPT)
%+ Laboratoire Charles Coulomb (L2C)
%A Dasanna, Anil, K.
%A Destainville, Nicolas
%A Palmeri, John
%A Manghi, Manoel
%< avec comité de lecture
%@ 1539-3755
%J Physical Review E : Statistical, Nonlinear, and Soft Matter Physics
%I American Physical Society
%V 87
%P 052703
%8 2013
%D 2013
%Z 1302.1673
%R 10.1103/PhysRevE.87.052703
%Z Physics [physics]/Condensed Matter [cond-mat]/Soft Condensed Matter [cond-mat.soft]
%Z Physics [physics]/Physics [physics]/Biological Physics [physics.bio-ph]Journal articles
%X The closure of long equilibrated denaturation bubbles in DNA is studied using Brownian dynamics simulations. A minimal mesoscopic model is used where the double-helix is made of two interacting bead-spring freely rotating strands, with a non-zero torsional modulus in the duplex state, $\kappa_\phi=$200 to 300 kT. For DNAs of lengths N=40 to 100 base-pairs (bps) with a large initial bubble in their middle, long closure times of 0.1 to 100 microseconds are found. The bubble starts winding from both ends until it reaches a 10 bp metastable state. The final closure is limited by three competing mechanisms depending on $\kappa_\phi$ and N: arms diffusion until their alignment, bubble diffusion along the DNA until one end is reached, or local Kramers process (crossing over a torsional energy barrier). For clamped ends or long DNAs, the closure occurs via this latter temperature activated mechanism, yielding for the first time a good quantitative agreement with experiments.
%G English
%2 https://hal.science/hal-00822680/document
%2 https://hal.science/hal-00822680/file/PhysRe7.pdf
%L hal-00822680
%U https://hal.science/hal-00822680
%~ UNIV-TLSE3
%~ IRSAMC
%~ LPT
%~ CNRS
%~ L2C
%~ LPT_PHY
%~ MIPS
%~ UNIV-MONTPELLIER
%~ UNIV-UT3
%~ UT3-INP
%~ UT3-TOULOUSEINP
%~ UM-2015-2021