title: Slow closure of denaturation bubbles in DNA: twist matters.
abstract: 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 nonzero torsional modulus in the duplex state, κ(φ)=200 to 300k(B)T. 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 100μs are found. The bubble starts winding from both ends until it reaches a ≈10 bp metastable state due to the large elastic energy stored in the bubble. The final closure is limited by three competing mechanisms depending on κ(φ) 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 last temperature-activated mechanism, yielding a good quantitative agreement with the experiments.
authors.affiliation: Université de Toulouse, Université Paul Sabatier (UPS), Laboratoire de Physique Théorique (IRSAMC), F-31062 Toulouse, France.
authors.forename: Anil Kumar
authors.initials: AK
authors.lastname: Dasanna
authors.forename: Nicolas
authors.initials: N
authors.lastname: Destainville
authors.forename: John
authors.initials: J
authors.lastname: Palmeri
authors.forename: Manoel
authors.initials: M
authors.lastname: Manghi
mesh_terms: D003198:Computer Simulation; D004247:DNA / Q000737:chemistry* / Q000648:ultrastructure*; D008956:Models, Chemical; D008958:Models, Molecular; D009690:Nucleic Acid Conformation; D009691:Nucleic Acid Denaturation; D013696:Temperature
chemical_list: D004247:DNA