title: Pore translocation of knotted DNA rings.
abstract: We use an accurate coarse-grained model for DNA and stochastic molecular dynamics simulations to study the pore translocation of 10-kbp-long DNA rings that are knotted. By monitoring various topological and physical observables we find that there is not one, as previously assumed, but rather two qualitatively different modes of knot translocation. For both modes the pore obstruction caused by knot passage has a brief duration and typically occurs at a late translocation stage. Both effects are well in agreement with experiments and can be rationalized with a transparent model based on the concurrent tensioning and sliding of the translocating knotted chains. We also observed that the duration of the pore obstruction event is more controlled by the knot translocation velocity than the knot size. These features should advance the interpretation and design of future experiments aimed at probing the spontaneous knotting of biopolymers.
authors.affiliation: Molecular and Statistical Biophysics, International School for Advanced Studies (SISSA), I-34136 Trieste, Italy.
authors.forename: Antonio
authors.identifier: 0000-0002-5049-9255
authors.initials: A
authors.lastname: Suma
authors.affiliation: Molecular and Statistical Biophysics, International School for Advanced Studies (SISSA), I-34136 Trieste, Italy michelet@sissa.it.
authors.forename: Cristian
authors.identifier: 0000-0002-1022-1638
authors.initials: C
authors.lastname: Micheletti
mesh_terms: D004247:DNA / Q000737:chemistry*; D006801:Humans; D008958:Models, Molecular; D056004:Molecular Dynamics Simulation; D058608:Nanopores; D009690:Nucleic Acid Conformation
chemical_list: D004247:DNA
keywords: DNA knotting; molecular dynamics simulations; pore translocation