FisMat2017 - Submission - View

Abstract's title: Pore translocation of knotted DNA rings
Submitting author: Antonio Suma
Affiliation: SISSA - Scuola Internazionale Superiore di Studi Avanzati
Affiliation Address: via Bonomea, 265 - 34136 Trieste ITALY
Country: Italy
Oral presentation/Poster (Author's request): Oral presentation
Other authors and affiliations: Cristian Micheletti (SISSA)

Biopolymers, such as DNA, can be long enough to become spontaneously knotted. This can have detrimental effects on their functionality in biological contexts, and in single-molecule manipulation experiments too. A relevant example is the translocation of DNA through biological or solid-state nanopores, which can become hindered by the presence of knots.  Here, to advance the understanding of the process and its relationship with DNA knotting in equilibrium, we present a detailed study based on molecular dynamics simulations of an accurate mesoscopic DNA model. Specifically, we consider equilibrated knotted DNA rings of 10 kbp represented with the oxDNA model and use Langevin dynamics to simulate their driven passage through a 10-nm–wide pore. Such a theoretical and computational framework allows us to investigate the translocation process and the geometry–topology interplay with unprecedented structural and dynamical detail [1].

[1] A. Suma and C. Micheletti "Pore translocation of knotted DNA rings", Proc. Natl. Acad. Sci. USA, (2017)