title: DNA-DNA interactions in tight supercoils are described by a small effective charge density.
abstract: DNA-DNA interactions are important for genome compaction and transcription regulation. In studies of such complex processes, DNA is often modeled as a homogeneously charged cylinder and its electrostatic interactions are calculated within the framework of the Poisson-Boltzmann equation. Commonly, a charge adaptation factor is used to address limitations of this theoretical approach. Despite considerable theoretical and experimental efforts, a rigorous quantitative assessment of this parameter is lacking. Here, we comprehensively characterized DNA-DNA interactions in the presence of monovalent ions by analyzing the supercoiling behavior of single DNA molecules held under constant tension. Both a theoretical model and coarse-grained simulations of this process revealed a surprisingly small effective DNA charge of 40% of the nominal charge density, which was additionally supported by all-atom molecular dynamics simulations.
authors.affiliation: Department of Physics, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, USA.
authors.forename: Christopher
authors.initials: C
authors.lastname: Maffeo
authors.forename: Robert
authors.initials: R
authors.lastname: Schöpflin
authors.forename: Hergen
authors.initials: H
authors.lastname: Brutzer
authors.forename: René
authors.initials: R
authors.lastname: Stehr
authors.forename: Aleksei
authors.initials: A
authors.lastname: Aksimentiev
authors.forename: Gero
authors.initials: G
authors.lastname: Wedemann
authors.forename: Ralf
authors.initials: R
authors.lastname: Seidel
mesh_terms: D001696:Biomechanical Phenomena / Q000187:drug effects; D004278:DNA, Superhelical / Q000737:chemistry* / Q000378:metabolism*; D056004:Molecular Dynamics Simulation; D009010:Monte Carlo Method; D012492:Salts / Q000494:pharmacology; D055672:Static Electricity
chemical_list: D004278:DNA, Superhelical; D012492:Salts