title: Probing the elasticity of DNA on short length scales by modeling supercoiling under tension.
abstract: The wormlike-chain (WLC) model is widely used to describe the energetics of DNA bending. Motivated by recent experiments, alternative, so-called subelastic chain models were proposed that predict a lower elastic energy of highly bent DNA conformations. Until now, no unambiguous verification of these models has been obtained because probing the elasticity of DNA on short length scales remains challenging. Here we investigate the limits of the WLC model using coarse-grained Monte Carlo simulations to model the supercoiling of linear DNA molecules under tension. At a critical supercoiling density, the DNA extension decreases abruptly due to the sudden formation of a plectonemic structure. This buckling transition is caused by the large energy required to form the tightly bent end-loop of the plectoneme and should therefore provide a sensitive benchmark for model evaluation. Although simulations based on the WLC energetics could quantitatively reproduce the buckling measured in magnetic tweezers experiments, the buckling almost disappears for the tested linear subelastic chain model. Thus, our data support the validity of a harmonic bending potential even for small bending radii down to 3.5 nm.
authors.affiliation: CC Bioinformatics, University of Applied Sciences Stralsund, Stralsund, Germany.
authors.forename: Robert
authors.initials: R
authors.lastname: Schöpflin
authors.forename: Hergen
authors.initials: H
authors.lastname: Brutzer
authors.forename: Oliver
authors.initials: O
authors.lastname: Müller
authors.forename: Ralf
authors.initials: R
authors.lastname: Seidel
authors.forename: Gero
authors.initials: G
authors.lastname: Wedemann
mesh_terms: D003198:Computer Simulation; D004247:DNA / Q000737:chemistry*; D004278:DNA, Superhelical / Q000737:chemistry*; D004548:Elasticity; D008958:Models, Molecular; D013314:Stress, Mechanical
chemical_list: D004278:DNA, Superhelical; D004247:DNA