title: Twist propagation in dinucleosome arrays.
abstract: We present a Monte Carlo simulation study of the distribution and propagation of twist from one DNA linker to another for a two-nucleosome array subjected to externally applied twist. A mesoscopic model of the array that incorporates nucleosome geometry along with the bending and twisting mechanics of the linkers is employed and external twist is applied in stepwise increments to mimic quasistatic twisting of chromatin fibers. Simulation results reveal that the magnitude and sign of the imposed and induced twist on contiguous linkers depend strongly on their relative orientation. Remarkably, the relative direction of the induced and applied twist can become inverted for a subset of linker orientations-a phenomenon we refer to as "twist inversion". We characterize the twist inversion, as a function of relative linker orientation, in a phase diagram and explain its key features using a simple model based on the geometry of the nucleosome/linker complex. In addition to twist inversion, our simulations reveal "nucleosome flipping", whereby nucleosomes may undergo sudden flipping in response to applied twist, causing a rapid bending of the linker and a significant change in the overall twist and writhe of the array. Our findings shed light on the underlying mechanisms by which torsional stresses impact chromatin organization.
authors.affiliation: Department of NanoEngineering, University of California at San Diego, La Jolla, CA, USA.
authors.forename: Irina V
authors.initials: IV
authors.lastname: Dobrovolskaia
authors.forename: Martin
authors.initials: M
authors.lastname: Kenward
authors.forename: Gaurav
authors.initials: G
authors.lastname: Arya
mesh_terms: D000818:Animals; D002645:Chickens; D003198:Computer Simulation; D009010:Monte Carlo Method; D009690:Nucleic Acid Conformation; D009707:Nucleosomes / Q000737:chemistry*; D012399:Rotation; D013816:Thermodynamics
chemical_list: D009707:Nucleosomes