Dynamics of forced nucleosome unraveling and role of nonuniform histone-DNA interactions.

No abstract is available for this paper.

• Publication year

  2012

• Venue

  Biophysical Journal

• Publication date

  2012-09-05

• Fields of study

  Biology, Medicine, Physics, Chemistry

• Identifiers
  DOI 10.1016/J.BPJ.2012.07.043PMID 23009848PMCID PMC3433614
• External record

  Open on Semantic Scholar

• Source metadata

  Semantic Scholar, PubMed

• No claims are published for this paper.

• No concepts are published for this paper.

• Histone fold modifications control nucleosome unwrapping and disassembly

  2011cited by this paper
• Dissecting DNA-histone interactions in the nucleosome by molecular dynamics simulations of DNA unwrapping.

  2011cited by this paper
• Influence of pulling handles and device stiffness in single-molecule force spectroscopy.

  2011cited by this paper
• A quantitative model of nucleosome dynamics

  2011cited by this paper
• Tension-dependent structural deformation alters single-molecule transition kinetics

  2011cited by this paper
• Model accounting for the effects of pulling-device stiffness in the analyses of single-molecule force measurements.

  2010cited by this paper
• Synergistic action of RNA polymerases in overcoming the nucleosomal barrier

  2010cited by this paper
• Mechanisms of ATP-dependent nucleosome sliding.

  2010cited by this paper
• Twist propagation in dinucleosome arrays.

  2010cited by this paper
• A Structural Perspective on the Where, How, Why, and What of Nucleosome Positioning

  2010influential reference
• Evidence for heteromorphic chromatin fibers from analysis of nucleosome interactions

  2009cited by this paper
• Brownian dynamics simulation of DNA unrolling from the nucleosome.

  2009cited by this paper
• A tale of tails: how histone tails mediate chromatin compaction in different salt and linker histone environments.

  2009cited by this paper
• Nucleosome disassembly intermediates characterized by single-molecule FRET

  2009cited by this paper
• High resolution dynamic mapping of histone-DNA interactions in a nucleosome

  2008cited by this paper
• Fast , long-range , reversible conformational fluctuations in nucleosomes revealed by single-pair fluorescence resonance energy transfer

  2008cited by this paper
• Chromatin remodeling: insights and intrigue from single-molecule studies

  2007cited by this paper
• Effect of force on mononucleosomal dynamics

  2006cited by this paper
• Flexible histone tails in a new mesoscopic oligonucleosome model.

  2006cited by this paper
• Intrinsic rates and activation free energies from single-molecule pulling experiments.

  2006cited by this paper
• Single chromatin fiber stretching reveals physically distinct populations of disassembly events.

  2005cited by this paper
• Fast, long-range, reversible conformational fluctuations in nucleosomes revealed by single-pair fluorescence resonance energy transfer.

  2005cited by this paper
• Forced unraveling of nucleosomes assembled on heterogeneous DNA using core histones, NAP-1, and ACF.

  2005cited by this paper
• DNA spools under tension.

  2003cited by this paper
• Controlling the double helix

  2003cited by this paper
• Solvent mediated interactions in the structure of the nucleosome core particle at 1.9 a resolution.

  2002influential reference
• Mechanical disruption of individual nucleosomes reveals a reversible multistage release of DNA

  2002influential reference
• Unfolding individual nucleosomes by stretching single chromatin fibers with optical tweezers

  2001cited by this paper
• Rotational and Translational Self-Diffusion in Colloidal Sphere Suspensions and the Applicability of Generalized Stokes−Einstein Relations

  2000cited by this paper
• DNA binding within the nucleosome core.

  1998cited by this paper
• Crystal structure of the nucleosome core particle at 2.8 Å resolution

  1997cited by this paper
• A model for the cooperative binding of eukaryotic regulatory proteins to nucleosomal target sites.

  1996influential reference
• Overcoming a nucleosomal barrier to transcription.

  1995cited by this paper
• A second‐order algorithm for the simulation of the Brownian dynamics of macromolecular models

  1990cited by this paper
• Interactions of highly charged colloidal cylinders with applications to double-stranded.

  1977cited by this paper
• Interactions of highly charged colloidal cylinders with applications to double‐stranded DNA

  1977cited by this paper

• DNA spontaneously wrapping around a histone core prefers negative supercoiling: A Brownian dynamics study

  2024cites this paper
• How Do Nucleosome Dynamics Regulate Protein Search on DNA?

  2023cites this paper
• High-yield ligation-free assembly of DNA constructs with nucleosome positioning sequence repeats for single-molecule manipulation assays

  2023cites this paper
• Nucleosome breathing facilitates cooperative binding of pluripotency factors Sox2 and Oct4 to DNA.

  2022cites this paper
• Stochastic models of nucleosome dynamics reveal regulatory rules of stimulus-induced epigenome remodeling.

  2022cites this paper
• Multiscale modeling of genome organization with maximum entropy optimization

  2021cites this paper
• Constructing arrays of nucleosome positioning sequences using Gibson Assembly for single-molecule studies

  2020cites this paper
• Quantitative Modeling of Nucleosome Unwrapping from Both Ends.

  2019cites this paper
• Nucleosomal DNA Dynamics Mediate Oct4 Pioneer Factor Binding

  2019cites this paper
• Title Partial Unwrapping and Histone Tail Dynamics in NucleosomeRevealed by Coarse-Grained Molecular Simulations

  2018cites this paper
• Transfer-matrix calculations of the effects of tension and torque constraints on DNA–protein interactions

  2018cites this paper
• Dynamics of Chromatin Fibers: Comparison of Monte Carlo Simulations with Force Spectroscopy

  2018cites this paper
• Critical Role of Histone Tail Entropy in Nucleosome Unwinding

  2018cites this paper
• Critical Role of Histone Tail Entropy in Nucleosome Unwinding

  2018cites this paper
• Designing nucleosomal force sensors.

  2017cites this paper
• Effects of Nucleosome Structure on DNA Photoproduct Formation and Deamination

  2017cites this paper
• Dynamique et stabilité du nucléosome

  2017cites this paper
• Modulation of cyclobutane thymine photodimer formation in T11-tracts in rotationally phased nucleosome core particles and DNA minicircles

  2017cites this paper
• Quantitative Analysis of Single-Molecule Force Spectroscopy on Folded Chromatin Fibers

  2016cites this paper
• Free-energy landscape of mono- and dinucleosomes: Enhanced rotational flexibility of interconnected nucleosomes.

  2016cites this paper
• Nucleosome dynamics: Sequence matters.

  2016cites this paper
• Computational strategies to address chromatin structure problems

  2016cites this paper
• Elastic model for dinucleosome structure and energy.

  2016cites this paper
• Why Do Nucleosomes Unwrap Asymmetrically?

  2016cites this paper
• Exploring the Free Energy Landscape of Nucleosomes.

  2016cites this paper
• Dynamic unwrapping of nucleosomes by HsRAD51 that includes sliding and rotational motion of histone octamers

  2016cites this paper
• Structural dynamics of nucleosome mediated by acetylations at H3K56 and H3K115,122

  2016cites this paper
• The chromatin fiber: multiscale problems and approaches.

  2015cites this paper
• Partial Unwrapping and Histone Tail Dynamics in Nucleosome Revealed by Coarse-Grained Molecular Simulations

  2015cites this paper
• Bayesian Uncertainty Quantification for Bond Energies and Mobilities Using Path Integral Analysis.

  2015cites this paper
• Quantitative analysis of single-molecule force spectroscopy on folded chromatin fibers

  2015cites this paper
• Invincible DNA tethers: covalent DNA anchoring for enhanced temporal and force stability in magnetic tweezers experiments

  2014cites this paper
• Nanopores Suggest a Negligible Influence of CpG Methylation on Nucleosome Packaging and Stability

  2014cites this paper
• Chromatin Fiber Structure Revealed through Quantitative Analysis of Single-Molecule Force Spectroscopy1

  2014cites this paper
• Topological constraints strongly affect chromatin reconstitution in silico

  2014cites this paper
• Monte-Carlo simulations of PAMAM dendrimer-DNA interactions.

  2014cites this paper
• An Advanced Coarse-Grained Nucleosome Core Particle Model for Computer Simulations of Nucleosome-Nucleosome Interactions under Varying Ionic Conditions

  2013cites this paper
• Unwinding and rewinding the nucleosome inner turn: force dependence of the kinetic rate constants.

  2012cites this paper
• Annals of the New York Academy of Sciences Evolutionary Dynamics and Information Hierarchies in Biological Systems

  year unknowncites this paper