Related papers: Elastic Model for Dinucleosome Structure and Energ…
The structure of DNA in the nucleosome core particle is studied using an elastic model that incorporates anisotropy in the bending energetics and twist-bend coupling. Using the experimentally determined structure of nucleosomal DNA [T.J.…
We examine the conformations of a model for under- and overwound DNA. The molecule is represented as a cylindrically symmetric elastic string subjected to a stretching force and to constraints corresponding to a specification of the link…
A versatile approach to modeling the conformations and energetics of DNA loops is presented. The model is based on the classical theory of elasticity, modified to describe the intrinsic twist and curvature of DNA, the DNA bending…
A theoretical framework for evaluating the approximate energy and dynamic properties associated with the folding of DNA into nucleosomes and chromatin is presented. For this purpose experimentally determined elastic constants of linear DNA…
Simple elastic network models of DNA were developed to reveal the structure-dynamics relationships for several nucleotide sequences. First, we propose a simple all-atom elastic network model of DNA that can explain the profiles of…
Within a simple elastic theory, we study the elongation versus force characteristics of a supercoiled DNA molecule at thermal equilibrium in the regime of small supercoiling. The partition function is mapped to the path integral…
Nucleosomes organize the folding of DNA into chromatin and significantly influence transcription, replication, regulation and repair. All atom molecular dynamics simulations of a nucleosome and of its 146 basepairs of DNA free in solution…
Eukaryotic DNA is packaged into chromatin: one-dimensional arrays of nucleosomes separated by stretches of linker DNA are folded into 30-nm chromatin fibers which in turn form higher-order structures. Each nucleosome, the fundamental unit…
Chromatin is a complex of DNA and specific proteins forming an intermediary level of organization of eukaryotic genomes, between double-stranded DNA and chromosome. Within a generic modeling of the chromatin assembly, we investigate the…
Dynamics of nucleosomes, the building blocks of the chromatin, has crucial effects on expression, replication and repair of genomes in eukaryotes. Beside constant movements of nucleosomes by thermal fluctuations, ATP-dependent chromatin…
This paper aims at a comprehensive understanding on the novel elastic property of double-stranded DNA (dsDNA) discovered very recently through single-molecule manipulation techniques. A general elastic model for double-stranded biopolymers…
We present Monte-Carlo (MC) simulations of the stretching of a single 30 nm chromatin fiber. The model approximates the DNA by a flexible polymer chain with Debye-H\"uckel electrostatics and uses a two-angle zig-zag model for the geometry…
We examine the conformations of a model for a short segment of closed DNA. The molecule is represented as a cylindrically symmetric elastic rod with a constraint corresponding to a specification of the linking number. We obtain analytic…
The structural origin of the size of the 11 nm nucleosomal disc is addressed. On the nanometer length-scale the organization of DNA as chromatin in the chromosomes involves a coiling of DNA around the histone core of the nucleosome. We…
We present a self-contained theory for the mechanical response of DNA in single molecule experiments. Our model is based on a 1D continuum description of the DNA molecule and accounts both for its elasticity and for DNA-DNA electrostatic…
The response of a short DNA segment to bending is studied, taking into account the anisotropy in the bending rigidities caused by the double-helical structure. It is shown that the anisotropy introduces an effective nonlinear twist-bend…
We present an elastic model of B-form DNA as a stack of thin, rigid plates or base pairs that are not permitted to deform. The symmetry of DNA and the constraint of plate rigidity limit the number of bulk elastic constants contributing to a…
We study numerically the mechanical stability and elasticity properties of duplex DNA molecules within the frame of a network model incorporating microscopic degrees of freedom related with the arrangement of the base pairs. We pay special…
We examine the elastic model of short circular DNA. We obtain analytic expressions for configurations, elastic energy, twist and linking number of our solutions. We find the onset of the plectonemic transition. We suggest ways to use our…
The approach for the description of the DNA conformational transformations on the mesoscopic scales in the frame of the double helix is presented. Due to consideration of the joint motions of DNA structural elements along the conformational…