Related papers: RSC remodeling of oligo-nucleosomes: an atomic for…
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…
Chromatin is a complex of DNA, RNA and proteins whose primary function is to package genomic DNA into the tight confines of a cell nucleus. A fundamental repeating unit of chromatin is the nucleosome, an octamer of histone proteins around…
By observing reconstituted chromatin by fluorescence microscopy (FM) and atomic force microscopy (AFM), we found that the density of nucleosomes exhibits a bimodal profile, i.e., there is a large transition between the dense and dispersed…
Chromatin remodeling machineries are abundant and diverse in eukaryotic cells. They have been involved in a variety of situations such as histone exchange and DNA repair, but their importance in gene expression remains unclear. Although the…
We propose a combined experimental (Atomic Force Microscopy) and theoretical study of the structural and dynamical properties of nucleosomes. In contrast to biochemical approaches, this method allows to determine simultaneously the DNA…
Atomic Force Microscopy (AFM) allows to reconstruct the topography of surface with a resolution in the nanometer range. The exceptional resolution attainable with the AFM makes this instrument a key tool in nanoscience and technology. The…
Atomic-scale investigation on mechanical behaviors is highly necessary to fully understand the fracture mechanics especially of brittle materials, which are determined by atomic-scale phenomena (e.g., lattice trapping). Here, exfoliated…
We develop a stochastic model for the programmed frameshift of ribosomes synthesizing a protein while moving along a mRNA template. Normally the reading frame of a ribosome decodes successive triplets of nucleotides on the mRNA in a…
Nucleosomes are the fundamental building blocks of chromatin that not only help in the folding of chromatin but also in carrying epigenetic information. It is known that nucleosome sliding is responsible for dynamically organizing chromatin…
Histone octamers show a heat-induced mobility along DNA. Recent theoretical studies have established two mechanisms that are qualitatively and quantitatively compatible with in vitro experiments on nucleosome sliding: Octamer repositiong…
Chromatin loop extrusion by Structural Maintenance of Chromosome (SMC) complexes is thought to underlie intermediate-scale chromatin organization inside cells. Motivated by a number of experiments suggesting that nucleosomes may block loop…
Active (catalysed) and passive (intrinsic) nucleosome repositioning is known to be a crucial event during the transcriptional activation of certain eucaryotic genes. Here we consider theoretically the intrinsic mechanism and study in detail…
Nucleosomes form the basic unit of compaction within eukaryotic genomes and their locations represent an important, yet poorly understood, mechanism of genetic regulation. Quantifying the strength of interactions within the nucleosome is a…
We construct and analyze monomeric and multimeric models of the stochastic disassembly of a single nucleosome. Our monomeric model predicts the time needed for a number of histone-DNA contacts to spontaneously break, leading to dissociation…
Atomic force microscopy (AFM) enables high-resolution imaging and quantitative force measurement, which is critical for understanding nanoscale mechanical, chemical, and biological interactions. In dynamic AFM modes, however, interaction…
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…
One-dimensional arrays of nucleosomes (DNA-bound histone octamers separated by stretches of linker DNA) fold into higher-order chromatin structures which ultimately make up eukaryotic chromosomes. Chromatin structure formation leads to…
High-speed atomic force microscopy (HS-AFM) is an indispensable technique in the biological field owing to its excellent imaging capability for the real-time observation of biomolecules with high spatial resolution. Furthermore, recent…
Rotations of microscopic magnetic particles, magnetosomes, embedded into the cytoskeleton and subjected to the influence of an ac magnetic field and thermal noise are considered. Magnetosome dynamics is shown to comply with the conditions…
We present a statistical-mechanical analysis of the positioning of nucleosomes along one of the chromosomes of yeast DNA as a function of the strength of the binding potential and of the chemical potential of the nucleosomes. We find a…