相关论文: Nucleosome repositioning via loop formation
From a nanoscience perspective, cellular processes and their reduced in vitro imitations provide extraordinary examples for highly robust few or single molecule reaction pathways. A prime example are biochemical reactions involving DNA…
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…
The eukaryotic cell nucleus harbors the DNA genome that is organized in a dynamic chromatin network and embedded in a viscous crowded fluid. This environment directly affects enzymatic reactions and target search processes that access the…
Recent experiments indicated that disorder effect in DNA may lead to a transition of the charge transport mechanism from band resonant tunnelling to thermal activated hopping. In this letter, based on Mott's variable-range hopping theory we…
The dynamics of polymer translocation through a pore has been the subject of recent theoretical and experimental works. We have considered theoretical estimates and performed computer simulations to understand the mechanism of DNA uptake…
Genetic information is stored in a linear sequence of base-pairs; however, thermal fluctuations and complex DNA conformations such as folds and loops make it challenging to order genomic material for in vitro analysis. In this work, we…
It is generally difficult to predict the positions of mutations in genomic DNA at the nucleotide level. Retroviral DNA insertion is one mode of mutation, resulting in host infections that are difficult to treat. This mutation process…
Gene sequences in the vicinity of splice sites are found to possess dinucleotide periodicities, especially RR and YY, with the period close to the pitch of nucleosome DNA. This confirms previously reported finding about preferential…
DNA loop formation is one of several mechanisms used by organisms to regulate genes. The free energy of forming a loop is an important factor in determining whether the associated gene is switched on or off. In this paper we use an elastic…
The molecular network in an organism consists of transcription/translation regulation, protein-protein interactions/modifications and a metabolic network, together forming a system that allows the cell to respond sensibly to the multiple…
During the eukaryotic cell cycle, chromatin undergoes several conformational changes, which are believed to play key roles in gene expression regulation during interphase, and in genome replication and division during mitosis. In this…
Recent works on localized charge transport along DNA, based on a three--dimensional, tight--binding model (Eur. Phys. J. B 30:211, 2002; Phys. D 180:256, 2003), suggest that charge transport is mediated by the coupling of the radial and…
In solution, DNA is a highly charged macromolecule which bears a unit of negative charge on each phosphate of its sugar-phosphate backbone. Although partially compensated by counterions adsorbed at or condensed near it, DNA still produces a…
This paper deals with the possible motion of nucleons in the nucleus, which is due to realistic inter-nucleonic forces. This approach provides new or more substantiated conclusions about the nuclear structure than those based on the…
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…
DNA methylation is an epigenetic mechanism whose important role in development has been widely recognized. This epigenetic modification results in heritable changes in gene expression not encoded by the DNA sequence. The underlying…
The electrical properties of DNA molecules are investigated by charge injection and electric force microscopy experiments. Prior to injection, DNA molecules exhibit a weak positively charged state. We probe the electrical behaviour of DNA…
We present Brownian dynamics simulations of the facilitated diffusion of a protein, modelled as a sphere with a binding site on its surface, along DNA, modelled as a semi-flexible polymer. We consider both the effect of DNA organisation in…
In living systems, DNA undergoes continuous and rhythmic mechanical remodeling through condensation, looping, and disentangling to regulate gene expression, segregate chromosomes, and guide morphogenesis. Here, we demonstrate a purely…
As the chief informational molecule of life, DNA is subject to extensive physical manipulations. The energy required to deform double-helical DNA depends on sequence, and this mechanical code of DNA influences gene regulation, such as…