Related papers: DNA Spools under Tension
Most living systems rely on double-stranded DNA (dsDNA) to store their genetic information and perpetuate themselves. This biological information has been considered the main target of evolution. However, here we show that symmetries and…
It is well known that transcription can induce torsional stress in DNA, affecting the activity of nearby genes or even inducing structural transitions in the DNA duplex. It has long been assumed that the generation of significant torsional…
The influence of tension on DNA looping has been studied both experimentally and theoretically in the past. However, different theoretical models have yielded different predictions, leaving uncertainty about their validity. We briefly…
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…
DNA plays a special role in polymer science not just because of the highly selective recognition of complementary single DNA strands but also because bacteria can express DNA chains that are very long yet perfectly monodisperse. The latter…
It is a standard exercise in mechanical engineering to infer the external forces and torques on a body from its static shape and known elastic properties. Here we apply this kind of analysis to distorted double-helical DNA in complexes with…
Debates about conductivity of DNAs have been recently renewed due to contradictory results of direct measurements by use of electrical contacts to molecules. In several works it was discovered that double-stranded (ds)DNAs are conductors:…
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…
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…
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…
The binding of proteins onto DNA contributes to the shaping and packaging of genome as well as to the expression of specific genetic messages. With a view to understanding the interplay between the presence of proteins and the deformation…
We propose that semiflexible polymers in poor solvent collapse in two stages. The first stage is the well known formation of a dense toroidal aggregate. However, if the solvent is sufficiently poor, the condensate will undergo a second…
Solid state nanopores have emerged as powerful tools for single-molecule sensing, yet the rapid uncontrolled translocation of the molecule through the pore remains a key limitation. We have previously demonstrated that an active…
The competition between toroidal and rod-like conformations as possible ground states for DNA condensation is studied as a function of the stiffness, the length of the DNA and the form of the long-range interactions between neighboring…
We study the nonlinear dynamics of a protein-DNA molecular system by treating DNA as a set of two coupled linear chains and protein in the form of a single linear chain sliding along the DNA at the physiological temperature in a viscous…
Cells regulate gene expression in part by forming DNA-protein condensates in the nucleus. While existing theories describe the equilibrium size and stability of such condensates, their dynamics remain less understood. Here, we use…
Due to its polyionic character the DNA double helix is stable and biologically active only in salty aqueous media where its charge is compensated by solvent counterions. Monovalent metal ions are ubiquitous in DNA environment and they are…
In mechanical manipulation experiments, a single DNA molecule overwound at constant force undergoes a discontinuous drop in extension as it buckles and forms a superhelical loop (a plectoneme). Further overwinding the DNA, we observe an…
Based on the result of an unzipping phase transition by a force in a model of DNA, we hypothesize that the DnaA-type proteins act as a pulling agent with a force slightly less than the critical force for unzipping. The dynamic (space-time)…
Genomic DNA is constantly subjected to various mechanical stresses arising from its biological functions and cell packaging. If the local mechanical properties of DNA change under torsional and tensional stress, the activity of…