相关论文: DNA loop statistics and torsional modulus

DNA looping participates in transcriptional regulation, for instance, by allowing distal binding sites to act synergistically. Here we study this process and compare different regulatory mechanisms based on repression with and without…

By combining analytical and numerical calculations, we investigate the minimal-energy shape of short DNA loops of approximately $100$ base pairs (bp). We show that in these loops the excess twist density oscillates as a response to an…

The continuum-rod model has emerged as an efficient tool to describe the long-length-scale structural-deformations of DNA which are critical to understanding the nature of many biological processes such as gene expression. However, a…

The symmetries of the DNA double helix require a new term in its linear response to stress: the coupling between twist and stretch. Recent experiments with torsionally-constrained single molecules give the first direct measurement of this…

DNA is subject to large deformations in a wide range of biological processes. Two key examples illustrate how such deformations influence the readout of the genetic information: the sequestering of eukaryotic genes by nucleosomes, and DNA…

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…

Storage and retrieval of the genetic information in cells is a dynamic process that requires the DNA to undergo dramatic structural rearrangements. DNA looping is a prominent example of such a structural rearrangement that is essential for…

Organization and maintenance of the chromosomal DNA in living cells strongly depends on the DNA interactions with a plethora of DNA-binding proteins. Single-molecule studies show that formation of nucleoprotein complexes on DNA by such…

DNA loop extrusion is arguably one of the most important players in genome organization. The precise mechanism by which loop extruding factors (LEFs) work is still unresolved and much debated. One of the major open questions in this field…

Chromatin loop extrusion is a popular model for the formation of CTCF loops and topological domains. Recent HiC data have revealed a strong bias in favour of a particular arrangement of the CTCF binding motifs that stabilize loops, and…

We calculate the probability of DNA loop formation mediated by regulatory proteins such as Lac repressor (LacI), using a mathematical model of DNA elasticity. Our model is adapted to calculating quantities directly observable in Tethered…

Recent advances in the understanding of the melting behavior of double-stranded DNA with statistical mechanics methods lead to improved estimates of the weight factors for the dissociation events of the chains, in particular for interior…

We use a statistical mechanical model to study nonthermal denaturation of DNA in the presence of protein-mediated loops. We find that looping proteins which randomly link DNA bases located at a distance along the chain could cause a…

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…

We calculate the spectrum of torsional vibrations of a double-stranded structure that models the double helix of the DNA. We come to the conclusion that within the framework of the model elementary excitations may display an asymmetry as…

In this work, we combine coarse-grained Brownian dynamics simulations and mean-field theory to study supercoiling dynamics, as well as the steady-state profiles of twist and writhe, in an open DNA polymer where one of the free ends is…

Early literature on genome rearrangement modelling views the problem of computing evolutionary distances as an inherently combinatorial one. In particular, attention was given to estimating distances using the minimum number of events…

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…

In columnar assemblies of helical bio-molecules the azimuthal degrees of freedom, i.e. rotations about the long axes of molecules, may be important in determining the structure of the assemblies especially when the interaction energy…

We deduced the torque applied on a single stretched and twisted DNA by integrating with respect to force the change in the molecule's extension as it is coiled. While consistent with previous direct measurements of the torque at high forces…