Related papers: Spontaneous Unidirectional Loop Extrusion Emerges …
Condensation of hundreds of mega-base-pair-long human chromosomes in a small nuclear volume is a spectacular phenomenon. This process is driven by the formation of chromosome loops. ATP consuming motor, condensin, interacts with chromatin…
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…
Loop extrusion convincingly describes how certain Structural Maintenance of Chromosome (SMC) proteins mediate the formation of large DNA loops. Yet, most of the existing computational models cannot reconcile recent in vitro observations…
The spatial organization of DNA involves DNA loop extrusion and the formation of protein-DNA condensates. While the significance of each process is increasingly recognized, their interplay remains unexplored. Using molecular dynamics…
Structural Maintenance Complexes (SMC) are energy consuming motors that are important in folding the genome by loop extrusion (LE) in all stages of the cell cycle. Single molecule magnetic tweezer pulling experiments have revealed that…
Loop extrusion is one of the main processes shaping chromosome organisation across the cell cycle, yet its role in regulating DNA entanglement and nucleoplasm viscoelasticity remains overlooked. We simulate entangled solutions of linear…
Using Langevin dynamics simulations, we study the hysteresis in unzipping of longer double stranded DNA chains whose ends are subjected to a time dependent periodic force with frequency $\omega$ and amplitude $G$ keeping the other end…
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 develop a kinetic theory of cohesin-driven loop extrusion on a disordered chromatin track with transient barriers. In the stationary state, the mean loop size is shown to obey a universal law determined by the bare processivity and a…
Active loop extrusion - the process of formation of dynamically growing chromatin loops due to the motor activity of DNA-binding protein complexes - is firmly established mechanism responsible for chromatin spatial organization at different…
We derive the single molecule equation of state (force-extension relation) for DNA molecules bearing sliding loops and deflection defects. Analytical results are obtained in the large force limit by employing an analogy with instantons in…
Both animal and plant tissue exhibit a nonlinear rheological phenomenon known as compression stiffening, or an increase in moduli with increasing uniaxial compressive strain. Does such a phenomenon exist in single cells, which are the…
An active loop-extrusion mechanism is regarded as the main out--of--equilibrium mechanism responsible for the structuring of megabase-sized domains in chromosomes. We developed a model to study the dynamics of the chromosome fibre by…
Force extension curves (FECs), which quantify the response of a variety of biomolecules subject to mechanical force ($f$), are often quantitatively fit using worm-like chain (WLC) or freely-jointed chain (FJC) models. These models predict…
Motivated by the recent experimental observations of the DNA loop extrusion by protein motors, in this paper we investigate the statistical properties of the growing polymer loops within the ideal chain model. The loop conformation is…
We calculate the equation of state of DNA under tension for the case that the DNA features loops. Such loops occur transiently during DNA condensation in the presence of multivalent ions or sliding cationic protein linkers. The…
We propose a generic model of driven DNA under the influence of an oscillatory force of amplitude $F$ and frequency $\nu$ and show the existence of a dynamical transition for a chain of finite length. We find that the area of the hysteresis…
Effect of bending anisotropy on a planar DNA loop, using energy minimization and neglecting entropic effects, is studied. We show that the anisotropy results in polygonal shape of the loop and increasing the anisotropy makes the edges…
The macroscopic curvature induced in double helical B-DNA by regularly repeated adenine tracts (A-tracts) is a long known, but still unexplained phenomenon. This effect plays a key role in DNA studies because it is unique in the amount and…
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…