相关论文: Looping and Clustering model for the organization …
We investigate the measurement of DNA supercoiling density ($\sigma$) along chromosomes using interaction frequencies between DNA and DNA-anchored clusters of proteins. Specifically, we show how the physics of DNA supercoiling leads, in…
Bacterial chromosome replication occurs in the absence of a canonical spindle apparatus; yet it reliably produces organised and segregated genomes. While both passive and active mechanisms have been investigated, DNA replication itself is a…
Liquid-liquid phase separated (LLPS) states are key to compartmentalise components in the absence of membranes, however it is unclear whether LLPS condensates are actively and specifically organized in the sub-cellular space and by which…
Recent experimental and theoretical approaches have attempted to quantify the physical organization (compaction and geometry) of the bacterial chromosome with its complement of proteins (the nucleoid). The genomic DNA exists in a complex…
The genomic DNA of bacteria occupies only a fraction of the cell called the nucleoid, although it is not bounded by any membrane and would occupy a volume hundreds of times larger than the cell in the absence of constraints. The two most…
We showed in our previous studies that just $3\%$ cross-links, at special points along the contour of the bacterial DNA help the DNA-polymer to get organized at micron length scales \cite{jpcm,epl}. In this work, we investigate how does the…
The unconstrained genomic DNA of bacteria forms a coil, which volume exceeds 1000 times the volume of the cell. Since prokaryotes lack a membrane-bound nucleus, in sharp contrast with eukaryotes, the DNA may consequently be expected to…
Using data from contact maps of the DNA-polymer of $E. Coli$ (at kilobase pair resolution) as an input to our model, we introduce cross-links between monomers in a bead-spring model of a ring polymer at very specific points along the chain.…
Using a bead-spring model of bacterial DNA polymers of {\em C. crescentus} and {\em E. coli} we show that just $33$ and $38$ effective cross-links at special positions along the chain contour of the DNA can lead to the large-scale…
Protein-DNA complexes with loops play a fundamental role in a wide variety of cellular processes, ranging from the regulation of DNA transcription to telomere maintenance. As ubiquitous as they are, their precise in vivo properties and…
The chromosomal DNA of bacteria is folded into a compact body called the nucleoid, which is composed essentially of DNA (80%), RNA (10%), and a number of different proteins (10%). These nucleoid proteins act as regulators of gene expression…
A prominent organizational feature of bacterial chromosomes was revealed by Hi-C experiments, indicating anomalously high contacts between the left and right chromosomal arms. These long-range contacts have been attributed to various…
While bacterial chromosomes were long thought to be amorphous, recent experiments reveal pronounced organizational features. However, the extent of bacterial chromosome organization remains unclear. Here, we develop a fully data-driven…
In-vivo DNA organization at large length scales ($\sim 100nm$) is highly debated and polymer models have proved useful to understand the principle of DNA-organization. Here, we show that $<2$% cross-links at specific points in a ring…
Entropic repulsion between DNA ring polymers under confinement is the key mechanism governing the spatial segregation of bacterial chromosomes, although it remains incompletely understood how proteins aid the process of entropic…
The formation of DNA loops by proteins and protein complexes that bind at distal DNA sites plays a central role in many cellular processes, such as transcription, recombination, and replication. Here we review the basic thermodynamic…
DNA looping is important in DNA condensation and regulation. One method for forming a DNA loop, thought to be used by the condensing agent protamine, is bind-and-bend. In bind-and-bend, molecules bind all along the DNA, each creating a bend…
Many fundamental biological processes are regulated by protein-DNA complexes called {\it synaptosomes}, which possess multiple interaction sites. Despite the critical importance of synaptosomes, the mechanisms of their formation remain not…
The native conformation of structured proteins is stabilized by a complex network of interactions. We analyzed the elementary patterns that constitute such network and ranked them according to their importance in shaping protein sequence…
The mechanism and driving forces of chromosome segregation in the bacterial cell cycle of E. coli is one of the least understood events in its life cycle. Using principles of entropic repulsion between polymer loops confined in a cylinder,…