相关论文: Nucleoid clustering drives stepwise expansion and …
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 mechanism responsible for the compaction of the genomic DNA of bacteria inside a structure called the nucleoid is a longstanding but still lively debated question. Most puzzling is the fact that the nucleoid occupies only a small…
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…
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,…
The volume occupied by the unconstrained genomic DNA of prokaryotes in saline solutions is thousand times larger than the cell. Moreover, it is not separated from the rest of the cell by a membrane. Nevertheless, it occupies only a small…
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…
In recent years significant attention has been attracted to proposals which utilize DNA for nanotechnological applications. Potential applications of these ideas range from the programmable self-assembly of colloidal crystals, to biosensors…
Focusing on the DNA-bridging nucleoid proteins Fis and H-NS, and integrating several independent experimental and bioinformatic data sources, we investigate the links between chromosomal spatial organization and global transcriptional…
We study the compression and extension dynamics of a DNA-like polymer interacting with non-DNA binding and DNA-binding proteins, by means of computer simulations. The geometry we consider is inspired by recent experiments probing the…
The bacterial genome is organized in a structure called the nucleoid by a variety of associated proteins. These proteins can form complexes on DNA that play a central role in various biological processes, including chromosome segregation. A…
The volume occupied by unconstrained bacterial DNA in physiological solutions exceeds 1000 times the volume of the cell. Still, it is confined to a well defined region of the cell called the nucleoid, which occupies only a fraction of the…
Different numerical mappings of the DNA sequences have been studied using a new cluster-scaling method and the well known spectral methods. It is shown, in particular, that the nucleotide sequences in DNA molecules have robust…
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…
In living cells, proteins involved in specialized biochemical functions are often spatially organized within biomolecular condensates. Increasing evidence suggests that some of these condensates, including DNA repair condensates, emerge…
Fluorescence microscopy reveals that the contents of many (membrane-free) nuclear "bodies" exchange rapidly with the soluble pool whilst the underlying structure persists; such observations await a satisfactory biophysical explanation. To…
Recent experiments have been able to visualise chromosome organization in fast-growing E.coli cells. However, the mechanism underlying the spatio-temporal organization remains poorly understood. We propose that the DNA adopts a specific…
Transcriptional activity has been shown to relate to the organization of chromosomes in the eukaryotic nucleus and in the bacterial nucleoid. In particular, highly transcribed genes, RNA polymerases and transcription factors gather into…
This work addresses the question of the interplay of DNA demixing and supercoiling in bacterial cells. Demixing of DNA from other globular macromolecules results from the overall repulsion between all components of the system and leads to…
Molecular motor proteins form the basis of cellular dynamics. Recently, notable efforts have led to the creation of their DNA-based mimics, which can carry out complex nanoscale motion. However, such functional analogues have not yet been…
DNA-mediated multivalent interactions between colloidal particles have been extensively applied for their ability to program bulk phase behaviour and dynamic processes. Exploiting the competition between different types of DNA-DNA bonds,…