Related papers: Active Loop Extrusion guides DNA-Protein Condensat…
Biomolecular condensates form by phase separation of biological polymers and have important functions in the cell $-$ functions that are inherently connected to their physical properties. A remarkable aspect of such condensates is that…
We show that minuscule entropic forces, on the order of 100 fN, can prevent the formation of DNA loops--a ubiquitous means of regulating the expression of genes. We observe a tenfold decrease in the rate of LacI-mediated DNA loop formation…
We study the influence of a structural disorder on the thermodynamical properties of 2D-elastic chains submitted to mechanical/topological constraint as loops. The disorder is introduced via a spontaneous curvature whose distribution along…
Using Langevin dynamics simulations, we study elastic response of single semiflexible polyelectrolytes to an external force pulling on the chain ends, to mimic the stretching of DNA molecules by optical tweezers. The linear chains are…
Transcription is the first step of gene expression, in which a particular segment of DNA is copied to RNA by the enzyme RNA polymerase (RNAP). Despite many details of the complex interactions between DNA and RNA synthesis disclosed…
The twisting deformation of mechanically stretched DNA molecules is studied by a coarse grained Hamiltonian model incorporating the fundamental interactions that stabilize the double helix and accounting for the radial and angular base pair…
The jumping-droplet condensation, namely the out-of-plane jumping of condensed droplets upon coalescence, has been a promising technical innovation in the fields of energy harvesting, droplet manipulation, thermal management, etc., yet is…
The chiral nature of DNA plays a crucial role in cellular processes. Here we use magnetic tweezers to explore one of the signatures of this chirality, the coupling between stretch and twist deformations. We show that the extension of a…
Protein folding and evolution are intimately linked phenomena. Here, we revisit the concept of exons as potential protein folding modules across 38 abundant and conserved protein families. Taking advantage of genomic exon-intron…
We propose a nonlinear model derived from first principles, to describe bubble dynamics of DNA. Our model equations include a term derived from the dissipative effect of intermolecular vibrational modes. Such modes are excited by the…
Structural-Maintenance-of-Chromosome (SMC) complexes such as condensins organise the folding of chromosomes. However, their role in modulating the entanglement of DNA and chromatin is not fully understood. To address this question, we…
Capturing the physical organisation and dynamics of genomic regions is one of the major open challenges in biology. The kinetoplast DNA (kDNA) is a topologically complex genome, made by thousands of DNA (mini and maxi) circles interlinked…
DNA-interacting proteins have roles multiple processes, many operating as molecular machines which undergo dynamic metastable transitions to bring about their biological function. To fully understand this molecular heterogeneity, DNA and…
Topological entanglements severely interfere with important biological processes. For this reason, genomes must be kept unknotted and unlinked during most of a cell cycle. Type II Topoisomerase (TopoII) enzymes play an important role in…
With the help of one-dimensional random Potts-like model we study the origins of fine structure observed on differential melting profiles of double-stranded DNA. We assess the effects of sequence arrangement on DNA melting curves through…
Gene transcription by a RNA Polymerase (RNAP) enzyme requires that double-stranded DNA be locally and transiently opened, which results in an increase of DNA supercoiling downstream of the RNAP and a decrease of supercoiling upstream of it.…
The local opening of DNA is an intriguing phenomenon from a statistical physics point of view, but is also essential for its biological function. For instance, the transcription and replication of our genetic code can not take place without…
RNA-binding proteins form biomolecular condensates with RNA through phase separation, playing crucial roles in various cellular processes. While intrinsically disordered regions (IDRs) are key drivers of phase separation, additional factors…
In this letter, we characterize experimentally the diffusiophoretic motion of colloids and lambda- DNA toward higher concentration of solutes, using microfluidic technology to build spatially- and temporally-controlled concentration…
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…