Related papers: Energetic funnel facilitates facilitated diffusion
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…
Transcription factors (TFs) are regulatory proteins that bind DNA in promoter regions of the genome and either promote or repress gene expression. Here we predict analytically that enhanced homo-oligonucleotide sequence correlations, such…
We study the propagation of very large amplitude localized excitations in a model of DNA that takes explicitly into account the helicoidal structure. These excitations represent the ``transcription bubble'', where the hydrogen bonds between…
Many cellular responses to surrounding cues require temporally concerted transcriptional regulation of multiple genes. In prokaryotic cells, a single-input-module motif with one transcription factor regulating multiple target genes can…
The transcription of DNA into mRNA is initiated and aided by a number of transcription factors (TFs), proteins with DNA-binding regions that attach themselves to binding sites in the DNA (transcription factor binding sites, TFBSs). As it…
The control over DNA elongation in nanofluidic devices holds great potential for large-scale genomic analysis. So far, the manipulation of DNA in nanochannels has been mostly carried out with electrophoresis and seldom with hydrodynamics,…
A theory is presented of the longitudinal dispersion of DNA under equilibrium confined in a nanochannel. Orientational fluctuations of the DNA chain build up to give rise to substantial fluctuations of the coil in the longitudinal direction…
We explore the consequences of very high dimensionality in the dynamical landscape of protein folding. Consideration of both typical range of stabilising interactions, and folding rates themselves, leads to a model of the energy…
The energy landscapes of proteins have evolved to be different from most random heteropolymers. Many studies have concluded that evolutionary selection for rapid and reliable folding to a given structure that is stable at biological…
Several processes in the cell, such as gene regulation, start when key proteins recognise and bind to short DNA sequences. However, as these sequences can be hundreds of million times shorter than the genome, they are hard to find by simple…
The transcriptional regulation of gene expression is orchestrated by complex networks of interacting genes. Increasing evidence indicates that these transcriptional regulatory networks (TRNs) in bacteria have an inherently hierarchical…
Identifying low-energy adsorption geometries on catalytic surfaces is a practical bottleneck for computational heterogeneous catalysis: the difficulty lies not only in the cost of density functional theory (DFT) but in proposing initial…
Evolution of gene regulation is crucial for our understanding of the phenotypic differences between species, populations and individuals. Sequence-specific binding of transcription factors to the regulatory regions on the DNA is a key…
The scaling properties of DNA knots of different complexities were studied by atomic force microscope. Following two different protocols DNA knots are adsorbed onto a mica surface in regimes of (i) strong binding, that induces a kinetic…
In the course of various biological processes, specific DNA-binding proteins must find a particular target sequence/protein or a damaged site on the DNA efficiently. DNA-binding proteins perform this task based on diffusion. Yet,…
We report results showing that thermally-induced openings of double stranded DNA coincide with the location of functionally relevant sites for transcription. Investigating both viral and bacterial DNA gene promoter segments, we found that…
Swimming bacteria create long-range velocity fields that stir a large volume of fluid and move around passive particles dispersed in the fluid. Recent experiments and simulations have shown that long-time mean-squared displacement of…
Transcription factors (TFs) are key regulators of gene expression. Based on the classical scenario in which the TF search process switches between one-dimensional motion along the DNA molecule and free Brownian motion in the nucleus, we…
We developed a method for estimating the positional distribution of transcription fac-tor (TF) binding sites using ChIP-chip data, and applied it to recently published experiments on binding sites of nine TFs; OCT4, SOX2, NANOG, HNF1A,…
Current models for the folding of the human genome see a hierarchy stretching down from chromosome territories, through A/B compartments and TADs (topologically-associating domains), to contact domains stabilized by cohesin and CTCF.…