Related papers: Dynamical model of DNA-protein interaction: effect…
There is now a certain consensus that Transcription Factors (TFs) reach their target sites, where they regulate gene transcription, via a mechanism dubbed facilitated diffusion (FD). In FD, the TF cycles between events of 3D-diffusion in…
The subject of this report is the dynamics of elastic system in conjunction with hydrogen bonds of the DNA. We draw attention to the draw-back of the familiar rod model of the DNA, and make a case of constructing models that could…
It is shown that information transmission inside a cell can occur by means of mechanical waves transmitted through DNA. The propagation of the waves is strongly dependent on the shape of the DNA thus proteins that change the shape of DNA…
Modeling of DNA-protein interactions is a complex process involving many important time and length scales. This can be facilitated through the use of coarse-grained models which reduce the number of degrees of freedom and allow efficient…
Strong experimental and theoretical evidence shows that transcription factors and other specific DNA-binding proteins find their sites using a two-mode search: alternating between 3D diffusion through the cell and 1D sliding along the DNA.…
Three coarse-grained models of the double-stranded DNA are proposed and compared in the context of mechanical manipulation such as twisting and various schemes of stretching. The models differ in the number of effective beads (between two…
Time-resolved single-molecule biophysical experiments yield data that contain a wealth of dynamic information, in addition to the equilibrium distributions derived from histograms of the time series. In typical force spectroscopic setups…
The model of facilitated diffusion describes how DNA-binding proteins, such as transcription factors (TFs), find their chromosomal targets by combining 3D diffusion through the cytoplasm and 1D sliding along nonspecific DNA sequences. The…
We study a model for a protein searching for a target, using facilitated diffusion, on a DNA molecule confined in a finite volume. The model includes three distinct pathways for facilitated diffusion: (a) sliding - in which the protein…
We present a dynamical model of DNA mechanical unzipping under the action of a force. The model includes the motion of the fork in the sequence-dependent landscape, the trap(s) acting on the bead(s), and the polymeric components of the…
Heat-induced mobility of nucleosomes along DNA is an experimentally well-studied phenomenon. A recent experiment shows that the repositioning is modified in the presence of minor-groove binding DNA ligands. We present here a stochastic…
The percentage and sequence of AT and GC base pairs and charges on the DNA backbone contribute significantly to the stiffness of DNA. This elastic property of DNA also changes with small interacting ligands. The single-molecule force…
In this paper, a new method to efficiently simulate diffusion controlled second order chemical reactions is derived and applied to site-specific DNA-binding proteins. The protein enters a spherical cell and propagates via two competing…
By exploring a recent model [Palmeri, J., M. Manghi, and N. Destainville. 2007. Phys. Rev. Lett. 99:088103] where DNA bending elasticity, described by the wormlike chain model, is coupled to base-pair denaturation, we demonstrate that small…
In this review we focus on the idea of establishing connections between the mechanical properties of DNAligand complexes and the physical chemistry of DNA-ligand interactions. This type of connection is interesting because it opens the…
DNA-functionalized particles have great potential for the design of complex self-assembled materials. The major hurdle in realizing crystal structures from DNA-functionalized particles is expected to be kinetic barriers that trap the system…
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…
Despite significant progress in static protein structure collection and prediction, the dynamic behavior of proteins, one of their most vital characteristics, has been largely overlooked in prior research. This oversight can be attributed…
All living systems can function only far away from equilibrium, and for this reason chemical kinetic methods are critically important for uncovering the mechanisms of biological processes. Here we present a new theoretical method of…
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…