相关论文: Stepwise bending of DNA by a single TATA-box Bindi…
Previous numerical investigations of an one-dimensional DNA model with an extended modified coupling constant by transcripting enzyme are integrated to longer time and demonstrated explicitly the trapping of breathers by DNA chains with…
Functionalization of nanoparticles or colloids is increasingly being used to develop customizable "atoms". Functionalization by attaching single strands of DNA allows for direct control of the binding between nanoparticles, since…
A detailed description of the conformational plasticity of double stranded DNA (ds) is a necessary framework for understanding protein-DNA interactions. Until now, however structure and kinetics of the transition from the basic conformation…
A model for the unidirectional movement of dynein is presented based on structural observations and biochemical experimental results available. In this model, the binding affinity of dynein for microtubule is independent of its nucleotide…
A model is presented to describe the nucleotide and repeat addition processivity by the telomerase. In the model, the processive nucleotide addition is implemented on the basis of two requirements: One is that stem IV loop stimulates the…
The mechanical model based on beads and springs, which we recently proposed to study non-specific DNA-protein interactions [J. Chem. Phys. 130, 015103 (2009)], was improved by describing proteins as sets of interconnected beads instead of…
The issue of the nucleation and slow closure mechanisms of non superhelical stress-induced denaturation bubbles in DNA is tackled using coarse-grained MetaDynamics and Brownian simulations. A minimal mesoscopic model is used where the…
Solid state nanopores have emerged as powerful tools for single-molecule sensing, yet the rapid uncontrolled translocation of the molecule through the pore remains a key limitation. We have previously demonstrated that an active…
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…
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,…
Recent work indicates that twist-bend coupling plays an important role in DNA micromechanics. Here we investigate its effect on bent DNA. We provide an analytical solution of the minimum-energy shape of circular DNA, showing that twist-bend…
We use the "magnetic tweezers" technique to reveal the structural transitions that DNA undergoes in the force-torsion space. In particular, we focus on regions corresponding to negative supercoiling. These regions are characterized by the…
Transcription factors (TFs) are macromolecules that bind to \textit{cis}-regulatory specific sub-regions of DNA promoters and initiate transcription. Finding the exact location of these binding sites (aka motifs) is important in a variety…
In biology, there are several processes in which unfolded protein chains are transported along narrow-tube channels. Normally, without such a severe configurational constraint, unfolded polypeptides would not bind to each other. However,…
We study DNA self-assembly and DNA computation using a coarse-grained DNA model within the directional dynamic bonding framework {[}C. Svaneborg, Comp. Phys. Comm. 183, 1793 (2012){]}. In our model, a single nucleotide or domain is…
DNA looping plays a fundamental role in a wide variety of biological processes, providing the backbone for long range interactions on DNA. Here we develop the first model for DNA looping by an arbitrarily large number of proteins and solve…
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…
Evolutionary trajectories and phenotypic states available to cell populations are ultimately dictated by intermolecular interactions between DNA, RNA, proteins, and other molecular species. Here we study how evolution of gene regulation in…
The spatial organization of DNA involves DNA loop extrusion and the formation of protein-DNA condensates. While the significance of each process is increasingly recognized, their interplay remains unexplored. Using molecular dynamics…
Using Brownian dynamics simulations, we study the migration of long charged chains in an electrophoretic microchannel device consisting of an array of microscopic entropic traps with alternating deep regions and narrow constrictions. Such a…