Related papers: Base sequence dependent sliding of proteins on DNA
We introduce a probabilistic model for protein sliding motion along DNA during the search of a target sequence. The model accounts for possible effects due to sequence-dependent interaction between the nonspecific DNA and the protein. As an…
The two strands of a DNA molecule with a repetitive sequence can pair into many different basepairing patterns. For perfectly periodic sequences, early bulk experiments of Poerschke indicate the existence of a sliding process, permitting…
Recognition and binding of specific sites on DNA by proteins is central for many cellular functions such as transcription, replication, and recombination. In the process of recognition, a protein rapidly searches for its specific site on a…
The structure of DNA Binding Proteins enables a strong interaction with their specific target site on DNA. However, recent single molecule experiment reported that proteins can diffuse on DNA. This suggests that the interactions between…
Gene expression and regulation rely on an apparently finely tuned set of reactions between some proteins and DNA. Such DNA-binding proteins have to find specific sequences on very long DNA molecules and they mostly do so in absence of any…
We investigate the dynamics of DNA translocation through a nanopore using 2D Langevin dynamics simulations, focusing on the dependence of the translocation dynamics on the details of DNA sequences. The DNA molecules studied in this work are…
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,…
The effect of sequence heterogeneity on polynucleotide translocation across a pore and on simple models of molecular motors such as helicases, DNA polymerase/exonuclease and RNA polymerase is studied in detail. Pore translocation of RNA or…
We investigate the sequence-dependent behaviour of localised excitations in a toy, nonlinear model of DNA base-pair opening originally proposed by Salerno. Specifically we ask whether ``breather'' solitons could play a role in the…
Solid-state nanopore DNA sequencers present mechanical and chemical stability, reusability, and large-scale integrability. However, their development is hindered by the absence of a protein-free mechanism for controlling DNA translocation,…
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 precision of biochemical signaling is limited by randomness in the diffusive arrival of molecules at their targets. For proteins binding to the specific sites on the DNA and regulating transcription, the ability of the proteins to…
The diffusion-controlled limit of reaction times for site-specific DNA-binding proteins is derived from first principles. We follow the generally accepted concept that a protein propagates via two competitive modes, a three-dimensional…
We propose a dynamical model for non-specific DNA-protein interaction, which is based on the 'bead-spring' model previously developed by other groups, and investigate its properties using Brownian Dynamics simulations. We show that the…
Using Monte-Carlo simulations, we deconvolved the sliding and hopping kinetics of GFP-LacI proteins on elongated DNA from their experimentally observed seconds-long diffusion trajectories. Our simulations suggest the following results: (1)…
Complex DNA topological structures, including polymer loops, are frequently observed in biological processes when protein molecules simultaneously bind to several distant sites on DNA. However, the molecular mechanisms of formation of these…
The translocation of structured RNA or DNA molecules through narrow pores necessitates the opening of all base pairs. Here, we study the interplay between the dynamics of translocation and base-pairing theoretically, using kinetic Monte…
We investigate diffusion-limited reactions between a diffusing particle and a target site on a semiflexible polymer, a key factor determining the kinetics of DNA-protein binding and polymerization of cytoskeletal filaments. Our theory…
Although mechanical properties of DNA are well characterized at the kilo base-pair range, a number of recent experiments have suggested that DNA is more flexible at shorter length scales, which correspond to the regime that is crucial for…
We considered a dsDNA polymer in which distribution of bases are random at the base pair level but ordered at a length of 18 base pairs and calculated its force elongation behaviour in the constant extension ensemble. The unzipping force…