Related papers: DNA twist stability changes with magnesium(2+) con…
Storage and retrieval of the genetic information in cells is a dynamic process that requires the DNA to undergo dramatic structural rearrangements. DNA looping is a prominent example of such a structural rearrangement that is essential for…
We use the worm-like chain model to study supercoiling of DNA under tension and torque. The model reproduces experimental data for a broad range of forces, salt concentrations and contour lengths. We find a plane of first order phase…
We investigate the role of bubble positioning in the force-induced melting of double-stranded DNA using two distinct approaches: Brownian Dynamics simulations and the Gaussian Network Model. We isolate the effect of bubble positioning by…
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…
A simple model of DNA based on two interacting polymers has been used to study the unzipping of a double stranded DNA subjected to a periodic force. We propose a dynamical transition, where without changing the physiological condition, it…
Single T4-DNA molecules were confined in rectangular-shaped channels with a depth of 300 nm and a width in the range 150-300 nm casted in a poly(dimethylsiloxane) nanofluidic chip. The extensions of the DNA molecules were measured with…
Most of the anticancer drugs bind to double-stranded DNA (dsDNA) by intercalative-binding mode. Although experimental studies have become available recently, a molecular-level understanding of the interactions between the drug and dsDNA…
A dynamical model is presented for chiral change in DNA molecules. The model is an extension of the conventional elastic model which incorporates the structure of base pairs and uses a spinor representation for the DNA configuration…
Although DNA is often bent in vivo, it is unclear how DNA-bending forces modulate DNA-protein binding affinity. Here, we report how a range of DNA-bending forces modulates the binding of the Integration Host Factor (IHF) protein to various…
Coarse-grained models have emerged as valuable tools to simulate long DNA molecules while maintaining computational efficiency. These models aim at preserving interactions among coarse-grained variables in a manner that mirrors the…
By equilibrating condensed DNA arrays against reservoirs of known osmotic stress and examining them with several structural probes, it has been possible to achieve a detailed thermodynamic and structural characterization of the change…
We develop a robust coarse-grained model for single and double stranded DNA by representing each nucleotide by three interaction sites (TIS) located at the centers of mass of sugar, phosphate, and base. The resulting TIS model includes…
The functioning of double-stranded (ds) nucleic acids (NAs) in cellular processes is strongly mediated by their elastic response. These processes involve proteins that interact with dsDNA or dsRNA and distort their structures. The…
Plectonemes are intertwined helically looped domains which form when a DNA molecule is supercoiled, i.e. over- or under-wounded. They are ubiquitous in cellular DNA and their physical properties have attracted significant interest both from…
The dependence of DNA assemblies conductance on relative humidity is investigated theoretically. Following earlier suggestions, we consider the ionic conductivity through the layers of water adsorbed by DNA molecules. The increase in…
We propose a model for DNA dynamics by introducing the helical structure through twist deformation in analogy with the structure of helimagnet and cholesteric liquid crystal system. The dynamics in this case is found to be governed by the…
While analyzing the persistence length of DNA atomistic simulations Wu et al. [J. Chem. Phys. 142, 125103 (2015)] introduced an empirical formula to account for the observed length-dependence. In particular they found that the persistence…
The equilibrium structure of a Dinucleosome is studied using an elastic model that takes into account the force and torque balance conditions. Using the proper boundary conditions, it is found that the conformational energy of the problem…
We use a recently developed coarse-grained model to simulate the overstretching of duplex DNA. Overstretching at 23C occurs at 74 pN in the model, about 6-7 pN higher than the experimental value at equivalent salt conditions. Furthermore,…
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…