Related papers: Topological interactions in DNA catenanes
The topological interaction arising in interlinked polymeric rings such as DNA catenanes is considered. More specifically, the free energy for a pair of linked random walk rings is derived where the distance $R$ between two segments each of…
Gel electrophoresis is a powerful experimental method to probe the topology of DNA and other biopolymers. While there is a large body of experimental work which allows us to accurately separate different topoisomers of a molecule, a full…
The structure of DNA in the nucleosome core particle is studied using an elastic model that incorporates anisotropy in the bending energetics and twist-bend coupling. Using the experimentally determined structure of nucleosomal DNA [T.J.…
Understanding the relationship between the microscopic structure and topology of a material and its macroscopic properties is a fundamental challenge across a wide range of systems. Here, we investigate the viscoelasticity of DNA nanostar…
This paper aims at a comprehensive understanding on the novel elastic property of double-stranded DNA (dsDNA) discovered very recently through single-molecule manipulation techniques. A general elastic model for double-stranded biopolymers…
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…
Allosteric interactions in DNA are crucial for various biological processes. These interactions are quantified by measuring the change in free energy as a function of the distance between the binding sites for two ligands. Here we show that…
In this paper we study the role of topology in DNA gel electrophoresis experiments via molecular dynamics simulations. The gel is modelled as a 3D array of obstacles from which half edges are removed at random with probability p, thereby…
We introduce a coarse-grained model of DNA with bases modeled as rigid-body ellipsoids to capture their anisotropic stereochemistry. Interaction potentials are all physicochemical and generated from all-atom simulation/parameterization with…
A unified model is constructed to study the recently observed DNA entropic elasticity, cooperative extensibility, and supercoiling property. With the introduction of a new structural parameter (the folding angle $\phi$), bending…
A versatile approach to modeling the conformations and energetics of DNA loops is presented. The model is based on the classical theory of elasticity, modified to describe the intrinsic twist and curvature of DNA, the DNA bending…
A model for the motion of ring-shaped DNA in a gel is introduced and studied by numerical simulations and a mean-field approximation. The ring motion is mediated by finger-shaped loops (hernias) that move in an amoeba-like fashion around…
Conformational transitions are ubiquitous in biomolecular systems, have significant functional roles and are subject to evolutionary pressures. Here we provide a first theoretical framework for topological transition, i.e. conformational…
In this work, we show that by varying the experimental conditions, the driving amplitude, a dynamic force microscope allows DNA properties to be selectively imaged. The substrate on which the DNA is fixed is a silica surface grafted with…
The effect of electrostatic interactions on the stretching of DNA is investigated using a simple worm like chain model. In the limit of small force there are large conformational fluctuations which are treated using a self-consistent…
We investigate quantum transport characteristics of a ladder model, which effectively mimics the topology of a double-stranded DNA molecule. We consider the interaction of tunneling charges with a selected internal vibrational degree of…
Simple elastic network models of DNA were developed to reveal the structure-dynamics relationships for several nucleotide sequences. First, we propose a simple all-atom elastic network model of DNA that can explain the profiles of…
Dynamics of topological solitons describing open states in the DNA double helix are studied in the frameworks of the model which takes into account asymmetry of the helix. It is shown that three types of topological solitons can occur in…
In this paper we study properties of topological RNA structures, i.e.~RNA contact structures with cross-serial interactions that are filtered by their topological genus. RNA secondary structures within this framework are topological…
The mechanical properties of DNA are typically described by elastic theories with purely local couplings (on-site models). We discuss and analyze coarse-grained (oxDNA) and all-atom simulations, which indicate that in DNA distal sites are…