Thermodynamics of G.A mispairs in DNA: continuum electrostatic model

Sequence-dependent B-A transitions in DNA in silico: Electrostatic condensation mechanism

Dynamics of the polymorphic A<->B transitions in DNA is compared for two polypurine sequences, poly(dA).poly(dT) and poly(dG).poly(dC), long known to exhibit contrasting properties in experiments. In free molecular dynamics simulations reversible transitions are induced by changing the size of a water drop around DNA neutralized by Na ions. In poly(dG).poly(dC) the B<->A transitions are easy, smooth and perfectly reversible. In contrast, a B->A transition in poly(dA).poly(dT) dodecamer fragment could not be obtained even though its A-form is stable under low hydration. Normal B->A transitions …

Protein-DNA electrostatics: toward a new paradigm for protein sliding

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 active process. It has been rapidly recognized that to achieve this task these proteins should be efficient at both searching (i.e. sampling fast relevant parts of DNA) and finding (i.e. recognizing the specific site). A two-mode search and variants of it have been suggested since the 70s to explain either a fast search or an efficient recognition. Combining …

On the ion-mediated interaction between protein and DNA

The mechanism allowing a protein to search of a target sequence on DNA is currently described as an intermittent process composed of 3D diffusion in bulk and 1D diffusion along the DNA molecule. Due to the relevant charge of protein and DNA, electrostatic interaction should play a crucial role during this search. In this paper, we explicitly derive the mean field theory allowing for a description of the protein-DNA electrostatics in solution. This approach leads to a unified model of the search process, where 1D and 3D diffusion appear as a natural consequence of the diffusion on an extended i…

Self-consistent treatment of electrostatics in molecular DNA braiding through external forces

In this paper we consider a physical system in which two DNA molecules braid about each other. The distance between the two molecular ends, on either side of the braid, is held at a distance much larger than supercoiling radius of the braid. The system is subjected to an external pulling force, and a moment that induces the braiding. In a model, developed for understanding such a system, we assume that each molecule can be divided into a braided and unbraided section. We also suppose that the DNA is nicked so that there is no constraint of the individual linking numbers of the molecules. Inclu…

Electrostatic Binding and Hydrophobic Collapse of Peptide-Nucleic Acid Aggregates Quantified Using Force Spectroscopy

Knowledge of the mechanisms of interaction between self-aggregating peptides and nucleic acids or other polyanions is key to the understanding of many aggregation processes underlying several human diseases (e.g. Alzheimer's and Parkinson's diseases). Determining the affinity and kinetic steps of such interactions is challenging due to the competition between hydrophobic self-aggregating forces and electrostatic binding forces. Kahalalide F (KF) is an anticancer hydrophobic peptide which contains a single positive charge that confers strong aggregative properties with polyanions. This makes KF…

包装的DNA基因组设定病毒的长程静电各向异性

Packaged DNA genome sets the long-range electrostatic anisotropy of a virus

本研究通过泊松-玻尔兹曼理论揭示，包装的DNA基因组赋予病毒长程静电各向异性，其源于逆线轴DNA结构，影响病毒间及病毒-壁相互作用，并以噬菌体λ验证。

Phase Behavior of Columnar DNA Assemblies

The pair interaction between two stiff parallel linear DNA molecules depends not only on the distance between their axes but on their azimuthal orientation. The positional and orientational order in columnar B-DNA assemblies in solution is investigated, based on the DNA-DNA electrostatic pair potential that takes into account DNA helical symmetry and the amount and distribution of adsorbed counterions. A phase diagram obtained by lattice sum calculations predicts a variety of positionally and azimuthally ordered phases and bundling transitions strongly depending on the counterion adsorption pa…

New smoothly connecting open curves for modeling nucleosome-decorated DNA

We introduce an analytical method to generate the pathway of a closed protein-bound DNA minicircle. This is a general method which can be used to connect any two open curves with well defined mathematical definitions as well as pairs of discrete systems found experimentally. We used this method to describe the configurations of torsionally relaxed, 360-base pair DNA rings with two evenly-spaced, ideal nucleosomes. We considered superhelical nucleosomal pathways with different levels of DNA wrapping and allowed for different inter-nucleosome orientations. We completed the DNA circles with the s…

Sensing of DNA conformation based on change in FRET efficiency between laser dyes

This communication reports the effect of DNA conformation on fluorescence resonance energy transfer (FRET) efficiency between two laser dyes in layer by layer (LbL) self assembled film. The dyes Acraflavine and Rhodamine B were attached onto the negative phosphate backbones of DNA in LbL film through electrostatic attraction. Then FRET between these dyes was investigated. Increase in pH or temperature causes the denaturation of DNA followed by coil formation of single stranded DNA. As a result the FRET efficiency also changed along with it. These observations demonstrated that by observing the…

Modeling DNA loops using the theory of elasticity

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 anisotropy, and electrostatic properties. All the model parameters are considered to be functions of the loop arclength, so that the DNA sequence-specific properties can be modeled. The model is applied to the test case study of a DNA loop clamped by the lac repressor protein. Several topologically different conformations are predicted for various lengths of the loop.…

不同硫代喹啉浓度下DNA热稳定性的分析

Analysis of DNA thermal stability across a broad range of thionine concentrations

研究硫代喹啉与DNA的相互作用机制，揭示其浓度依赖的分子作用，为设计抗癌药物和核酸检测探针提供理论支持。

Thermodynamics of force-induced B-DNA melting: single-strand discreteness matters

Overstretching of B-DNA is currently understood as force-induced melting. Depending on the geometry of the stretching experiment, the force threshold for the overstretching transition is around 65 or 110 pN. Although the mechanisms behind force-induced melting have been correctly described by Rouzina and Bloomfield \cite{RouzinaBloomfield2001a}, neither force threshold has been exactly calculated by theory. In this work, a detailed analysis of the force-extension curve is presented, based on a description of single-stranded DNA in terms of the discrete Kratky-Porod model, consistent with (i) t…