Electrostatic interactions in biological DNA-related systems

Sequence-dependent Kink-and-Slide Deformations of Nucleosomal DNA Facilitated by Histone Arginines Bound in the Minor Groove

(2012) Difei Wang et al.   JOURNAL OF BIOMOLECULAR STRUCTURE & DYNAMICS

Electrostatics of Strongly Charged Biological Polymers: Ion-Mediated Interactions and Self-Organization in Nucleic Acids and Proteins

(2010) Gerard C.L. Wong et al.   Annual Review of Physical Chemistry

Looping Probabilities in Model Interphase Chromosomes

(2010) Angelo Rosa et al.   BIOPHYSICAL JOURNAL

Visualizing the Formation and Collapse of DNA Toroids

(2010) Bram van den Broek et al.   BIOPHYSICAL JOURNAL

Mechanisms of Capsid Assembly around a Polymer

(2010) Aleksandr Kivenson et al.   BIOPHYSICAL JOURNAL

Cation Charge Dependence of the Forces Driving DNA Assembly

(2010) Jason DeRouchey et al.   BIOPHYSICAL JOURNAL

A Lattice Model for Transcription Factor Access to Nucleosomal DNA

(2010) Vladimir B. Teif et al.   BIOPHYSICAL JOURNAL

Charge State of the Globular Histone Core Controls Stability of the Nucleosome

(2010) Andrew T. Fenley et al.   BIOPHYSICAL JOURNAL

Squeezing Protein Shells: How Continuum Elastic Models, Molecular Dynamics Simulations, and Experiments Coalesce at the Nanoscale

(2010) W.H. Roos et al.   BIOPHYSICAL JOURNAL

Electrostatic Origin of Salt-Induced Nucleosome Array Compaction

(2010) Nikolay Korolev et al.   BIOPHYSICAL JOURNAL

Non-specific (entropic) forces as major determinants of the structure of mammalian chromosomes

(2010) Kieran Finan et al.   CHROMOSOME RESEARCH

Chromosome dynamics, molecular crowding, and diffusion in the interphase cell nucleus: a Monte Carlo lattice simulation study

(2010) Christian C. Fritsch et al.   CHROMOSOME RESEARCH

Chromatin structure: does the 30-nm fibre exist in vivo?

(2010) Kazuhiro Maeshima et al.   CURRENT OPINION IN CELL BIOLOGY

First-order–like transition in salt-induced macroion-polyelectrolyte desorption

(2010) S. J. de Carvalho   EPL

Looping charged elastic rods: applications to protein-induced DNA loop formation

(2010) A. G. Cherstvy   EUROPEAN BIOPHYSICS JOURNAL WITH BIOPHYSICS LETTERS

Symmetry of electrostatic interaction between pyrophosphate DNA molecules

(2010) V. L. Golo et al.   EUROPEAN PHYSICAL JOURNAL E

Counterion-mediated weak and strong coupling electrostatic interaction between like-charged cylindrical dielectrics

(2010) Matej Kanduč et al.   JOURNAL OF CHEMICAL PHYSICS

Electric potential and bending rigidity of a wormlike particle in electrolyte solution

(2010) V. A. Andreev et al.   JOURNAL OF CHEMICAL PHYSICS

DNA-protein binding rates: Bending fluctuation and hydrodynamic coupling effects

(2010) Yann von Hansen et al.   JOURNAL OF CHEMICAL PHYSICS

Polymer translocation through α-hemolysin pore with tunable polymer-pore electrostatic interaction

(2010) Chiu Tai Andrew Wong et al.   JOURNAL OF CHEMICAL PHYSICS

Modeling Studies of Chromatin Fiber Structure as a Function of DNA Linker Length

(2010) Ognjen Perišić et al.   JOURNAL OF MOLECULAR BIOLOGY

Effects of Salts on Internal DNA Pressure and Mechanical Properties of Phage Capsids

(2010) Alex Evilevitch et al.   JOURNAL OF MOLECULAR BIOLOGY

DNA-DNA sequence homology recognition: physical mechanisms and open questions

(2010) A. G. Cherstvy   JOURNAL OF MOLECULAR RECOGNITION

Comparison of Kinetic and Dynamical Models of DNA−Protein Interaction and Facilitated Diffusion†

(2010) Ana-Maria Florescu et al.   JOURNAL OF PHYSICAL CHEMISTRY A

Undulations Enhance the Effect of Helical Structure on DNA Interactions

(2010) D. J. Lee et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Electrostatic Persistence Length

(2010) Marshall Fixman   JOURNAL OF PHYSICAL CHEMISTRY B

Self-Assembly of Lamellar Lipid−DNA Complexes Simulated by Explicit Solvent Counterion Model

(2010) Lianghui Gao et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Linker Formation in an Overcharged Complex of Two Dendrimers and Linear Polyelectrolyte

(2010) Sergey V. Larin et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Universality of DNA Adsorption Behavior on the Cationic Membranes of Nanolipoplexes

(2010) Giulio Caracciolo et al.   JOURNAL OF PHYSICAL CHEMISTRY B

An Accurate Prediction of Hydration Free Energies by Combination of Molecular Integral Equations Theory with Structural Descriptors

(2010) Ekaterina L. Ratkova et al.   JOURNAL OF PHYSICAL CHEMISTRY B

DNA Surface Hybridization: Comparison of Theory and Experiment

(2010) Damion Irving et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Multishell Structures of Virus Coat Proteins

(2010) Peter Prinsen et al.   JOURNAL OF PHYSICAL CHEMISTRY B

All-Atom Multiscale Simulation of Cowpea Chlorotic Mottle Virus Capsid Swelling

(2010) Yinglong Miao et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Using DNA to Link Gold Nanoparticles, Polymers, and Molecules: A Theoretical Perspective

(2010) One-Sun Lee et al.   Journal of Physical Chemistry Letters

Long-Range Architecture of Single Lipid-Based Complex Nanoparticles with Local Hexagonal Packing

(2010) Guillaume Tresset et al.   Journal of Physical Chemistry Letters

Fluctuations and interactions of semi-flexible polyelectrolytes in columnar assemblies

(2010) D J Lee et al.   JOURNAL OF PHYSICS-CONDENSED MATTER

Charge renormalization of helical macromolecules

(2010) D J Lee   JOURNAL OF PHYSICS-CONDENSED MATTER

Statistical–mechanical lattice models for protein–DNA binding in chromatin

(2010) Vladimir B Teif et al.   JOURNAL OF PHYSICS-CONDENSED MATTER

Towards a universal method for calculating hydration free energies: a 3D reference interaction site model with partial molar volume correction

(2010) David S Palmer et al.   JOURNAL OF PHYSICS-CONDENSED MATTER

Biopolymer organization upon confinement

(2010) D Marenduzzo et al.   JOURNAL OF PHYSICS-CONDENSED MATTER

Cooperative Melting in Caged Dimers with Only Two DNA Duplexes

(2010) Ibrahim Eryazici et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Tailoring DNA Structure To Increase Target Hybridization Kinetics on Surfaces

(2010) Andrew E. Prigodich et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Effect of the Electrostatic Interactions on Stretching of Semiflexible and Biological Polyelectrolytes

(2010) Jan-Michael Y. Carrillo et al.   MACROMOLECULES

Physical virology

(2010) W. H. Roos et al.   Nature Physics

Structure and DNA binding activity of the mouse condensin hinge domain highlight common and diverse features of SMC proteins

(2010) Julia J. Griese et al.   NUCLEIC ACIDS RESEARCH

Electrostatic hot spot on DNA-binding domains mediates phosphate desolvation and the pre-organization of specificity determinant side chains

(2010) Alpay N. Temiz et al.   NUCLEIC ACIDS RESEARCH

Differential stability of DNA crossovers in solution mediated by divalent cations

(2010) Péter Várnai et al.   NUCLEIC ACIDS RESEARCH

Interpreting protein/DNA interactions: distinguishing specific from non-specific and electrostatic from non-electrostatic components

(2010) P. L. Privalov et al.   NUCLEIC ACIDS RESEARCH

Physics of DNA: unravelling hidden abilities encoded in the structure of ‘the most important molecule’

(2010) Alexei A. Kornyshev   PHYSICAL CHEMISTRY CHEMICAL PHYSICS

Facilitated search of proteins on DNA: correlations are important

(2010) Rahul K. Das et al.   PHYSICAL CHEMISTRY CHEMICAL PHYSICS

Physics of protein–DNA interactions: mechanisms of facilitated target search

(2010) Anatoly B. Kolomeisky   PHYSICAL CHEMISTRY CHEMICAL PHYSICS

Thermodynamics of nanospheres encapsulated in virus capsids

(2010) Antonio Šiber et al.   PHYSICAL REVIEW E

Symmetries of interacting helices of charge

(2010) Jonathan Landy et al.   PHYSICAL REVIEW E

Torsional effect on the wrapping transition of a semiflexible polymer around a core as a model of nucleosome

(2010) Yuji Higuchi et al.   PHYSICAL REVIEW E

Confined nematic polymers: Order and packing in a nematic drop

(2010) Daniel Svenšek et al.   PHYSICAL REVIEW E

Simple electrostatic model applicable to biomolecular recognition

(2010) T. P. Doerr et al.   PHYSICAL REVIEW E

DNA Condensation at Freestanding Cationic Lipid Bilayers

(2010) C. Herold et al.   PHYSICAL REVIEW LETTERS

Multibond Dynamics of Nanoscale Friction: The Role of Temperature

(2010) Itay Barel et al.   PHYSICAL REVIEW LETTERS

Helical Chirality: a Link between Local Interactions and Global Topology in DNA

(2010) Youri Timsit et al.   PLoS One

Divalent counterion-induced condensation of triple-strand DNA

(2010) X. Qiu et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Right-handed double-helix ultrashort DNA yields chiral nematic phases with both right- and left-handed director twist

(2010) Giuliano Zanchetta et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Single-base resolution mapping of H1-nucleosome interactions and 3D organization of the nucleosome

(2010) S. H. Syed et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Condensed DNA: Condensing the concepts

(2010) Vladimir B. Teif et al.   PROGRESS IN BIOPHYSICS & MOLECULAR BIOLOGY

Virus engineering: functionalization and stabilization

(2010) M. G. Mateu   PROTEIN ENGINEERING DESIGN & SELECTION

DNA curvature and flexibility in vitro and in vivo

(2010) Justin P. Peters et al.   QUARTERLY REVIEWS OF BIOPHYSICS

Long range interactions in nanoscale science

(2010) Roger H. French et al.   REVIEWS OF MODERN PHYSICS

Imaging and manipulation of single viruses by atomic force microscopy

(2010) M. Baclayon et al.   Soft Matter

Liquid crystal phase formation by biopolymers

(2010) I. W. Hamley   Soft Matter

Liquid crystal models of biological materials and processes

(2010) Alejandro D. Rey   Soft Matter

Chromatin Higher-order Structure and Dynamics

(2010) C. L. Woodcock et al.   Cold Spring Harbor Perspectives in Biology

Nanoindentation Studies Reveal Material Properties of Viruses

(2009) Wouter H. Roos et al.   ADVANCED MATERIALS

Cation-induced polyelectrolyte–polyelectrolyte attraction in solutions of DNA and nucleosome core particles

(2009) Nikolay Korolev et al.   ADVANCES IN COLLOID AND INTERFACE SCIENCE

An end to 40 years of mistakes in DNA–protein association kinetics?

(2009) Stephen E. Halford   BIOCHEMICAL SOCIETY TRANSACTIONS

Analytical Model Study of Dendrimer/DNA Complexes

(2009) Khawla Qamhieh et al.   BIOMACROMOLECULES

Depletion Effects Massively Change Chromatin Properties and Influence Genome Folding

(2009) Philipp M. Diesinger et al.   BIOPHYSICAL JOURNAL

Elucidating the Mechanism behind Irreversible Deformation of Viral Capsids

(2009) Anton Arkhipov et al.   BIOPHYSICAL JOURNAL

Nucleosome Shape Dictates Chromatin Fiber Structure

(2009) Martin Depken et al.   BIOPHYSICAL JOURNAL

Computer Modeling Reveals that Modifications of the Histone Tail Charges Define Salt-Dependent Interaction of the Nucleosome Core Particles

(2009) Ye Yang et al.   BIOPHYSICAL JOURNAL

Elasticity and Electrostatics of Plectonemic DNA

(2009) N. Clauvelin et al.   BIOPHYSICAL JOURNAL

Fundamental Aspects of Protein−Protein Association Kinetics

(2009) G. Schreiber et al.   CHEMICAL REVIEWS

Spermidine-induced two-dimensional DNA condensations on mica surfaces: A different pathway from condensations in solution

(2009) XingHua Zhang et al.   CHINESE SCIENCE BULLETIN

Adding a new dimension to DNA melting curves

(2009) S. Cuesta-Lopez et al.   EPL

Homology recognition funnel

(2009) Dominic Lee et al.   JOURNAL OF CHEMICAL PHYSICS

A theory for viral capsid assembly around electrostatic cores

(2009) Michael F. Hagan   JOURNAL OF CHEMICAL PHYSICS

Electrostatics of capsid-induced viral RNA organization

(2009) Christopher Forrey et al.   JOURNAL OF CHEMICAL PHYSICS

The Bacteriophage Genome Undergoes a Succession of Intracapsid Phase Transitions upon DNA Ejection

(2009) Amélie Leforestier et al.   JOURNAL OF MOLECULAR BIOLOGY

Probing DNA−DNA Electrostatic Friction in Tight Superhelical DNA Plies

(2009) A. G. Cherstvy   JOURNAL OF PHYSICAL CHEMISTRY B

Positively Charged Residues in DNA-Binding Domains of Structural Proteins Follow Sequence-specific Positions of DNA Phosphate Groups

(2009) A. G. Cherstvy   JOURNAL OF PHYSICAL CHEMISTRY B

Electrostatics in soft matter

(2009) René Messina   JOURNAL OF PHYSICS-CONDENSED MATTER

Simulation of Self-Assembly of Cationic Lipids and DNA into Structured Complexes

(2009) Oded Farago et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

To Switch or Not To Switch: The Effects of Potassium and Sodium Ions on α-Poly-l-glutamate Conformations in Aqueous Solutions

(2009) Maxim V. Fedorov et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Directed Hybridization and Melting of DNA Linkers using Counterion-Screened Electric Fields

(2009) Ian Y. Wong et al.   NANO LETTERS

Self-assembly of DNA into nanoscale three-dimensional shapes

(2009) Shawn M. Douglas et al.   NATURE

The role of DNA shape in protein–DNA recognition

(2009) Remo Rohs et al.   NATURE

The renaissance of friction

(2009) Michael Urbakh et al.   NATURE MATERIALS

Origin of the electrophoretic force on DNA in solid-state nanopores

(2009) Stijn van Dorp et al.   Nature Physics

Recombinational DNA repair in a cellular context: a search for the homology search

(2009) Allon Weiner et al.   NATURE REVIEWS MICROBIOLOGY

Single-molecule force spectroscopy reveals a highly compliant helical folding for the 30-nm chromatin fiber

(2009) Maarten Kruithof et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Both helix topology and counterion distribution contribute to the more effective charge screening in dsRNA compared with dsDNA

(2009) Suzette A. Pabit et al.   NUCLEIC ACIDS RESEARCH

Predicting nucleosome positions on the DNA: combining intrinsic sequence preferences and remodeler activities

(2009) Vladimir B. Teif et al.   NUCLEIC ACIDS RESEARCH

Viral assembly: a molecular modeling perspective

(2009) Stephen C. Harvey et al.   PHYSICAL CHEMISTRY CHEMICAL PHYSICS

DNA stretching and multivalent-cation-induced condensation

(2009) Yevgeni Sh. Mamasakhlisov et al.   PHYSICAL REVIEW E

Unraveling DNA tori under tension

(2009) C. Battle et al.   PHYSICAL REVIEW E

Stochastic model for nucleosome sliding under an external force

(2009) L. Mollazadeh-Beidokhti et al.   PHYSICAL REVIEW E

The homology recognition well as an innate property of DNA structure

(2009) A. A. Kornyshev et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Structure of toroidal DNA collapsed inside the phage capsid

(2009) A. Leforestier et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

DNA–DNA interactions in bacteriophage capsids are responsible for the observed DNA knotting

(2009) Davide Marenduzzo et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Single molecule detection of direct, homologous, DNA/DNA pairing

(2009) C. Danilowicz et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

VIROLOGY: Pressurized Viruses

(2009) W. M. Gelbart et al.   SCIENCE

Folding DNA into Twisted and Curved Nanoscale Shapes

(2009) H. Dietz et al.   SCIENCE

Comprehensive Mapping of Long-Range Interactions Reveals Folding Principles of the Human Genome

(2009) E. Lieberman-Aiden et al.   SCIENCE

RNA Folding: Conformational Statistics, Folding Kinetics, and Ion Electrostatics

(2008) Shi-Jie Chen   Annual Review of Biophysics

Physical Chemistry of DNA Viruses

(2008) Charles M. Knobler et al.   Annual Review of Physical Chemistry

The Effect of Internucleosomal Interaction on Folding of the Chromatin Fiber

(2008) René Stehr et al.   BIOPHYSICAL JOURNAL

RNA Folding: Thermodynamic and Molecular Descriptions of the Roles of Ions

(2008) David E. Draper   BIOPHYSICAL JOURNAL

Attractive Forces between Cation Condensed DNA Double Helices

(2008) Brian A. Todd et al.   BIOPHYSICAL JOURNAL

Influence of Nonuniform Geometry on Nanoindentation of Viral Capsids

(2008) Melissa M. Gibbons et al.   BIOPHYSICAL JOURNAL

A Unified Poland-Scheraga Model of Oligo- and Polynucleotide DNA Melting: Salt Effects and Predictive Power

(2008) Daniel Jost et al.   BIOPHYSICAL JOURNAL

Principles of Protein−Protein Interactions: What are the Preferred Ways For Proteins To Interact?

(2008) Ozlem Keskin et al.   CHEMICAL REVIEWS

Expression of chirality in columnar hexagonal phases or DNA and nucleosomes

(2008) Amélie Leforestier et al.   COMPTES RENDUS CHIMIE

Structural transitions and soft modes in frustrated DNA crystals

(2008) G. M. Grason   EPL

Similia similibus: Pairing of homologous chromosomes driven by the physicochemical properties of DNA

(2008) Arturo Falaschi   HFSP Journal

An analytical approach to computing biomolecular electrostatic potential. I. Derivation and analysis

(2008) Andrew T. Fenley et al.   JOURNAL OF CHEMICAL PHYSICS

Theory of polyelectrolyte adsorption onto surfaces patterned with charge and topography

(2008) Nazish Hoda et al.   JOURNAL OF CHEMICAL PHYSICS

A formula for the minimal coordination number of a parallel bundle

(2008) E. L. Starostin   JOURNAL OF CHEMICAL PHYSICS

Protein−DNA Interactions:  Reaching and Recognizing the Targets

(2008) A. G. Cherstvy et al.   JOURNAL OF PHYSICAL CHEMISTRY B

DNA Cholesteric Phases: The Role of DNA Molecular Chirality and DNA−DNA Electrostatic Interactions

(2008) A. G. Cherstvy   JOURNAL OF PHYSICAL CHEMISTRY B

DNA Double Helices Recognize Mutual Sequence Homology in a Protein Free Environment

(2008) Geoff S. Baldwin et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Genome wide application of DNA melting analysis

(2008) Daniel Jost et al.   JOURNAL OF PHYSICS-CONDENSED MATTER

Dynamical versus statistical mesoscopic models for DNA denaturation

(2008) Marc Joyeux et al.   JOURNAL OF PHYSICS-CONDENSED MATTER

Liquid crystal ordering of DNA and RNA oligomers with partially overlapping sequences

(2008) G Zanchetta et al.   JOURNAL OF PHYSICS-CONDENSED MATTER

DNA Attraction in Monovalent and Divalent Electrolytes

(2008) Binquan Luan et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Engineering Viable Foot-and-Mouth Disease Viruses with Increased Thermostability as a Step in the Development of Improved Vaccines

(2008) R. Mateo et al.   JOURNAL OF VIROLOGY

Mechanical Response of Plectonemic DNA: An Analytical Solution

(2008) N. Clauvelin et al.   MACROMOLECULES

A multifaceted role for polyamines in bacterial pathogens

(2008) Pratik Shah et al.   MOLECULAR MICROBIOLOGY

Mechanisms of Size Control and Polymorphism in Viral Capsid Assembly

(2008) Oren M. Elrad et al.   NANO LETTERS

Helical coherence of DNA in crystals and solution

(2008) Aaron Wynveen et al.   NUCLEIC ACIDS RESEARCH

Nanotribology and nanomechanics in nano/biotechnology

(2008) B. Bhushan   PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY A-MATHEMATICAL PHYSICAL AND ENGINEERING SCIENCES

Electrostatic theory of viral self-assembly

(2008) Tao Hu et al.   PHYSICA A-STATISTICAL MECHANICS AND ITS APPLICATIONS

Electron spin resonance spectroscopy in drug delivery

(2008) Giacomo Martini et al.   PHYSICAL CHEMISTRY CHEMICAL PHYSICS

Nonspecific interactions in spontaneous assembly of empty versus functional single-stranded RNA viruses

(2008) Antonio Šiber et al.   PHYSICAL REVIEW E

The physics of phages

(2008) William M. Gelbart et al.   PHYSICS TODAY

Helical twist controls the thickness of F-actin bundles

(2008) M. M. A. E. Claessens et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Phase separation and liquid crystallization of complementary sequences in mixtures of nanoDNA oligomers

(2008) G. Zanchetta et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Nucleosome repeat length and linker histone stoichiometry determine chromatin fiber structure

(2008) Andrew Routh et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Manipulation of the mechanical properties of a virus by protein engineering

(2008) C. Carrasco et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Counterion-mediated electrostatic interactions between helical molecules

(2008) M. Kanduč et al.   Soft Matter

Effects of Salt Concentrations and Bending Energy on the Extent of Ejection of Phage Genomes

(2007) Alex Evilevitch et al.   BIOPHYSICAL JOURNAL

Packaging of a Polymer by a Viral Capsid: The Interplay between Polymer Length and Capsid Size

(2007) Yufang Hu et al.   BIOPHYSICAL JOURNAL

Finding a match: how do homologous sequences get together for recombination?

(2007) Adi Barzel et al.   NATURE REVIEWS GENETICS