- Home
- Publications
- Publication Search
- Publication Details
Title
Twisting DNA by salt
Authors
Keywords
-
Journal
NUCLEIC ACIDS RESEARCH
Volume -, Issue -, Pages -
Publisher
Oxford University Press (OUP)
Online
2022-05-11
DOI
10.1093/nar/gkac445
References
Ask authors/readers for more resources
Related references
Note: Only part of the references are listed.- Extended magnesium and calcium force field parameters for accurate ion–nucleic acid interactions in biomolecular simulations
- (2021) Sergio Cruz-León et al. JOURNAL OF CHEMICAL PHYSICS
- Optimized Magnesium Force Field Parameters for Biomolecular Simulations with Accurate Solvation, Ion-Binding, and Water-Exchange Properties
- (2021) Kara K. Grotz et al. Journal of Chemical Theory and Computation
- Accurate modeling of DNA conformational flexibility by a multivariate Ising model
- (2021) Korbinian Liebl et al. PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
- Surprising Twists in Nucleosomal DNA with Implication for Higher-order Folding
- (2021) Stefjord Todolli et al. JOURNAL OF MOLECULAR BIOLOGY
- Similarities and Differences between Na+ and K+ Distributions around DNA Obtained with Three Popular Water Models
- (2021) Egor S. Kolesnikov et al. Journal of Chemical Theory and Computation
- Opposite Effects of High-Valent Cations on the Elasticities of DNA and RNA Duplexes Revealed by Magnetic Tweezers
- (2020) Hang Fu et al. PHYSICAL REVIEW LETTERS
- Compensatory Mechanisms in Temperature Dependence of DNA Double Helical Structure: Bending and Elongation
- (2020) Hana Dohnalová et al. Journal of Chemical Theory and Computation
- Hofmeister Series for Metal-Cation–RNA Interactions: The Interplay of Binding Affinity and Exchange Kinetics
- (2020) Sergio Cruz-León et al. LANGMUIR
- How global DNA unwinding causes non-uniform stress distribution and melting of DNA
- (2020) Korbinian Liebl et al. PLoS One
- DNA Crookedness Regulates DNA Mechanical Properties at Short Length Scales
- (2019) Alberto Marin-Gonzalez et al. PHYSICAL REVIEW LETTERS
- Free energy of cylindrical polyions: Analytical results
- (2019) Gabriel Téllez et al. JOURNAL OF CHEMICAL PHYSICS
- RNA Structural Dynamics As Captured by Molecular Simulations: A Comprehensive Overview
- (2018) Jiří Šponer et al. CHEMICAL REVIEWS
- Force fields for monovalent and divalent metal cations in TIP3P water based on thermodynamic and kinetic properties
- (2018) Shavkat Mamatkulov et al. JOURNAL OF CHEMICAL PHYSICS
- OUP accepted manuscript
- (2018) NUCLEIC ACIDS RESEARCH
- GROmaρs: A GROMACS-Based Toolset to Analyze Density Maps Derived from Molecular Dynamics Simulations
- (2018) Rodolfo Briones et al. BIOPHYSICAL JOURNAL
- Influence of BII Backbone Substates on DNA Twist: A Unified View and Comparison of Simulation and Experiment for All 136 Distinct Tetranucleotide Sequences
- (2017) Marie Zgarbová et al. Journal of Chemical Information and Modeling
- rRNA C-Loops: Mechanical Properties of a Recurrent Structural Motif
- (2017) Tomáš Dršata et al. Journal of Chemical Theory and Computation
- Unwinding Induced Melting of Double-Stranded DNA Studied by Free Energy Simulations
- (2017) Korbinian Liebl et al. JOURNAL OF PHYSICAL CHEMISTRY B
- Beyond the Hofmeister Series: Ion-Specific Effects on Proteins and Their Biological Functions
- (2017) Halil I. Okur et al. JOURNAL OF PHYSICAL CHEMISTRY B
- Probing the mechanical properties, conformational changes, and interactions of nucleic acids with magnetic tweezers
- (2017) Franziska Kriegel et al. JOURNAL OF STRUCTURAL BIOLOGY
- Resolving the Conformational Dynamics of DNA with Ångstrom Resolution by Pulsed Electron–Electron Double Resonance and Molecular Dynamics
- (2017) Lukas S. Stelzl et al. JOURNAL OF THE AMERICAN CHEMICAL SOCIETY
- Understanding the mechanical response of double-stranded DNA and RNA under constant stretching forces using all-atom molecular dynamics
- (2017) Alberto Marin-Gonzalez et al. PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
- Unraveling Mg 2+ –RNA binding with atomistic molecular dynamics
- (2017) Richard A. Cunha et al. RNA
- Elastic Properties of Nucleic Acids by Single-Molecule Force Spectroscopy
- (2016) Joan Camunas-Soler et al. Annual Review of Biophysics
- Reversed Hofmeister series—The rule rather than the exception
- (2016) Nadine Schwierz et al. CURRENT OPINION IN COLLOID & INTERFACE SCIENCE
- Assessing the Current State of Amber Force Field Modifications for DNA
- (2016) Rodrigo Galindo-Murillo et al. Journal of Chemical Theory and Computation
- Does Cation Size Affect Occupancy and Electrostatic Screening of the Nucleic Acid Ion Atmosphere?
- (2016) Magdalena Gebala et al. JOURNAL OF THE AMERICAN CHEMICAL SOCIETY
- Calcium ions function as a booster of chromosome condensation
- (2016) Rinyaporn Phengchat et al. Scientific Reports
- do_x3dna: a tool to analyze structural fluctuations of dsDNA or dsRNA from molecular dynamics simulations: Fig. 1.
- (2015) Rajendra Kumar et al. BIOINFORMATICS
- Force Field for Mg2+, Mn2+, Zn2+, and Cd2+ Ions That Have Balanced Interactions with Nucleic Acids
- (2015) Maria T. Panteva et al. JOURNAL OF PHYSICAL CHEMISTRY B
- Cation–Anion Interactions within the Nucleic Acid Ion Atmosphere Revealed by Ion Counting
- (2015) Magdalena Gebala et al. JOURNAL OF THE AMERICAN CHEMICAL SOCIETY
- Parmbsc1: a refined force field for DNA simulations
- (2015) Ivan Ivani et al. NATURE METHODS
- Structural diversity of supercoiled DNA
- (2015) Rossitza N. Irobalieva et al. Nature Communications
- Understanding Nucleic Acid–Ion Interactions
- (2014) Jan Lipfert et al. Annual Review of Biochemistry
- Torque Spectroscopy for the Study of Rotary Motion in Biological Systems
- (2014) Jan Lipfert et al. CHEMICAL REVIEWS
- Analyzing ion distributions around DNA
- (2014) Richard Lavery et al. NUCLEIC ACIDS RESEARCH
- Unraveling the sequence-dependent polymorphic behavior of d(CpG) steps in B-DNA
- (2014) Pablo Daniel Dans et al. NUCLEIC ACIDS RESEARCH
- Double-stranded RNA under force and torque: Similarities to and striking differences from double-stranded DNA
- (2014) J. Lipfert et al. PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
- An optimized software framework for real-time, high-throughput tracking of spherical beads
- (2014) J. P. Cnossen et al. REVIEW OF SCIENTIFIC INSTRUMENTS
- Blind Predictions of DNA and RNA Tweezers Experiments with Force and Torque
- (2014) Fang-Chieh Chou et al. PLoS Computational Biology
- Rational Design of Particle Mesh Ewald Compatible Lennard-Jones Parameters for +2 Metal Cations in Explicit Solvent
- (2013) Pengfei Li et al. Journal of Chemical Theory and Computation
- Anionic and Cationic Hofmeister Effects on Hydrophobic and Hydrophilic Surfaces
- (2013) Nadine Schwierz et al. LANGMUIR
- Magnesium Ion–Water Coordination and Exchange in Biomolecular Simulations
- (2012) Olof Allnér et al. Journal of Chemical Theory and Computation
- Competitive Binding of Cations to Duplex DNA Revealed through Molecular Dynamics Simulations
- (2012) Jejoong Yoo et al. JOURNAL OF PHYSICAL CHEMISTRY B
- Slowing down DNA Translocation through a Nanopore in Lithium Chloride
- (2012) Stefan W. Kowalczyk et al. NANO LETTERS
- Monovalent Cation Size and DNA Conformational Stability
- (2011) Earle Stellwagen et al. BIOCHEMISTRY
- A primer to scaffolded DNA origami
- (2011) Carlos Ernesto Castro et al. NATURE METHODS
- Ionic strength-dependent persistence lengths of single-stranded RNA and DNA
- (2011) H. Chen et al. PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
- A Stability Concept for Metal Ion Coordination to Single-Stranded Nucleic Acids and Affinities of Individual Sites
- (2010) Roland K. O. Sigel et al. ACCOUNTS OF CHEMICAL RESEARCH
- 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
- Ionic force field optimization based on single-ion and ion-pair solvation properties
- (2010) Maria Fyta et al. JOURNAL OF CHEMICAL PHYSICS
- Coulombic Free Energy of Polymeric Nucleic Acid: Low- and High-Salt Analytical Approximations for the Cylindrical Poisson−Boltzmann Model
- (2010) Irina A. Shkel JOURNAL OF PHYSICAL CHEMISTRY B
- Magnetic torque tweezers: measuring torsional stiffness in DNA and RecA-DNA filaments
- (2010) Jan Lipfert et al. NATURE METHODS
- Quantitative Modeling and Optimization of Magnetic Tweezers
- (2009) Jan Lipfert et al. BIOPHYSICAL JOURNAL
- Two perspectives on the twist of DNA
- (2009) Lauren A. Britton et al. JOURNAL OF CHEMICAL PHYSICS
- Self-assembly of DNA into nanoscale three-dimensional shapes
- (2009) Shawn M. Douglas et al. NATURE
- Folding DNA into Twisted and Curved Nanoscale Shapes
- (2009) H. Dietz et al. SCIENCE
- Determination of Alkali and Halide Monovalent Ion Parameters for Use in Explicitly Solvated Biomolecular Simulations
- (2008) In Suk Joung et al. JOURNAL OF PHYSICAL CHEMISTRY B
- Critical Assessment of Nucleic Acid Electrostatics via Experimental and Computational Investigation of an Unfolded State Ensemble
- (2008) Yu Bai et al. JOURNAL OF THE AMERICAN CHEMICAL SOCIETY
- Single-molecule force spectroscopy: optical tweezers, magnetic tweezers and atomic force microscopy
- (2008) Keir C Neuman et al. NATURE METHODS
- 3DNA: a versatile, integrated software system for the analysis, rebuilding and visualization of three-dimensional nucleic-acid structures
- (2008) Xiang-Jun Lu et al. Nature Protocols
Find the ideal target journal for your manuscript
Explore over 38,000 international journals covering a vast array of academic fields.
SearchCreate your own webinar
Interested in hosting your own webinar? Check the schedule and propose your idea to the Peeref Content Team.
Create Now