RNA Captures More Cations than DNA: Insights from Molecular Dynamics Simulations

Artificial Intelligence Resolves Kinetic Pathways of Magnesium Binding to RNA

(2022) Jan Neumann et al.   Journal of Chemical Theory and Computation

Magnesium force fields for OPC water with accurate solvation, ion-binding, and water-exchange properties: Successful transfer from SPC/E

(2022) Kara K. Grotz et al.   JOURNAL OF CHEMICAL PHYSICS

Twisting DNA by salt

(2022) Sergio Cruz-León et al.   NUCLEIC ACIDS RESEARCH

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

The structural plasticity of nucleic acid duplexes revealed by WAXS and MD

(2021) Weiwei He et al.   Science Advances

Optimized Magnesium Force Field Parameters for Biomolecular Simulations with Accurate Solvation, Ion-Binding, and Water-Exchange Properties in SPC/E, TIP3P-fb, TIP4P/2005, TIP4P-Ew, and TIP4P-D

(2021) Kara K. Grotz 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

Hofmeister Series for Metal-Cation–RNA Interactions: The Interplay of Binding Affinity and Exchange Kinetics

(2020) Sergio Cruz-León et al.   LANGMUIR

Kinetic pathways of water exchange in the first hydration shell of magnesium

(2020) Nadine Schwierz   JOURNAL OF CHEMICAL PHYSICS

Ion-Specific and pH-Dependent Hydration of Mica–Electrolyte Interfaces

(2019) Simone R. van Lin et al.   LANGMUIR

Quantitative Studies of an RNA Duplex Electrostatics by Ion Counting

(2019) Magdalena Gebala et al.   BIOPHYSICAL JOURNAL

The Contribution of Backbone Electrostatic Repulsion to DNA Mechanical Properties is Length-Scale-Dependent

(2019) Shiyan Xiao et al.   Journal of Physical Chemistry Letters

Salt Dependence of A-Form RNA Duplexes: Structures and Implications

(2019) Yen-Lin Chen et al.   JOURNAL OF PHYSICAL CHEMISTRY B

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

Unraveling Mg 2+ –RNA binding with atomistic molecular dynamics

(2017) Richard A. Cunha et al.   RNA

Reversed Hofmeister series—The rule rather than the exception

(2016) Nadine Schwierz et al.   CURRENT OPINION IN COLLOID & INTERFACE SCIENCE

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

Opposing Effects of Multivalent Ions on the Flexibility of DNA and RNA

(2016) Aleksander V. Drozdetski et al.   PHYSICAL REVIEW LETTERS

DNA Immobilization and Hybridization Detection by the Intrinsic Molecular Charge Using Capacitive Field-Effect Sensors Modified with a Charged Weak Polyelectrolyte Layer

(2015) Thomas S. Bronder et al.   ACS Applied Materials & Interfaces

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

Competition among Li+, Na+, K+, and Rb+ Monovalent Ions for DNA in Molecular Dynamics Simulations Using the Additive CHARMM36 and Drude Polarizable Force Fields

(2015) Alexey Savelyev 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

Multivalent ion-mediated nucleic acid helix-helix interactions: RNA versus DNA

(2015) Yuan-Yan Wu et al.   NUCLEIC ACIDS RESEARCH

Analyzing ion distributions around DNA: sequence-dependence of potassium ion distributions from microsecond molecular dynamics

(2015) Marco Pasi et al.   NUCLEIC ACIDS RESEARCH

Understanding Nucleic Acid–Ion Interactions

(2014) Jan Lipfert et al.   Annual Review of Biochemistry

Ion Counting from Explicit-Solvent Simulations and 3D-RISM

(2014) George M. Giambaşu et al.   BIOPHYSICAL JOURNAL

Comparison of monovalent and divalent ion distributions around a DNA duplex with molecular dynamics simulation and a Poisson-Boltzmann approach

(2014) Timothy J. Robbins et al.   BIOPOLYMERS

Ion distributions around left- and right-handed DNA and RNA duplexes: a comparative study

(2014) Feng Pan et al.   NUCLEIC ACIDS RESEARCH

Why double-stranded RNA resists condensation

(2014) Igor S. Tolokh et al.   NUCLEIC ACIDS RESEARCH

Analyzing ion distributions around DNA

(2014) Richard Lavery et al.   NUCLEIC ACIDS RESEARCH

Anionic and Cationic Hofmeister Effects on Hydrophobic and Hydrophilic Surfaces

(2013) Nadine Schwierz et al.   LANGMUIR

RNA and Its Ionic Cloud: Solution Scattering Experiments and Atomically Detailed Simulations

(2012) Serdal Kirmizialtin et al.   BIOPHYSICAL JOURNAL

Influence of divalent magnesium ion on DNA: molecular dynamics simulation studies

(2012) Sanchita Mukherjee et al.   JOURNAL OF BIOMOLECULAR STRUCTURE & DYNAMICS

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

Refinement of the Cornell et al. Nucleic Acids Force Field Based on Reference Quantum Chemical Calculations of Glycosidic Torsion Profiles

(2011) Marie Zgarbová et al.   Journal of Chemical Theory and Computation

Double-Stranded RNA Resists Condensation

(2011) Li Li et al.   PHYSICAL REVIEW LETTERS

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

Controlling ribozyme activity by metal ions

(2010) Joachim Schnabl et al.   CURRENT OPINION IN CHEMICAL BIOLOGY

Ionic force field optimization based on single-ion and ion-pair solvation properties

(2010) Maria Fyta et al.   JOURNAL OF CHEMICAL PHYSICS

Counting Ions around DNA with Anomalous Small-Angle X-ray Scattering

(2010) Suzette A. Pabit et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Reversed Anionic Hofmeister Series: The Interplay of Surface Charge and Surface Polarity

(2010) Nadine Schwierz et al.   LANGMUIR

The role of DNA shape in protein–DNA recognition

(2009) Remo Rohs et al.   NATURE

Multinuclear NMR studies of the interaction of metal ions with adenine-nucleotides

(2008) Zoltán Szabó   COORDINATION CHEMISTRY REVIEWS