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

Speed of Conformational Change: Comparing Explicit and Implicit Solvent Molecular Dynamics Simulations

(2015) Ramu Anandakrishnan et al.   BIOPHYSICAL JOURNAL

Flexibility of short DNA helices with finite-length effect: From base pairs to tens of base pairs

(2015) Yuan-Yan Wu et al.   JOURNAL OF CHEMICAL PHYSICS

Understanding Nucleic Acid–Ion Interactions

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

DNA Binding Dynamics and Energetics of Cobalt, Nickel, and Copper Metallopeptides

(2014) Rodrigo Galindo-Murillo et al.   ChemMedChem

Excluded volume and ion-ion correlation effects on the ionic atmosphere around B-DNA: Theory, simulations, and experiments

(2014) Zaven Ovanesyan et al.   JOURNAL OF CHEMICAL PHYSICS

A coarse-grained model with implicit salt for RNAs: Predicting 3D structure, stability and salt effect

(2014) Ya-Zhou Shi et al.   JOURNAL OF CHEMICAL PHYSICS

Conformation-dependent DNA attraction

(2014) Weifeng Li et al.   Nanoscale

Why double-stranded RNA resists condensation

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

Insights into Ligand Binding to PreQ1 Riboswitch Aptamer from Molecular Dynamics Simulations

(2014) Zhou Gong et al.   PLoS One

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

Ion Competition in Condensed DNA Arrays in the Attractive Regime

(2013) Xiangyun Qiu et al.   BIOPHYSICAL JOURNAL

Helical Structure Determines Different Susceptibilities of dsDNA, dsRNA, and tsDNA to Counterion-Induced Condensation

(2013) Alexei A. Kornyshev et al.   BIOPHYSICAL JOURNAL

Quantifying Coulombic and Solvent Polarization-Mediated Forces Between DNA Helices

(2013) Zhaojian He et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Interaction between functionalized gold nanoparticles in physiological saline

(2013) Shada A. Alsharif et al.   PHYSICAL CHEMISTRY CHEMICAL PHYSICS

Calculating potential of mean force between like-charged nanoparticles: A comprehensive study on salt effects

(2013) Yuan-Yan Wu et al.   PHYSICS LETTERS A

Ion-Mediated RNA Structural Collapse: Effect of Spatial Confinement

(2012) Zhi-Jie Tan et al.   BIOPHYSICAL JOURNAL

The Ionic Atmosphere around A-RNA: Poisson-Boltzmann and Molecular Dynamics Simulations

(2012) Serdal Kirmizialtin et al.   BIOPHYSICAL JOURNAL

Salt contribution to the flexibility of single-stranded nucleic acid of finite length

(2012) Feng-Hua Wang et al.   BIOPOLYMERS

Influences of Mutations on the Electrostatic Binding Free Energies of Chloride Ions in Escherichia coli ClC

(2012) Tao Yu et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Mechanical Identities of RNA and DNA Double Helices Unveiled at the Single-Molecule Level

(2012) Elías Herrero-Galán et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

A universal description for the experimental behavior of salt-(in)dependent oligocation-induced DNA condensation

(2012) Nikolay Korolev et al.   NUCLEIC ACIDS RESEARCH

End-to-end attraction of duplex DNA

(2012) Christopher Maffeo et al.   NUCLEIC ACIDS RESEARCH

H++ 3.0: automating pK prediction and the preparation of biomolecular structures for atomistic molecular modeling and simulations

(2012) R. Anandakrishnan et al.   NUCLEIC ACIDS RESEARCH

Variational Multiscale Models for Charge Transport

(2012) Guo-Wei Wei et al.   SIAM REVIEW

Salt Contribution to RNA Tertiary Structure Folding Stability

(2011) Zhi-Jie Tan et al.   BIOPHYSICAL JOURNAL

Atomistic Analysis of Pseudoknotted RNA Unfolding

(2011) Yujie Zhang et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Salt-Dependent DNA-DNA Spacings in Intact BacteriophageλReflect Relative Importance of DNA Self-Repulsion and Bending Energies

(2011) Xiangyun Qiu et al.   PHYSICAL REVIEW LETTERS

Double-Stranded RNA Resists Condensation

(2011) Li Li et al.   PHYSICAL REVIEW LETTERS

Compact Intermediates in RNA Folding

(2010) Sarah A. Woodson   Annual Review of Biophysics

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

A Three-State Multi-Ion Kinetic Model for Conduction Properties of ClC-0 Chloride Channel

(2010) Xiao-Qing Wang et al.   BIOPHYSICAL JOURNAL

Cation Charge Dependence of the Forces Driving DNA Assembly

(2010) Jason DeRouchey et al.   BIOPHYSICAL JOURNAL

Predicting Ion Binding Properties for RNA Tertiary Structures

(2010) Zhi-Jie Tan et al.   BIOPHYSICAL JOURNAL

AFMPB: An adaptive fast multipole Poisson–Boltzmann solver for calculating electrostatics in biomolecular systems

(2010) Benzhuo Lu et al.   COMPUTER PHYSICS COMMUNICATIONS

MIBPB: A software package for electrostatic analysis

(2010) Duan Chen et al.   JOURNAL OF COMPUTATIONAL CHEMISTRY

Differential stability of DNA crossovers in solution mediated by divalent cations

(2010) Péter Várnai et al.   NUCLEIC ACIDS RESEARCH

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

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

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

(2008) Shi-Jie Chen   Annual Review of Biophysics

Attractive Forces between Cation Condensed DNA Double Helices

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

GROMACS 4:  Algorithms for Highly Efficient, Load-Balanced, and Scalable Molecular Simulation

(2008) Berk Hess et al.   Journal of Chemical Theory and Computation

DNA Attraction in Monovalent and Divalent Electrolytes

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

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

Molecular Dynamics Simulation of Multivalent-Ion Mediated Attraction between DNA Molecules

(2008) Liang Dai et al.   PHYSICAL REVIEW LETTERS