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

Solution scattering at the Life Science X-ray Scattering (LiX) beamline

(2020) Lin Yang et al.   JOURNAL OF SYNCHROTRON RADIATION

Quantitative Studies of an RNA Duplex Electrostatics by Ion Counting

(2019) Magdalena Gebala et al.   BIOPHYSICAL JOURNAL

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

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

Revealing the distinct folding phases of an RNA three-helix junction

(2018) Alex Plumridge et al.   NUCLEIC ACIDS RESEARCH

Conformational ensembles of RNA oligonucleotides from integrating NMR and molecular simulations

(2018) Sandro Bottaro et al.   Science Advances

Conformations of an RNA Helix-Junction-Helix Construct Revealed by SAXS Refinement of MD Simulations

(2018) Yen-Lin Chen et al.   BIOPHYSICAL JOURNAL

SAS profile correlations reveal SAS hierarchical nature and information content

(2017) Yannick G. Spill et al.   PLoS One

Multi-shell model of ion-induced nucleic acid condensation

(2016) Igor S. Tolokh et al.   JOURNAL OF CHEMICAL PHYSICS

Combining Simulations and Solution Experiments as a Paradigm for RNA Force Field Refinement

(2016) Andrea Cesari et al.   Journal of Chemical Theory and Computation

Anisotropy of B-DNA Groove Bending

(2016) Ning Ma 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

Direct evidence for sequence-dependent attraction between double-stranded DNA controlled by methylation

(2016) Jejoong Yoo et al.   Nature Communications

Correlation Map, a goodness-of-fit test for one-dimensional X-ray scattering spectra

(2015) Daniel Franke 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

WAXSiS: a web server for the calculation of SAXS/WAXS curves based on explicit-solvent molecular dynamics

(2015) Christopher J. Knight et al.   NUCLEIC ACIDS RESEARCH

Allosteric transcriptional regulation via changes in the overall topology of the core promoter

(2015) S. J. Philips et al.   SCIENCE

Molecular Dynamics Simulations of Ribosomes: Integrating Theory and Experiment

(2015) Serdal Kirmizialtin et al.   BIOPHYSICAL JOURNAL

Validating Solution Ensembles from Molecular Dynamics Simulation by Wide-Angle X-ray Scattering Data

(2014) Po-chia Chen 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

Why double-stranded RNA resists condensation

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

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

(2012) Serdal Kirmizialtin et al.   BIOPHYSICAL JOURNAL

RNA recognition by double-stranded RNA binding domains: a matter of shape and sequence

(2012) Grégoire Masliah et al.   CELLULAR AND MOLECULAR LIFE SCIENCES

DNA Bending through Large Angles Is Aided by Ionic Screening

(2012) Justin Spiriti 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

Improved Parametrization of Li+, Na+, K+, and Mg2+ Ions for All-Atom Molecular Dynamics Simulations of Nucleic Acid Systems

(2011) Jejoong Yoo et al.   Journal of Physical Chemistry Letters

Characterizing RNA dynamics at atomic resolution using solution-state NMR spectroscopy

(2011) Jameson R Bothe et al.   NATURE METHODS

Major groove width variations in RNA structures determined by NMR and impact of 13C residual chemical shift anisotropy and 1H–13C residual dipolar coupling on refinement

(2010) Blanton S. Tolbert et al.   JOURNAL OF BIOMOLECULAR NMR

Computational Exploration of Mobile Ion Distributions around RNA Duplex

(2010) Serdal Kirmizialtin et al.   JOURNAL OF PHYSICAL CHEMISTRY B

A measure of bending in nucleic acids structures applied to A-tract DNA

(2010) F. Lankaš et al.   NUCLEIC ACIDS RESEARCH

Improved side-chain torsion potentials for the Amber ff99SB protein force field

(2010) Kresten Lindorff-Larsen et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

Monovalent Cation Binding in the Minor Groove of DNA A-Tracts†

(2009) Qian Dong et al.   BIOCHEMISTRY

Simulated x-ray scattering of protein solutions using explicit-solvent models

(2009) Sanghyun Park et al.   JOURNAL OF CHEMICAL PHYSICS

Constructing RNA dynamical ensembles by combining MD and motionally decoupled NMR RDCs: new insights into RNA dynamics and adaptive ligand recognition

(2009) Aaron T. Frank et al.   NUCLEIC ACIDS RESEARCH

The unique structure of A-tracts and intrinsic DNA bending

(2009) Tali E. Haran et al.   QUARTERLY REVIEWS OF BIOPHYSICS

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

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

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

Single-molecule FRET measures bends and kinks in DNA

(2008) A. K. Wozniak et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA