ArticleBiophysical journal2012
RNA and its ionic cloud: solution scattering experiments and atomically detailed simulations.
Article in Biophysical journal, 2012. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 64 papers.
What it found
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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
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Who cites it
64 citing papers in PubMed, 103 citations in OpenAlex.
- Article
- Predicting RNA structure and dynamics with deep learning and solution scattering.Biophysical journal · 2025Article
- Principles of ion binding to RNA inferred from the analysis of a 1.55 Å resolution bacterial ribosome structure - Part I: Mg2.Nucleic acids research · 2025Article
- Predicting RNA Structure and Dynamics with Deep Learning and Solution Scattering.bioRxiv : the preprint server for biology · 2024Article
- Influence of MgACS omega · 2023Article
- Sensitivity of the RNA Structure to Ion Conditions as Probed by Molecular Dynamics Simulations of Common Canonical RNA Duplexes.Journal of chemical information and modeling · 2023Article
- Computational Study of the pH-Dependent Ionic Environment around β-Lactoglobulin.The journal of physical chemistry. B · 2022Article
- RNA Captures More Cations than DNA: Insights from Molecular Dynamics Simulations.The journal of physical chemistry. B · 2022Article
- Insights into the structural stability of major groove RNA triplexes by WAXS-guided MD simulations.Cell reports. Physical science · 2022Article
- Nearest neighbor rules for RNA helix folding thermodynamics: improved end effects.Nucleic acids research · 2022Article
- Dynamics of Cations around DNA and Protein as Revealed byAnalytical chemistry · 2022Article
- Visualizing RNA Structures by SAXS-Driven MD Simulations.Frontiers in bioinformatics · 2022Article
- Aggregates Sealed by Ions.Methods in molecular biology (Clifton, N.J.) · 2022Article
- Contact pairs of RNA with magnesium ions-electrostatics beyond the Poisson-Boltzmann equation.Biophysical journal · 2021Article
- The structural plasticity of nucleic acid duplexes revealed by WAXS and MD.Science advances · 2021Article
- Experimental approaches for investigating ion atmospheres around nucleic acids and proteins.Computational and structural biotechnology journal · 2021Review
- Contributions and competition of MgRNA (New York, N.Y.) · 2020Article
- Dynamics of Ionic Interactions at Protein-Nucleic Acid Interfaces.Accounts of chemical research · 2020Article
- Multivalent ions and biomolecules: Attempting a comprehensive perspective.Chemphyschem : a European journal of chemical physics and physical chemistry · 2020Review
- Salt effect on thermodynamics and kinetics of a single RNA base pair.RNA (New York, N.Y.) · 2020Article
4 more citing papers are in PubMed but not listed here.
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
5 authors at 2 institutions in 1 country.
Funding
Abstract
RNA molecules play critical roles in many cellular processes. Traditionally viewed as genetic messengers, RNA molecules were recently discovered to have diverse functions related to gene regulation and expression. RNA also has great potential as a therapeutic and a tool for further investigation of gene regulation. Metal ions are an integral part of RNA structure and should be considered in any experimental or theoretical study of RNA. Here, we report a multidisciplinary approach that combines anomalous small-angle x-ray scattering and molecular-dynamics (MD) simulations with explicit solvent and ions around RNA. From experiment and simulation results, we find excellent agreement in the number and distribution of excess monovalent and divalent ions around a short RNA duplex. Although similar agreement can be obtained from a continuum description of the solvent and mobile ions (by solving the Poisson-Boltzmann equation and accounting for finite ion size), the use of MD is easily extended to flexible RNA systems with thermal fluctuations. Therefore, we also model a short RNA pseudoknot and find good agreement between the MD results and the experimentally derived solution structures. Surprisingly, both deviate from crystal structure predictions. These favorable comparisons of experiment and simulations encourage work on RNA in all-atom dynamic models.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.