ArticleNucleic acids research2018
Influence of Na+ and Mg2+ ions on RNA structures studied with molecular dynamics simulations.
Article in Nucleic acids research, 2018. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 48 papers.
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Who cites it
48 citing papers in PubMed.
- Building RNA coarse-grained force fields: Design principles and training strategies.Biophysical journal · 2026Review
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- A cooperative effect of ligands, MgThe Journal of biological chemistry · 2026Article
- Beyond Partitioning: Using Force Field Science to Evaluate Electrostatics Models.Journal of chemical theory and computation · 2026Article
- Human lncRNAProceedings of the National Academy of Sciences of the United States of America · 2026Article
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- Peptide Nucleic Acid Probes for MicroRNA Detection: MgACS measurement science au · 2025Article
- Structural basis of double-stranded RNA recognition by the J2 monoclonal antibody.Nature communications · 2025Article
- Blind prediction of complex water and ion ensembles around RNA in CASP16.bioRxiv : the preprint server for biology · 2025Article
- GC Content and Thermal Stability of Double-Stranded RNA: Fragments of MicrosporidiaInternational journal of molecular sciences · 2025Article
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- Phylogenetic history and temperature adaptation contribute to structural and functional stability of proteins in marine mollusks.Communications biology · 2025Article
- Complex Water Networks Visualized through 2.2-2.3 Å Cryogenic Electron Microscopy of RNA.bioRxiv : the preprint server for biology · 2025Article
- RNA Order Regulates Its Interactions with Zwitterionic Lipid Bilayers.Nano letters · 2025Article
- RNA Stability: A Review of the Role of Structural Features and Environmental Conditions.Molecules (Basel, Switzerland) · 2024Review
- Mechanistic insights into ASO-RNA complexation: Advancing antisense oligonucleotide design strategies.Molecular therapy. Nucleic acids · 2024Article
- Atomistic Simulations Reveal Crucial Role of Metal Ions for Ligand Binding in Guanidine-I Riboswitch.Macromolecular rapid communications · 2024Article
- Structure of Essential RNA Regulatory Elements in the West Nile Virus 3'-Terminal Stem Loop.Journal of molecular biology · 2024Article
- Implicit Solvent with Explicit Ions Generalized Born Model in Molecular Dynamics: Application to DNA.Journal of chemical theory and computation · 2024Article
- Atomistic insights into the reentrant phase-transitions in polyuracil and polylysine mixtures.The Journal of chemical physics · 2024Article
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Authors and funding
4 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
The structure of ribonucleic acid (RNA) polymers is strongly dependent on the presence of, in particular Mg2+ cations to stabilize structural features. Only in high-resolution X-ray crystallography structures can ions be identified reliably. Here, we perform molecular dynamics simulations of 24 RNA structures with varying ion concentrations. Twelve of the structures were helical and the others complex folded. The aim of the study is to predict ion positions but also to evaluate the impact of different types of ions (Na+ or Mg2+) and the ionic strength on structural stability and variations of RNA. As a general conclusion Mg2+ is found to conserve the experimental structure better than Na+ and, where experimental ion positions are available, they can be reproduced with reasonable accuracy. If a large surplus of ions is present the added electrostatic screening makes prediction of binding-sites less reproducible. Distinct differences in ion-binding between helical and complex folded structures are found. The strength of binding (ΔG‡ for breaking RNA atom-ion interactions) is found to differ between roughly 10 and 26 kJ/mol for the different RNA atoms. Differences in stability between helical and complex folded structures and of the influence of metal ions on either are discussed.
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