ArticlePhysical review letters2015
Generalized Manning Condensation Model Captures the RNA Ion Atmosphere.
Article in Physical review letters, 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 42 papers.
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Who cites it
42 citing papers in PubMed.
- Exploring functional transitions of the 2'-dG riboswitch aptamer.Proceedings of the National Academy of Sciences of the United States of America · 2026Article
- Transient ion-mediated interactions regulate subunit rotation in a eukaryotic ribosome.Proceedings of the National Academy of Sciences of the United States of America · 2026Article
- Driving forces of RNA condensation revealed through coarse-grained modeling with explicit MgProceedings of the National Academy of Sciences of the United States of America · 2025Article
- Critical Role of MgThe journal of physical chemistry. B · 2025Article
- Transient ion-mediated interactions regulate subunit rotation in a eukaryotic ribosome.bioRxiv : the preprint server for biology · 2025Article
- 3D structure and stability prediction of DNA with multi-way junctions in ionic solutions.PLoS computational biology · 2025Article
- Structural Prediction of Coronavirus s2m Kissing Complexes and Extended Duplexes.ACS physical chemistry Au · 2025Article
- Modeling riboswitches: The impact of concentration of MgBiophysical journal · 2025Article
- Magnesium ions mitigate metastable states in the regulatory landscape of mRNA elements.RNA (New York, N.Y.) · 2024Article
- Article
- Explicit Ion Modeling Predicts Physicochemical Interactions for Chromatin Organization.bioRxiv : the preprint server for biology · 2023Article
- Geometric alignment of aminoacyl-tRNA relative to catalytic centers of the ribosome underpins accurate mRNA decoding.Nature communications · 2023Article
- Influence of MgACS omega · 2023Article
- Structural, Dynamical, and Entropic Differences between SARS-CoV and SARS-CoV-2 s2m Elements Using Molecular Dynamics Simulations.ACS physical chemistry Au · 2023Article
- Exploring the Energy Landscape of Riboswitches Using Collective Variables Based on Tertiary Contacts.Journal of molecular biology · 2022Article
- Getting to the bottom of lncRNA mechanism: structure-function relationships.Mammalian genome : official journal of the International Mammalian Genome Society · 2022Review
- Graph deep learning locates magnesium ions in RNA.QRB discovery · 2022Article
- Lipid nanoparticles for antisense oligonucleotide gene interference into brain border-associated macrophages.Frontiers in molecular biosciences · 2022Article
- Chelated Magnesium Logic Gate Regulates Riboswitch Pseudoknot Formation.The journal of physical chemistry. B · 2021Article
- Stability and folding pathways of tetra-nucleosome from six-dimensional free energy surface.Nature communications · 2021Article
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Authors and funding
7 authors.
Funding
Abstract
RNA is highly sensitive to the ionic environment and typically requires Mg(2+) to form compact structures. There is a need for models capable of describing the ion atmosphere surrounding RNA with quantitative accuracy. We present a model of RNA electrostatics and apply it within coarse-grained molecular dynamics simulation. The model treats Mg(2+) ions explicitly to account for ion-ion correlations neglected by mean-field theories. Since mean-field theories capture KCl well, it is treated implicitly by a generalized Manning counterion condensation model. The model extends Manning condensation to deal with arbitrary RNA conformations, nonlimiting KCl concentrations, and the ion inaccessible volume of RNA. The model is tested against experimental measurements of the excess Mg(2+) associated with the RNA, Γ(2+), because Γ(2+) is directly related to the Mg(2+)-RNA interaction free energy. The excellent agreement with experiment demonstrates that the model captures the ionic dependence of the RNA free energy landscape.
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