ArticleScience advances2022
Differences in ion-RNA binding modes due to charge density variations explain the stability of RNA in monovalent salts.
Article in Science advances, 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 12 papers.
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Who cites it
12 citing papers in PubMed, 24 citations in OpenAlex.
- Protein crowders remodel RNA electrostatics, hydration, and dynamics: a challenge to steric crowding models.Nucleic acids research · 2026Article
- Local cation-clamping distorts and softens RNA duplex.Communications biology · 2026Article
- Characterizing the Energy Surfaces of Competing Pathways in Gas-Phase Charge Inversion Ion/Ion Reactions Involving Cationized Lipids and Anionic Diacids.Journal of the American Society for Mass Spectrometry · 2025Article
- Essential Considerations for Free Energy Calculations of RNA-Small Molecule Complexes: Lessons from the Theophylline-Binding RNA Aptamer.Journal of chemical information and modeling · 2025Article
- Mechanistic insights into ASO-RNA complexation: Advancing antisense oligonucleotide design strategies.Molecular therapy. Nucleic acids · 2024Article
- Elucidating the Role of Groove Hydration on Stability and Functions of Biased DNA Duplexes in Cell-Like Chemical Environments.Journal of the American Chemical Society · 2024Article
- A Coarse-Grained SPICA Makeover for Solvated and Bare Sodium and Chloride Ions.Journal of chemical theory and computation · 2024Article
- Competitive Influence of Alkali Metals in the Ion Atmosphere on Nucleic Acid Duplex Stability.ACS omega · 2024Article
- Structural and computational studies of HIV-1 RNA.RNA biology · 2024Review
- Sequence-Dependent Orientational Coupling and Electrostatic Attraction in Cation-Mediated DNA-DNA Interactions.Journal of chemical theory and computation · 2023Article
- Decoding the dual recognition mechanism of the glucocorticoid receptor for DNA and RNA: sequence versus shape.Scientific reports · 2023Article
- Nearest-neighbor parameters for the prediction of RNA duplex stability in diverse in vitro and cellular-like crowding conditions.Nucleic acids research · 2023Article
Corrections and comments
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Authors and funding
3 authors at 1 institution in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
The stability of RNA increases as the charge density of the alkali metal cations increases. The molecular mechanism for this phenomenon remains elusive. To fill this gap, we performed all-atom molecular dynamics pulling simulations of HIV-1 trans-activation response RNA. We first established that the free energy landscape obtained in the simulations is in excellent agreement with the single-molecule optical tweezer experiments. The origin of the stronger stability in sodium compared to potassium is found to be due to the differences in the charge density-related binding modes. The smaller hydrated sodium ion preferentially binds to the highly charged phosphates that have high surface area. In contrast, the larger potassium ions interact with the major grooves. As a result, more cations condense around phosphate groups in the case of sodium ions, leading to the reduction of electrostatic repulsion. Because the proposed mechanism is generic, we predict that the same conclusions are valid for divalent alkaline earth metal cations.
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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.