ArticleBiophysical journal2012
Ion-mediated RNA structural collapse: effect of spatial confinement.
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 24 papers.
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Who cites it
24 citing papers in PubMed, 44 citations in OpenAlex.
- Coarse-Grained Modeling and Simulation of Multistranded RNA Nanostars.Chem & bio engineering · 2026Article
- Structural basis for Mg²⁺-glycine synergy in the tandem glycine riboswitch revealed by cryo-EM.Npj structural biology · 2026Article
- Space-Confined Hydrogel Particle-Based Biosensor for Early Warning of Aflatoxin B1 via Rapid Label-Free Fluorescence Detection of theAnalytical chemistry · 2025Article
- Cryo-EM reveals remodeling of a tandem riboswitch at 2.9 Å resolution.Research square · 2025Article
- RNA 3D Structure Prediction: Progress and Perspective.Molecules (Basel, Switzerland) · 2023Review
- Encapsulation of ribozymes inside model protocells leads to faster evolutionary adaptation.Proceedings of the National Academy of Sciences of the United States of America · 2021Article
- Multivalent Ion-Mediated Attraction between Like-Charged Colloidal Particles: Nonmonotonic Dependence on the Particle Charge.ACS omega · 2021Article
- IsRNA1:Journal of chemical theory and computation · 2021Article
- Salt-Dependent RNA Pseudoknot Stability: Effect of Spatial Confinement.Frontiers in molecular biosciences · 2021Article
- Ion-mediated interactions between like-charged polyelectrolytes with bending flexibility.Scientific reports · 2020Article
- Modeling Loop Composition and Ion Concentration Effects in RNA Hairpin Folding Stability.Biophysical journal · 2020Article
- Thermal stability and conformation of DNA and proteins under the confined condition in the matrix of hydrogels.Molecular biology reports · 2018Article
- Competitive Binding of MgBiophysical journal · 2018Article
- Electrostatic Interactions in Protein Structure, Folding, Binding, and Condensation.Chemical reviews · 2018Review
- Soft Interactions with Model Crowders and Non-canonical Interactions with Cellular Proteins Stabilize RNA Folding.Journal of molecular biology · 2018Article
- Potential of mean force between oppositely charged nanoparticles: A comprehensive comparison between Poisson-Boltzmann theory and Monte Carlo simulations.Scientific reports · 2017Article
- Divalent Ion-Mediated DNA-DNA Interactions: A Comparative Study of Triplex and Duplex.Biophysical journal · 2017Article
- Entropic stabilization of folded RNA in crowded solutions measured by SAXS.Nucleic acids research · 2016Article
- Potential of mean force between like-charged nanoparticles: Many-body effect.Scientific reports · 2016Article
- Multivalent ion-mediated nucleic acid helix-helix interactions: RNA versus DNA.Nucleic acids research · 2015Article
Corrections and comments
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Authors and funding
2 authors at 2 institutions in 2 countries.
Funding
Abstract
RNAs are negatively charged molecules that reside in cellular environments with macromolecular crowding. Macromolecular confinement can influence the ion effects in RNA folding. In this work, using the recently developed tightly bound ion model for ion fluctuation and correlation, we investigate the effect of confinement on ion-mediated RNA structural collapse for a simple model system. We find that for both Na(+) and Mg(2+), the ion efficiencies in mediating structural collapse/folding are significantly enhanced by the structural confinement. This enhancement of ion efficiency is attributed to the decreased electrostatic free-energy difference between the compact conformation ensemble and the (restricted) extended conformation ensemble due to the spatial restriction.
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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.