ArticleBiophysical journal2010
Predicting ion binding properties for RNA tertiary structures.
Article in Biophysical journal, 2010. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 34 papers.
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Who cites it
34 citing papers in PubMed.
- 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
- When does molecular dynamics improve RNA models? Insights from CASP15 and practical guidelines.Computational and structural biotechnology journal · 2025Article
- The origin of different bending stiffness between double-stranded RNA and DNA revealed by magnetic tweezers and simulations.Nucleic acids research · 2024Article
- RNA 3D Structure Prediction: Progress and Perspective.Molecules (Basel, Switzerland) · 2023Review
- rsRNASP: A residue-separation-based statistical potential for RNA 3D structure evaluation.Biophysical journal · 2022Article
- Salt-Dependent RNA Pseudoknot Stability: Effect of Spatial Confinement.Frontiers in molecular biosciences · 2021Article
- Hofmeister Series for Metal-Cation-RNA Interactions: The Interplay of Binding Affinity and Exchange Kinetics.Langmuir : the ACS journal of surfaces and colloids · 2020Article
- Structure folding of RNA kissing complexes in salt solutions: predicting 3D structure, stability, and folding pathway.RNA (New York, N.Y.) · 2019Article
- Predicting Monovalent Ion Correlation Effects in Nucleic Acids.ACS omega · 2019Article
- What is the best reference state for building statistical potentials in RNA 3D structure evaluation?RNA (New York, N.Y.) · 2019Article
- Predicting RNA-Metal Ion Binding with Ion Dehydration Effects.Biophysical journal · 2019Article
- Modeling Structure, Stability, and Flexibility of Double-Stranded RNAs in Salt Solutions.Biophysical journal · 2018Article
- Effects of flanking regions on HDV cotranscriptional folding kinetics.RNA (New York, N.Y.) · 2018Article
- Predicting 3D structure and stability of RNA pseudoknots in monovalent and divalent ion solutions.PLoS computational biology · 2018Article
- Competitive Binding of MgBiophysical journal · 2018Article
- Potential of mean force between oppositely charged nanoparticles: A comprehensive comparison between Poisson-Boltzmann theory and Monte Carlo simulations.Scientific reports · 2017Article
- Predicting Ion Effects in an RNA Conformational Equilibrium.The journal of physical chemistry. B · 2017Article
- Divalent Ion-Mediated DNA-DNA Interactions: A Comparative Study of Triplex and Duplex.Biophysical journal · 2017Article
- MCTBI: a web server for predicting metal ion effects in RNA structures.RNA (New York, N.Y.) · 2017Article
- Counting the ions surrounding nucleic acids.Nucleic acids research · 2017Article
Corrections and comments
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Authors and funding
2 authors.
Funding
Abstract
Recent experiments pointed to the potential importance of ion correlation for multivalent ions such as Mg(2+) ions in RNA folding. In this study, we develop an all-atom model to predict the ion electrostatics in RNA folding. The model can treat ion correlation effects explicitly by considering an ensemble of discrete ion distributions. In contrast to the previous coarse-grained models that can treat ion correlation, this new model is based on all-atom nucleic acid structures. Thus, unlike the previous coarse-grained models, this new model allows us to treat complex tertiary structures such as HIV-1 DIS type RNA kissing complexes. Theory-experiment comparisons for a variety of tertiary structures indicate that the model gives improved predictions over the Poisson-Boltzmann theory, which underestimates the Mg(2+) binding in the competition with Na(+). Further systematic theory-experiment comparisons for a series of tertiary structures lead to a set of analytical formulas for Mg(2+)/Na(+) ion-binding to various RNA and DNA structures over a wide range of Mg(2+) and Na(+) concentrations.
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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.