ArticleBiochemistry2013
Effect of sodium ions on RNA duplex stability.
Article in Biochemistry, 2013. 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.
- Reparameterization of the Amber RNA Force Field Non-Bonded Terms.bioRxiv : the preprint server for biology · 2026Article
- Insights into siRNA Duplex Stability by UV Spectrophotometry Absorbance and Melting Temperature Analyses.ACS omega · 2026Article
- Competitive Influence of Alkali Metals in the Ion Atmosphere on Nucleic Acid Duplex Stability.ACS omega · 2024Article
- Thermodynamics and kinetics of DNA and RNA dinucleotide hybridization to gaps and overhangs.Biophysical journal · 2023Article
- Mono-valent salt corrections for RNA secondary structures in the ViennaRNA package.Algorithms for molecular biology : AMB · 2023Article
- Thermodynamic determination of RNA duplex stability in magnesium solutions.Biophysical journal · 2023Article
- Developing an Updated Strategy for Estimating the Free-Energy Parameters in RNA Duplexes.International journal of molecular sciences · 2021Article
- Improved nearest-neighbor parameters for the stability of RNA/DNA hybrids under a physiological condition.Nucleic acids research · 2020Article
- Salt effect on thermodynamics and kinetics of a single RNA base pair.RNA (New York, N.Y.) · 2020Article
- Replacing salt correction factors with optimized RNA nearest-neighbour enthalpy and entropy parameters.Chemical physics · 2019Article
- Modeling Structure, Stability, and Flexibility of Double-Stranded RNAs in Salt Solutions.Biophysical journal · 2018Article
- Blind tests of RNA nearest-neighbor energy prediction.Proceedings of the National Academy of Sciences of the United States of America · 2016Article
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Authors and funding
2 authors.
Funding
Abstract
The standard sodium concentration for RNA optical melting experiments is 1.021 M. Algorithms that predict Tm, ΔG°37, and secondary structure from sequence generally rely on parameters derived from optical melting experiments performed in 1.021 M sodium. Physiological monovalent cation concentrations are much lower than 1.021 M. In fact, many molecular biology techniques require buffers containing monovalent cation concentrations other than 1.021 M. Predictions based on the 1.021 M Na(+) parameters may not be accurate when the monovalent cation concentration is not 1.021 M. Here, we report thermodynamic data from optical melting experiments for a set of 18 RNA duplexes, each melted over a wide range of sodium ion concentrations (71, 121, 221, and 621 mM). Using these data and previously published data for the same sequences melted in 1.021 M Na(+), we report Tm and ΔG°37 correction factors to scale the standard 1.021 M Na(+) RNA parameters to other sodium ion concentrations. The recommended Tm correction factor predicts the melting temperature within 0.7 °C, and the recommended ΔG°37 correction factor predicts the free energy within 0.14 kcal/mol. These correction factors can be incorporated into prediction algorithms that predict RNA secondary structure from sequence and provide Tm and ΔG°37 values for RNA duplexes.
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