Effect of Sodium Ions on RNA Duplex Stability

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.