Nucleic acid research projects are often times guided by prediction of RNA stability and secondary structure from sequence. Currently, algorithms used to make these predictions are based on parameters from optical melting studies performed in 1.021 M NaCl. However, many physiological and biochemical buffers containing RNA include much lower concentrations of monovalent cations and the presence of divalent cations. Under these conditions, the current prediction algorithms may not be accurate. In order to improve these algorithms by accounting for variations in sodium concentration, thermodynamic data was previously collected from optical melting studies on a set of 18 RNA duplexes in sodium concentrations of 71, 121, 221, and 621 mM to derive correction factors for free energy (ΔG°37) and melting temperature (Tm). Despite these newly derived correction factors for sodium, they neglect the stabilizing effects of magnesium. Here, the same RNA duplexes were melted in magnesium concentrations of 0.5, 1.5, 3.0, and 10.0 mM in the absence of monovalent cations. With this data and the newly derived sodium correction factors serving as a model, correction factors for free energy and melting temperature were derived to scale the current parameters to a range of magnesium concentrations. Along with the sodium correction factors, the correction factors for RNA duplexes in magnesium can be incorporated into algorithms that predict RNA secondary structure and stability from sequence.

Thermodynamic determination of RNA duplex stability in magnesium solutions

249th National Meeting (2015)

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