A test of the model to predict unusually stable RNA hairpin loop stability

Abstract

To investigate the accuracy of a model [Giese et al., 1998, Biochemistry 37:1094–1100 and Mathews et al., 1999, J Mol Biol 288:911–940] that predicts the stability of RNA hairpin loops, optical melting studies were conducted on sets of hairpins previously determined to have unusually stable thermodynamic parameters. Included were the tetraloops GNRA and UNCG (where N is any nucleotide and R is a purine), hexaloops with UU first mismatches, and the hairpin loop of the iron responsive element, CAGUGC. The experimental values for the GNRA loops are in excellent agreement (ΔG°₃₇ within 0.2 kcal/mol and melting temperature (T_M) within 4 °C) with the values predicted by the model. When the UNCG hairpin loops are treated as tetraloops, and a bonus of 0.8 kcal/mol included in the prediction to account for the extra stable first mismatch (UG), the measured and predicted values are also in good agreement (ΔG°₃₇ within 0.7 kcal/mol and T_M within 3 °C). Six hairpins with unusually stable UU first mismatches also gave good agreement with the predictions (ΔG°₃₇ within 0.5 kcal/mol and T_M within 8 °C), except for hairpins closed by wobble base pairs. For these hairpins, exclusion of the additional stabilization term for UU first mismatches improved the prediction (ΔG°₃₇ within 0.1 kcal/mol and T_M within 3 °C). Hairpins with the iron-responsive element loop were not predicted well by the model, as measured ΔG°₃₇ values were at least 1 kcal/mol greater than predicted.