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

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 thermody namic parameters. Included were the tetraloops GNRA and UNCG (where N is an y nucleotide and R is a purine), hexaloops with UU first mismatches, and th e hairpin loop of the iron responsive element, CAGUGC. The experimental val ues for the GNRA loops are in excellent agreement (Delta G degrees(37) with in 0.2 kcal/mol and melting temperature (T-M) within 4 degrees C) with the values predicted by the model. When the UNCG hairpin loops are treated as t etraloops, and a bonus of 0.8 kcal/mol included in the prediction to accoun t for the extra stable first mismatch (UG), the measured and predicted valu es are also in good agreement (Delta G degrees(37) within 0.7 kcal/mol and T-M within 3 degrees C). Six hairpins with unusually stable UU first mismat ches also gave good agreement with the predictions (Delta G degrees(37) wit hin 0.5 kcal/mol and T-M within 8 degrees C), except for hairpins closed by wobble base pairs. For these hairpins, exclusion of the additional stabili zation term for UU first mismatches improved the prediction (Delta G degree s(37) within 0.1 kcal/mol and T-M within 3 degrees C). Hairpins with the ir on-responsive element loop were not predicted well by the model, as measure d Delta G degrees(37) values were at least 1 kcal/mol greater than predicte d.