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 (TM)
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
TM 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 TM 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 TM 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.