Improved Parameters for the Prediction of RNA Hairpin Stability

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Abstract
Thermodynamic parameters are reported for hairpin formation in 1 M NaCl by RNA sequences of the type where XY is the set of four Watson−Crick base pairs and the underlined loop sequences are three to nine nucleotides. A nearest neighbor analysis of the data indicates the free energy of loop formation at 37 °C is dependent upon loop size and closing base pair. The model previously developed to predict the stability for RNA hairpin loops (n > 3) includes contributions from the size of the loop, the identity of the closing base pair, the free energy increment (ΔG°37mm) for the interaction of the closing base pair with the first mismatch and an additional stabilization term for GA and UU first mismatches [Serra, M. J., Axenson, T. J., & Turner, D. H. (1994) Biochemistry 33, 14289]. The results presented here allow improvements in the parameters used to predict RNA hairpin stability. For hairpin loops of n = 4−9, ΔG°37iL(n) is 4.9, 5.0, 5.0, 5.0, 4.9, and 5.5 kcal/mol, respectively, and the penalty for hairpin closure by AU or UA is +0.6 kcal/mol. ΔG°37iL(n) is the free energy for initiating a loop of n nucleotides. The model for predicting hairpin loop stability for loops larger than three becomes ΔG°37L(n) = ΔG°37iL(n) + ΔG°37mm + 0.6(if closed by AU or UA) −0.7(if first mismatch is GA or UU). Hairpin loops of three are modeled as independent of loop sequence with ΔG°37iL(3) = 4.8 and the penalty for AU closure of +0.6 kcal/mol. Thermodynamic parameters for hairpin formation in 1 M NaCl for 11 naturally occurring RNA hairpin sequences are reported. The model provides good agreement with the measured values for both TM (within 10 °C of the measured value) and ΔG°37 (within 0.8 kcal/mol of the measured value) for hairpin formation. In general, the nearest neighbor model allows prediction of RNA hairpin stability to within 5−10% of the experimentally measured values.