Stability of RNA hairpins closed by wobble base pairs.

Thermodynamic parameters are reported for hairpin formation in 1 M NaCl by RNA sequences of the type GGXANmAYCC, where XY is the wobble base pair, GU or UG, and the underlined loop sequences are three to eight nucleotides. A nearest-neighbor analysis indicates the free energy of loop formation is dependent upon loop size and closing base pair. Hairpin loops closed by UG base pairs are on average 1.3 kcal/mol less stable than hairpins closed by GU base pairs. The hairpin loops closed by UG have approximately the same stability as hairpin loops closed by AU/UA base pairs, while the loops closed by GU are approximately 0.7 kcal/mol more stable than hairpins loops closed by GC/CG base pairs. These results, combined with the model previously developed [Serra et al. (1997) Biochemistry 36, 4844] to predict the stability for hairpin loops closed by Watson-Crick base pairs, allow for the following model to predict the stability of hairpin loops: delta G degree 37L(n) = delta G degree 37iL(n) + delta G degree 37mm + 0.6 (if closed by AU, UA, or UB) - 0.7 (if closed by GU) - 0.7 (if first mismatch is GA or UU except for loops closed by GU). Here, delta G degree 37iL(n) is the free energy increment for initiating a loop of n nucleotides with a CG or GC pair, and delta G degree 37mm is the free energy for the interaction of the first mismatch with the closing base pair. For hairpin loops of n = 4-9, delta G037iL(n) is 4.9, 5.0, 5.0, 5.0, 4.9, and 5.5 kcal/mol, respectively. For hairpin loops of n = 3, delta G degree 37L(3) = +4.8 + 0.6 (if closed by AU, UA, or UG) kcal/mol. Thermodynamic parameters for hairpin formation in 1 M NaCl for 13 naturally occurring RNA hairpin sequences closed by wobble base pairs are reported. The model provides good agreement for both TM and delta G degree 37 for most hairpins studied. Thermodynamic values for five terminal mismatches adjacent to wobble base pairs are also reported.

Improved parameters for the prediction of RNA hairpin stability.

Thermodynamic parameters are reported for hairpin formation in 1 M NaCl by RNA sequences of the type GGXANmAYCC, 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 degrees 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 (deltaGo(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, deltaGo(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. deltaGo(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 deltaGo(37L)(n) = deltaGo(37iL)(n) + deltaGo(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 deltaGo(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 T(M) (within 10 degrees C of the measured value) and deltaGo(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.