Stability of RNA hairpins closed by wobble base pairs

Thermodynamic parameters are reported for hairpin formation ill 1 M NaCl by RNA sequences of the type GGXAN(m)AVCC, 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 UC 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 degrees(37L)(n) = Delta G degrees(37iL)(n) + Delta G degrees(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 degrees 37iL(n) is the free energy increment for initiating a loop of rt nucleotides with a CC or GC pair, and Delta G degrees(37mm) is the free energy for the interaction of the first mismatch with the closing base pair, Fur hairpin]oops of n = 4-9, Delta G degrees(37iL)(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(37iL)(0)(3) = +4.8 + 0.6 (if closed by AU: VA, 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 fnr both T-M and Delta G degrees(37) for most hairpins studied. Thermodynamic values for five terminal mismatches adjacent to wobble base pairs are also reported.