IMPROVED PARAMETERS FOR THE PREDICTION OF RNA HAIRPIN STABILITY

Thermodynamic parameters are reported for hairpin formation in 1 M NaC l by RNA sequences of the type GGX<(AN)under bar>(m) (A) under bar YCC , where XY is the set of four Watson-Crick base pairs and the underlin ed loop sequences are three to nine nucleotides. A nearest neighbor an alysis of the data indicates the free energy of loop formation at 37 d egrees 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 o f the closing base pair, the free energy increment (Delta G degrees(37 mm)) for the interaction of the closing base pair with the first misma tch and an additional stabilization term for GA and UU first mismatche s [Serra, M. J., Axenson, T. J., & Turner, D. H. (1994) Biochemistry 3 3, 14289]. The results presented here allow improvements in the parame ters used to predict RNA hairpin stability. For hairpin loops 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, and the penalty for hairpin closure by AU or UA is +0.6 kcal/mol. Delta G degrees(37iL)(n) is the free energy for initiat ing a loop of it nucleotides. The model for predicting hairpin loop st ability for loops larger than three becomes Delta G degrees(37iL)-(n) = Delta G degrees(37iL)(n) + Delta G degrees(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 Delta G degrees(37iL) (3) = 4.8 and the penalty for AU closure of +0.6 kcal/mol. Thermodynam ic parameters for hairpin formation in 1 M NaCl for 11 naturally occur ring RNA hairpin sequences are reported. The model provides good agree ment with the measured values for both T-M (within 10 degrees C of the measured value) and Delta G degrees(37) (within 0.8 kcal/mol of the m easured value) for hairpin formation. In general, the nearest neighbor model allows prediction of RNA hairpin stability to within 5-10% of t he experimentally measured values.