TY - JOUR
T1 - Improved parameters for the prediction of RNA hairpin stability
AU - Serra, Martin J.
AU - Barnes, Thomas W.
AU - Betschart, Kelly
AU - Gutierrez, Mathew J.
AU - Sprouse, Kimberly J.
AU - Riley, Cheryl K.
AU - Stewart, Lora
AU - Temel, Ryan E.
PY - 1997/4/22
Y1 - 1997/4/22
N2 - Thermodynamic parameters are reported for hairpin formation in 1 M NaCl by RNA sequences of the type GGXAN AYCC, 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., and 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 T(M) (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.
AB - Thermodynamic parameters are reported for hairpin formation in 1 M NaCl by RNA sequences of the type GGXAN AYCC, 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., and 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 T(M) (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.
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U2 - 10.1021/bi962608j
DO - 10.1021/bi962608j
M3 - Article
C2 - 9125504
AN - SCOPUS:0030890755
SN - 0006-2960
VL - 36
SP - 4844
EP - 4851
JO - Biochemistry
JF - Biochemistry
IS - 16
ER -