Sequence Dependence of the Stability of RNA Hairpin Molecules with Six Nucleotide Loops
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- 作者：Christopher J. Vecenie ; Catherine V. Morrow ; Allison Zyra ; and Martin J. Serra
- 刊名：Biochemistry
- 出版年：2006
- 出版时间：February 7, 2006
- 年：2006
- 卷：45
- 期：5
- 页码：1400 - 1407
- 全文大小：211K
- 年卷期：v.45,no.5(February 7, 2006)
- ISSN：1520-4995
文摘
Thermodynamic parameters are reported for hairpin formation in 1 M NaCl by RNA sequenceof the types GCGXUAAUYCGC and GGUXUAAUYACC with Watson-Crick loop closure, where XYis the set of 10 possible mismatch base pairs. A nearest-neighbor analysis of the data indicates the freeenergy of loop formation at 37 
C varies from 3.1 to 5.1 kcal/mol. These results agree with the modelpreviously developed [Vecenie, C. J., and Serra, M. J. (2004) Biochemistry 43, 11813] to predict thestability of RNA hairpin loops: 
G37L(n) = G37i(n) + G37MM - 0.8 (if first mismatch is GA or UU)- 0.8 (if first mismatch is GG and loop is closed on the 5' side by a purine). Here, G37i(n) is the freeenergy for initiating a loop of n nucleotides, and G37MM is the free energy for the interaction of the firstmismatch with the closing base pair. Thermodynamic parameters are also reported for hairpin formationin 1 M NaCl by RNA sequence of the types GACGXUAAUYUGUC and GGUXUAAUYGCC with GUbase pair closure, where XY is the set of 10 possible mismatch base pairs. A nearest-neighbor analysisof the data indicates the free energy of loop formation at 37 C varies from 3.6 to 5.3 kcal/mol. Theseresults allow the development of a model for predicting the stability of hairpin loops closed by GU basepairs. G37L(n) (kcal/mol) = G37i(n) - 0.8 (if the first mismatch is GA) - 0.8 (if the first mismatch isGG and the loop is closed on the 5' side by a purine). Note that for these hairpins, the stability of theloops does not depend on G37MM. For hairpin loops closed by GU base pairs, the G37i(n) values,when n = 4, 5, 6, 7, and 8, are 4.9, 5.0, 4.6, 5.0, and 4.8 kcal/mol, respectively. The model gives goodagreement when tested against six naturally occurring hairpin sequences. Thermodynamic values forterminal mismatches adjacent to GC, GU, and UG base pairs are also reported.
C varies from 3.1 to 5.1 kcal/mol. These results agree with the modelpreviously developed [Vecenie, C. J., and Serra, M. J. (2004) Biochemistry 43, 11813] to predict thestability of RNA hairpin loops: G37L(n) = G37i(n) + G37MM - 0.8 (if first mismatch is GA or UU)- 0.8 (if first mismatch is GG and loop is closed on the 5' side by a purine). Here, G37i(n) is the freeenergy for initiating a loop of n nucleotides, and G37MM is the free energy for the interaction of the firstmismatch with the closing base pair. Thermodynamic parameters are also reported for hairpin formationin 1 M NaCl by RNA sequence of the types GACGXUAAUYUGUC and GGUXUAAUYGCC with GUbase pair closure, where XY is the set of 10 possible mismatch base pairs. A nearest-neighbor analysisof the data indicates the free energy of loop formation at 37 C varies from 3.6 to 5.3 kcal/mol. Theseresults allow the development of a model for predicting the stability of hairpin loops closed by GU basepairs. G37L(n) (kcal/mol) = G37i(n) - 0.8 (if the first mismatch is GA) - 0.8 (if the first mismatch isGG and the loop is closed on the 5' side by a purine). Note that for these hairpins, the stability of theloops does not depend on G37MM. For hairpin loops closed by GU base pairs, the G37i(n) values,when n = 4, 5, 6, 7, and 8, are 4.9, 5.0, 4.6, 5.0, and 4.8 kcal/mol, respectively. The model gives goodagreement when tested against six naturally occurring hairpin sequences. Thermodynamic values forterminal mismatches adjacent to GC, GU, and UG base pairs are also reported.