Sequence Dependence of the Stability of RNA Hairpin Molecules with Six Nucleotide Loops

• Published in: Biochemistry (Easton) 2006-02, Vol.45 (5), p.1400-1407
• Main Authors: Vecenie, Christopher J., Morrow, Catherine V., Zyra, Allison, Serra, Martin J.
• Format: Article
• Language: English
• Subjects: Base Composition; Base Pairing; Base Sequence; Models, Chemical; Models, Molecular; Nucleic Acid Conformation; Nucleic Acid Denaturation; Oligoribonucleotides - chemistry; RNA - chemical synthesis; RNA - chemistry; RNA - isolation & purification; RNA Stability; Sodium Chloride - chemistry; Thermodynamics
• ISSN: 0006-2960; 1520-4995
• DOI: 10.1021/bi051750u

Thermodynamic parameters are reported for hairpin formation in 1 M NaCl by RNA sequence of the types GCGXUAAUYCGC and GGUXUAAUYACC with Watson−Crick loop closure, where XY is the set of 10 possible mismatch base pairs. A nearest-neighbor analysis of the data indicates the free energy of loop formation at 37 °C varies from 3.1 to 5.1 kcal/mol. These results agree with the model previously developed [Vecenie, C. J., and Serra, M. J. (2004) Biochemistry 43, 11813] to predict the stability of RNA hairpin loops:  ΔG°37L( n ) = ΔG°37i( n ) + ΔG°37MM − 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, ΔG°37i( n ) is the free energy for initiating a loop of n nucleotides, and ΔG°37MM is the free energy for the interaction of the first mismatch with the closing base pair. Thermodynamic parameters are also reported for hairpin formation in 1 M NaCl by RNA sequence of the types GACGXUAAUYUGUC and GGUXUAAUYGCC with GU base pair closure, where XY is the set of 10 possible mismatch base pairs. A nearest-neighbor analysis of the data indicates the free energy of loop formation at 37 °C varies from 3.6 to 5.3 kcal/mol. These results allow the development of a model for predicting the stability of hairpin loops closed by GU base pairs. ΔG°37L( n ) (kcal/mol) = ΔG°37i( n ) − 0.8 (if the first mismatch is GA) − 0.8 (if the first mismatch is GG and the loop is closed on the 5‘ side by a purine). Note that for these hairpins, the stability of the loops does not depend on ΔG°37MM. For hairpin loops closed by GU base pairs, the ΔG°37i( 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 good agreement when tested against six naturally occurring hairpin sequences. Thermodynamic values for terminal mismatches adjacent to GC, GU, and UG base pairs are also reported.