Thermodynamic parameters for loop formation in RNA and DNA hairpin tetraloops
- 25 February 1992
- journal article
- research article
- Published by Oxford University Press (OUP) in Nucleic Acids Research
- Vol. 20 (4), 819-824
- https://doi.org/10.1093/nar/20.4.819
Abstract
We determined the melting temperatures (Tm) and thermodynamic parameters of 15 RNA and 19 DNA hairpins at 1 M NaCI, 0.01 M sodium phosphate, 0.1 mM EDTA, at pH 7. All these hairpins have loops of four bases, the most common loop size in 16S and 23S ribosomal RNAs. The RNA hairpins varied in loop sequence, loop-closing base pair (A.U, C G, or G.C), base sequence of the stem, and stem size (four or five base pairs). The DNA hairpins varied in loop sequence, loop-closing base pair (C-G, or G-C), and base sequence of the four base-pair stem. Thermodynamic properties of a hairpin may be represented by nearest-neighbor interactions of the stem plus contributions from the loop. Thus, we obtained thermodynamic parameters for the formation of RNA and DNA tetraloops. For the tetraloops we studied, a free energy of loop formation (at 37°C) of about +3 kcal/mol is most common for either RNA or DNA. There are extra stable loops with ΔG°37 near +1 kcal/mol, but the sequences are not necessarily the same for RNA and DNA. The closing base pair is also important; changing from C-G to G-C lowered the stability of several tetraloops in both RNA and DNA. These values will be useful in predicting RNA and DNA secondary structures.Keywords
This publication has 19 references indexed in Scilit:
- Stabilities of consecutive A.cntdot.C, C.cntdot.C, G.cntdot.G, U.cntdot.C, and U.cntdot.U mismatches in RNA internal loops: evidence for stable hydrogen-bonded U.cntdot.U and C.cntdot.C+ pairsBiochemistry, 1991
- Structural Features that Give Rise to the Unusual Stability of RNA Hairpins Containing GNRA LoopsScience, 1991
- A comparison of optimal and suboptimal RNA secondary structures predicted by free energy minimization with structures determined by phylogenetic comparisonNucleic Acids Research, 1991
- Structure of an unusually stable RNA hairpinBiochemistry, 1991
- A thermodynamic study of unusually stable RNA and DNA hairpinsNucleic Acids Research, 1991
- Oligoribonucleotide synthesis using T7 RNA polymerase and synthetic DNA templatesNucleic Acids Research, 1987
- Predicting DNA duplex stability from the base sequence.Proceedings of the National Academy of Sciences, 1986
- Comparative Anatomy of 16-S-like Ribosomal RNAProgress in Nucleic Acid Research and Molecular Biology, 1985
- Free energy of imperfect nucleic acid helices: II. Small Hairpin LoopsJournal of Molecular Biology, 1973
- Stability of RNA hairpin loops: A6-Cm-U6Journal of Molecular Biology, 1973