Turner 1999

hairpin loops




The hairpin loop nearest neighbor parameters for free energy change were reported in:

Mathews, D.H., Sabina, J., Zuker, M. and Turner, D.H. (1999) Expanded sequence dependence of thermodynamic parameters provides improved prediction of RNA secondary structure. J. Mol. Biol., 288, 911-940.


The experimental data for the fit of the parameters were taken from:

1.       Groebe, D.R. and Uhlenbeck, O.C. (1988) Characterization of RNA hairpin loop stability. Nucleic Acids Res., 16, 11725-11735.

2.       Antao, V.P., Lai, S.Y. and Tinoco, I., Jr. (1991) A thermodynamic study of unusually stable RNA and DNA hairpins. Nucleic Acids Res., 19, 5901-5905.

3.       Antao, V.P. and Tinoco, I., Jr. (1992) Thermodynamic parameters for loop formation in RNA and DNA hairpin tetraloops. Nucleic Acids Res., 20, 819-824.

4.       Serra, M.J., Lyttle, M.H., Axenson, T.J., Schadt, C.A. and Turner, D.H. (1993) RNA hairpin loop stability depends on closing pair. Nucleic Acids Res., 21, 3845-3849.

5.       Serra, M.J., Axenson, T.J. and Turner, D.H. (1994) A model for the stabilities of RNA hairpins based on a study of the sequence dependence of stability for hairpins of six nucleotides. Biochemistry, 33, 14289-14296.

6.       Laing, L.G. and Hall, K.B. (1996) A model of the iron responsive element RNA hairpin loop structure determined from NMR and thermodynamic data. Biochemistry, 35, 13586-13596.

7.       Serra, M.J., Barnes, T.W., Betschart, K., Gutierrez, M.J., Sprouse, K.J., Riley, C.K., Stewart, L. and Temel, R.E. (1997) Improved parameters for the prediction of RNA hairpin stability. Biochemistry, 36, 4844-4851.

8.       Giese, M.R., Betschart, K., Dale, T., Riley, C.K., Rowan, C., Sprouse, K.J. and Serra, M.J. (1998) Stability of RNA hairpins closed by wobble base pairs. Biochemistry, 37, 1094-1100.