Turner 2004

hairpin loops




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

Mathews, D.H., Disney, M.D., Childs, J.L., Schroeder, S.J., Zuker, M. and Turner, D.H. (2004) Incorporating chemical modification constraints into a dynamic programming algorithm for prediction of RNA secondary structure. Proc. Natl. Acad. Sci. USA, 101, 7287-7292.

The enthalpy change parameters were reported in:

Lu, Z.J., Turner, D.H. and Mathews, D.H. (2006) A set of nearest neighbor parameters for predicting the enthalpy change of RNA secondary structure formation. Nucleic Acids Res., 34 4912 - 4924.

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.

9.       Shu, Z. and Bevilacqua, P.C. (1999) Isolation and characterization of thermodynamically stable and unstable RNA hairpins from a triloop combinatorial library. Biochemistry, 38, 15369-15379.

10.     Dale, T., Smith, R. and Serra, M. (2000) A test of the model to predict unusually stable RNA hairpin loop stability. RNA, 6, 608-615.

11.     Proctor, D.J., Schaak, J.E., Bevilacqua, J.M., Falzone, C.J. and Bevilacqua, P.C. (2002) Isolation and characterization of stable tetraloops with the motif YNMG that participates in tertiary interactions. Biochemistry, 41, 12062-12075.