Turner 2004

Bulge Loops




The bulge 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.       Fink, T.R. and Crothers, D.M. (1972) Free energy of imperfect nucleic acid helices,  I.  The bulge defect. J. Mol. Biol., 66, 1-12.

2.       Groebe, D.R. and Uhlenbeck, O.C. (1989) Thermal stability of RNA hairpins containing a four-membered loop and a bulge nucleotide. Biochemistry, 28, 742-747.

3.       Longfellow, C.E., Kierzek, R. and Turner, D.H. (1990) Thermodynamic and spectroscopic study of bulge loops in oligoribonucleotides. Biochemistry, 29, 278-285.

4.       Znosko, B.M., Silvestri, S.B., Volkman, H., Boswell, B. and Serra, M.J. (2002) Thermodynamic parameters for an expanded nearest-neighbor model for the formation of RNA duplexes with single nucleotide bulges. Biochemistry, 41, 10406-10417.