Turner 1999

Bulge Loops




The bulge 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.       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.