The internal 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. Peritz, A.E., Kierzek, R.,
Sugimoto, N. and Turner, D.H. (1991) Thermodynamic study of internal loops in oligoribonucleotides: Symmetric loops are more stable than
asymmetric loops. Biochemistry, 30, 6428-6436.
2. SantaLucia, J.,
Jr., Kierzek, R. and Turner, D.H. (1991) Functional
group substitutions as probes of hydrogen bonding between GA mismatches in RNA
internal loops. J. Am. Chem. Soc., 113, 4313-4322.
3. SantaLucia, J.,
Jr., Kierzek, R. and Turner, D.H. (1991) Stabilities
of consecutive A.C, C.C, G.G, U.C,
and U.U mismatches in RNA internal loops: evidence for stable
hydrogen-bonded U.U and C.C+ pairs. Biochemistry, 30, 8242-8251.
4. Walter, A.E., Wu, M. and Turner, D.H.
(1994) The stability and structure of tandem GA
mismatches in RNA depend on closing base pairs. Biochemistry, 33,
11349-11354.
5. Wu, M., McDowell, J.A. and Turner, D.H.
(1995) A periodic table of symmetric tandem mismatches in RNA. Biochemistry, 34, 3204-3211.
6. Schroeder, S., Kim, J. and Turner, D.H.
(1996) G.A and U.U mismatches can stabilize RNA internal
loops of three nucleotides. Biochemistry, 35, 16105-16109.
7. Xia, T., McDowell, J.A. and Turner, D.H.
(1997) Thermodynamics of nonsymmetric tandem
mismatches adjacent to G.C base pairs in RNA. Biochemistry, 36,
12486-12487.
8. Kierzek, R., Burkard, M. and Turner, D. (1999) Thermodynamics of single
mismatches in RNA duplexes. Biochemistry, 38, 14214-14223.