Turner 2004

Internal loops




The internal 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.       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.

9.       Schroeder, S.J. and Turner, D.H. (2000) Factors affecting the thermodynamic stability of small asymmetric internal loops in RNA. Biochemistry, 39, 9257-9274.

10.     Burkard, M.E., Xia, T. and Turner, D.H. (2001) Thermodynamics of RNA internal loops with a guanosine-guanosine pair adjacent to another noncanonical pair. Biochemistry, 40, 2478-2483.

11.     Schroeder, S.J. and Turner, D.H. (2001) Thermodynamic stabilities of internal loops with GU closing pairs in RNA. Biochemistry, 40, 11509-11517.

12.     Schroeder, S.J., Fountain, M.A., Kennedy, S.D., Lukavsky, P.J., Puglisi, J.D., Krugh, T.R. and Turner, D.H. (2003) Thermodynamic stability and structural features of the J4/5 loop in a Pneumocystis carinii group I intron. Biochemistry, 42, 14184-14196.