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Turner 2004

Watson-Crick Helices

References

 

 

The Watson-Crick nearest neighbor parameters were reported in:

Xia, T., SantaLucia, J., Jr., Burkard, M.E., Kierzek, R., Schroeder, S.J., Jiao, X., Cox, C. and Turner, D.H. (1998) Thermodynamic parameters for an expanded nearest-neighbor model for formation of RNA duplexes with Watson-Crick pairs. Biochemistry, 37, 14719-14735.

The experimental data for the fit of the parameters were taken from:

1.       Nelson, J.W., Martin, F.H. and Tinoco, I., Jr. (1981) DNA and RNA oligomer thermodynamics: the effect of mismatched bases on double-helix stability. Biopolymers, 20, 2509-2531.

2.       Freier, S.M., Burger, B.J., Alkema, D., Neilson, T. and Turner, D.H. (1983) Effects of 3' dangling end stacking on the stability of GGCC and CCGG double helices. Biochemistry, 22, 6198-6206.

3.       Petersheim, M. and Turner, D.H. (1983) Base-stacking and base-pairing contributions to helix stability: thermodynamics of double-helix formation with CCGG, CCGGp, CCGGAp, ACCGGp, CCGGUp, and ACCGGUp. Biochemistry, 22, 256-263.

4.       Freier, S.M., Alkema, D., Sinclair, A., Neilson, T. and Turner, D.H. (1985) Contributions of dangling end stacking and terminal base-pair formation to the stabilities of XGGCCp, XCCGGp, XGGCCYp, and XCCGGYp helixes. Biochemistry, 24, 4533-4539.

5.       Freier, S.M., Sinclair, A., Neilson, T. and Turner, D.H. (1985) Improved free energies for G-C base-pairs. J. Mol. Biol., 185, 645-647.

6.       Hickey, D.R. and Turner, D.H. (1985) Solvent effects on the stability of A7U7p. Biochemistry, 24, 2086-2094.

7.       Freier, S.M., Kierzek, R., Caruthers, M.H., Neilson, T. and Turner, D.H. (1986) Free energy contributions of G.U and other terminal mismatches to helix stability. Biochemistry, 25, 3209-3223.

8.       Freier, S.M., Kierzek, R., Jaeger, J.A., Sugimoto, N., Caruthers, M.H., Neilson, T. and Turner, D.H. (1986) Improved free-energy parameters for predictions of RNA duplex stability. Proc. Natl. Acad. Sci. USA., 83, 9373-9377.

9.       Kierzek, R., Caruthers, M.H., Longfellow, C.E., Swinton, D., Turner, D.H. and Freier, S.M. (1986) Polymer-supported synthesis and its application to test the nearest-neighbor model for duplex stability. Biochemistry, 25, 7840-7846.

10.     Sugimoto, N., Kierzek, R., Freier, S.M. and Turner, D.H. (1986) Energetics of internal GU mismatches in ribooligonucleotide helixes. Biochemistry, 25, 5755-5759.

11.     Sugimoto, N., Kierzek, R. and Turner, D.H. (1987) Sequence dependence for the energetics of dangling ends and terminal base pairs in ribonucleic acid. Biochemistry, 26, 4554-4558.

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

13.     Hall, K.B. and McLaughlin, L.W. (1991) Thermodynamic and structural properties of pentamer DNA.DNA, RNA.RNA, and DNA.RNA duplexes of identical sequence. Biochemistry, 30, 10606-10613.

14.     He, L., Kierzek, R., SantaLucia, J., Jr., Walter, A.E. and Turner, D.H. (1991) Nearest-neighbor parameters for G.U mismatches. Biochemistry, 30, 11124-11132.

15.     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.

16.     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.

17.     Wu, M., McDowell, J.A. and Turner, D.H. (1995) A periodic table of symmetric tandem mismatches in RNA. Biochemistry, 34, 3204-3211.

18.     McDowell, J.A., He, L., Chen, X. and Turner, D.H. (1997) Investigation of the structural basis for thermodynamic stabilities of tandem GU wobble pairs: NMR structures of (rGGAGUUCC)2 and (rGGAUGUCC)2. Biochemistry, 36, 8030-8038.

19.     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.

20.     Xia, T., SantaLucia, J., Jr., Burkard, M.E., Kierzek, R., Schroeder, S.J., Jiao, X., Cox, C. and Turner, D.H. (1998) Thermodynamic parameters for an expanded nearest-neighbor model for formation of RNA duplexes with Watson-Crick pairs. Biochemistry, 37, 14719-14735.