Elements of thermodynamics in RNA evolution.

• Authors: Elżbieta Kierzek , Ewa Biała , Ryszard Kierzek
• Languages of publication: EN

Abstracts

EN

The paper presents some aspects correlating thermal stability of RNA folding and the occurrence of structural motifs in natural ribonucleic acids. Particularly, the thermodynamic stability of 2'-5' and 3'-5' linked RNA and the contribution of unpaired terminal nucleotides (dangling ends) in secondary (2D) and tertiary (3D) structures of RNA are discussed. Both examples suggest that during evolution nature selected sequences and structures of RNA which are the most thermally stable and efficient for their biological function.

Keywords

EN

thermodynamics; ribonucleic acids

• Publisher: Polish Biochemical Society
• Journal: Acta Biochimica Polonica
• Year: 2001
• Volume: 48
• Issue: 2
• Pages: 485-493

Dates

published

2001

received

2001-02-14

accepted

2001-05-23

revised

2001-05-9

Contributors

author

Elżbieta Kierzek

• Institute of Bioorganic Chemistry, Polish Academy of Sciences, Poznań, Poland

author

Ewa Biała

• Institute of Bioorganic Chemistry, Polish Academy of Sciences, Poznań, Poland

author

Ryszard Kierzek

• Institute of Bioorganic Chemistry, Polish Academy of Sciences, Poznań, Poland

References

• 1. Gesteland, R.F. & Atkins, J.F. (1993) The RNA world. Cold Spring Harbor Laboratory Press, Cold Spring Harbor.
• 2. Matysiak, M., Wrzesiński, J. & Ciesiołka, J. (1999) Sequentional folding of the genomic ribozyme of the hepatitis delta virus: Structural analysis of RNA transcription intermediates. J. Mol. Biol. 291, 283-294.
• 3. Jaeger, J.A., Turner, D.H. & Zucker, M. (1989) Improved prediction of secondary structure for RNA. Proc. Natl. Acad. Sci. U.S.A. 86, 7706-7710.
• 4. Baglioni, C., Minks, M.A. & Maroney, P.A. (1978) Interferon action may be mediated by activation of a nuclease by pppA2'p5'A2' p5'A. Nature 273, 684-687.
• 5. Orgel, L.E. (1987) Evolution of the genetic apparatus: A review. Cold Spring Harbor Symp. Quant. Biol. 52, 123-133.
• 6. Breslow, R., Anslyn, E. & Huang, D.L. (1991) Ribonuclease mimics. Tetrahedron 47, 2365- 2376.
• 7. Usher, D.A. (1972) RNA double helix and the evolution of the 3',5' linkage. Nat. New Biol. 235, 207-208.
• 8. Usher, D.A. & McHale, A.H. (1976) Hydrolytic stability of helical RNA: A selective advantage for the natural 3',5'-bond. Proc. Natl. Acad. Sci. U.S.A. 73, 1149-1153.
• 9. Kierzek, R., He, L. & Turner, D.H. (1992) Association of 2'-5' oligoribonucleotides. Nucleic Acids Res. 20, 1685-1690.
• 10. Xia, T., SantaLucia, J., Burkard, M.E., Kierzek, R., Schroeder, S.J., Cox, C. & Turner, D.H. (1998) Parameters for expanded nearest-neighbor model for formation of RNA duplexes with Watson-Crick base pair. Biochemistry 37, 14719-14735.
• 11. Kierzek, R., Burkard, M.E. & Turner, D.H. (1999) The thermodynamics of single mismatches in RNA duplexes. Biochemistry 38, 14214-14223.
• 12. Tunis-Schneider, M.J.B. & Maestre, M.F. (1970) Circular dichroism spectra of oriented and unoriented deoxyribonucleic acid films: A preliminary study. J. Mol. Biol. 52, 521-541.
• 13. Williams, A.P., Longfellow, C.L., Freier, S.M., Kierzek, R. & Turner, D.H. (1989) Laser temperature-jump, spectroscopic and thermodynamic study of salt effects on duplex formation by dGCATGC. Biochemistry 28, 4283-4291.
• 14. Xia, T., McDowell, J.A. & Turner, D.H. (1997) Thermodynamics of nonsymetric tandem mismatches adjacent to G-C base pairs in RNA. Biochemistry 36, 12486-12497.
• 15. Dougherty, J.P., Rizzo, C.J. & Breslow, R. (1992) Oligodeoxynucleotides that contain 2',5' linkages: Synthesis and hybridization properties. J. Am. Chem. Soc. 114, 6254- 6255.
• 16. Hashimoto, H. & Switzer, C. (1992) Self-association of 2',5'-linked deoxynucleotides: meta- DNA. J. Am. Chem. Soc. 114, 6255-6256.
• 17. Robinson, H., Jung, K.E., Switzer, C. & Wang, A.H.J. (1995) DNA with 2'-5' phosphodiester bonds forms a duplex structure in the A-type conformation. J. Am. Chem. Soc. 117, 837-838.
• 18. Freier, S.M., Kierzek, R., Jaeger, J.A., Sugimoto, N., Caruthers, M.H., Neilson, T. & Turner, D.H. (1986) Improved free energy parameters for predictions of RNA duplex stability. Proc. Natl. Acad. Sci. U.S.A. 83, 9373- 9377.
• 19. Sugimoto, N., Kierzek, R. & Turner, D.H. (1987) Sequence dependence for the energetics of dangling ends and terminal base pairs in ribonucleic acid. Biochemistry 26, 4554-4559.
• 20. Quigley, G.J. & Rich, A., (1976) Structural domains of transfer RNA molecules. Science 194, 796-806.
• 21. Protein Data Bank (http://www.pdb.bnl.gov), Nucleic Acid Data Base (http://ndbserver.rutgers.edu).
• 22. Burkard, M.E., Kierzek, R. & Turner, D.H. (1999) Thermodynamics of unpaired terminal nucleotides on short RNA helixes correlates with stacking at helix termini in larger RNAs. J. Mol. Biol. 290, 967-982.
• 23. Sprinzl, M., Horn, C., Brown, M., Ioudovitch, A. & Steinberg, S. (1998) Compilation of tRNA sequences and sequences of tRNA genes. Nucleic Acids Res. 26, 148-153.
• 24. Mathews, D.H., Sabina, J., Zucker, M. & Turner, D.H. (1999) Expanded sequence dependence of thermodynamic parameters improves prediction of RNA secondary structure. J. Mol. Biol. 288, 911-940.