Last modified on 29 December 2006.

Links are provided to online PubMed abstracts for journal articles at NCBI when available.

Prediction of RNA Structure From Single Sequences:

• Jaeger J.A., Turner D.H., and Zuker M. (1989). Improved predictions of secondary structures for RNA. Proceedings of the National Academy of Sciences (USA). 86(20):7706-7710.
• Zuker M., Jaeger J.A., and Turner D.H. (1991). A comparison of optimal and suboptimal RNA secondary structures predicted by free energy minimization with structures determined by phylogenetic comparison. Nucleic Acids Research. 19(10):2707-2714.
• Walter A.E., Turner D.H., Kim J., Lyttle M.H., Muller P., Mathews D.H., and Zuker M. (1994). Coaxial stacking of helixes enhances binding of oligoribonucleotides and improves predictions of RNA folding. Proceedings of the National Academy of Sciences (USA). 91(20):9218-9222.
• Gultyaev A.P., van Batenburg F.H., and Pleij C.W. (1995). The computer simulation of RNA folding pathways using a genetic algorithm. Journal of Molecular Biology. 250(1):37-51.
• Konings D.A.M. and Gutell R.R. (1995). A comparison of thermodynamic foldings with comparatively derived structures of 16S and 16S-like rRNAs. RNA. 1(6):559-574.
• Zuker M. and Jacobson A.B. (1995). "Well-determined" regions in RNA secondary structure prediction: analysis of small subunit ribosomal RNA. Nucleic Acids Research. 23(14):2791-2798.
• Fields D.S. and Gutell R.R. (1996) An Analysis of Large rRNA Sequences Folded by a Thermodynamic Method. Folding and Design. 1(6):419-430.
• Huynen M., Gutell R., and Konings D. (1997). Assessing the reliability of RNA folding using statistical mechanics. Journal of Molecular Biology. 267(5):1104-1112.

tRNA Crystal Structure:

• Kim S.H. (1976). Three-dimensional structure of transfer RNA. Prog Nucleic Acid Res Mol Biol 17:181-216.
• Quigley G.J. and Rich A. (1976). Structural domains of transfer RNA molecules. Science 194(4267):796-806.

Review Articles Describing Comparative Sequence Analysis:

• Gutell R.R. (1993). The Simplicity Behind the Elucidation of Complex Structure in Ribosomal RNA. In: The Translational Apparatus. Nierhaus K.H., Subramanian A.R., Erdmann V.A., Franceschi F., and Wittman-Liebold B. (eds.). pp. 477-488. Plenum Publishing Corporation. New York, New York.
• Woese C.R. and Pace N.R. (1993). Probing RNA Structure, Function, and History by Comparative Analysis. In: The RNA World. Gesteland R.F. and Atkins J.F. (eds.). pp. 91-118. Cold Spring Harbor Laboratory Press. Plainview, New York.
• Gutell R.R., Larsen N., and Woese C.R. (1994) Lessons from an Evolving Ribosomal RNA: 16S and 23S rRNA Structure from a Comparative Perspective. Microbiological Reviews. 58:10-26.
• Gutell R.R. (1996). Comparative Sequence Analysis and the Structure of 16S and 23S rRNA. In: Ribosomal RNA. Structure, Evolution, Processing, and Function in Protein Biosynthesis. pp. 111-128. Dahlberg A. and Zimmerman B. (eds.) CRC Press. Boca Raton.
• Gutell R.R. and Damberger S.H. (1996). Comparative Sequence Analysis of Experiments Performed During Evolution. In: Ribosomal RNA and Group I Introns. pp. 15-33. Green R., and Schroeder R. eds. R.G. Landes Company, Austin, Texas.

Number of Possible Structure Models:

Current Structure Models:

• tRNA:
  • Crystal: Kim S.H. (1976). Three-dimensional structure of transfer RNA. Prog Nucleic Acid Res Mol Biol 17:181-216.
  • Crystal: Quigley G.J. and Rich A. (1976). Structural domains of transfer RNA molecules. Science 194(4267):796-806.
• 5S rRNA:
  • Crystal: Correll C.C., Freeborn B., Moore P.B., and Steitz T.A. (1997). Metals, motifs, and recognition in the crystal structure of a 5S rRNA domain. Cell 91(5):705-712.
  • Comparative:
• Group I Intron:
  • Crystal (P456 Region): Cate J.H., Gooding A.R., Podell E., Zhou K., Golden B.L., Kundrot C.E., Cech T.R., and Doudna J.A. (1996). Crystal structure of a group I ribozyme domain: principles of RNA packing. Science 273(5282):1678-1685.
  • Comparative: