Last modified on 09 July 2013.


Manual drawing and comparative modeling of RNA sequences in the 1980s was an essential process to determine and refine the 16S (and 16S-like) and 23S (and 23S-like) rRNA secondary structures [1-3]. These efforts were also the foundation for the:

  1. determination of rRNA structure evolution, and characterization of sequence and structure conservation and variation [3-5],
  2. study of RNA structural motifs and higher-order structure, including pseudoknots and tetraloops [6-9], and
  3. process of structure-based alignment of RNA sequences [4, 5].

Carl Woese, in collaboration with Harry Noller, created large wall-size blueprints of the Escherichia coli 16S and 23S rRNAs secondary structure diagrams. Sequences from the 16S (and 16S-like) and 23S (and 23S-like) from other organisms were drawn, mapped, and threaded onto smaller versions of these diagrams. Initially, the second sequence was drawn over the E. coli sequence in pencil (see Bacterial MSB8 23S rRNAs), then finalized with blue letters to indicate similarity in nucleotides between E. coli and the other rRNA sequence, and red letters to indicate differences. Note that most base pairs in a helix are composed of two blue nucleotides or two red nucleotides (covariation). These hand drawings on blueprints were subsequently drawn with computers [4, 5, 10].


Links to PubMed (PM), PubMed Central (PMC), and DOI are provided, when available.

  1. Woese C.R., Magrum L.J., Gupta R., Siegel R.B., Stahl D.A., Kop J., Crawford N., Brosius J., Gutell R., Hogan J.J., and Noller H.F. (1980). Secondary structure model for bacterial 16S ribosomal RNA: phylogenetic, enzymatic and chemical evidence. Nucleic Acids Research, 8(10):2275-2293. [ PM | PMC | DOI ]
  2. Noller H.F., Kop J., Wheaton V., Brosius J., Gutell R.R., Kopylov A.M., Dohme F., Herr W., Stahl D.A., Gupta R., and Woese C.R. (1981). Secondary structure model for 23S ribosomal RNA. Nucleic Acids Research, 9(22):6167-6189. [ PM | PMC | DOI ]
  3. Woese C.R., Gutell R., Gupta R., and Noller H.F. (1983). Detailed analysis of the higher-order structure of 16S-like ribosomal ribonucleic acids. Microbiological Reviews, 47(4):621-669. [ PM | PMC | doi ]
  4. Gutell R.R. (1984). Comparative Structural Analysis of 16S Ribosomal-RNA. Dissertation: University of California, Santa Cruz; 1984.
  5. Gutell R.R., Weiser B., Woese C.R., and Noller H.F. (1985). Comparative anatomy of 16S-like ribosomal RNA. Progress in Nucleic Acid Research and Molecular Biology, 32:155-216. [ PM | pmc | DOI ]
  6. Woese C.R., Winker S. and Gutell R.R. (1990). Architecture of Ribosomal RNA: Constraints on the sequence of Tetra-loops. Proceedings of the National Academy of Sciences (USA), 87(21):8467-8471. [ PM | PMC | DOI ]
  7. Woese C.R. and Gutell R.R. (1989). Evidence for several higher order structural elements in ribosomal RNA. Proceedings of the National Academy of Sciences (USA), 86(9):3119-3122. [ PM | PMC | DOI ]
  8. Gutell R.R. and Woese C.R. (1990). Higher order structural elements in ribosomal RNAs: Pseudo-knots and the use of non-canonical pairs. Proceedings of the National Academy of Sciences (USA), 87(2):663-667. [ PM | PMC | DOI ]
  9. Gutell R.R., Noller H.F., and Woese C.R. (1986). Higher order structure in ribosomal RNA. The EMBO Journal, 5(5):1111-1113. [ PM | PMC | doi ]
  10. Gutell R.R. and Fox G.E. (1988). A compilation of large subunit RNA sequences presented in a structural format. Nucleic Acids Research, 16(Supplement):r175-r269. [ PM | PMC | doi ]

rRNA Secondary Structure Model Diagrams:

NOTE: Some of these image files are large enough that heavily-loaded web browsers may not display them. You may wish to view this page in a new browser window and open links in new browser windows to avoid this problem.

Taxonomy/Cell Location Organism SSU rRNA LSU rRNA, 5' half LSU rRNA, 3' half
Archaea Desulfurococcus mobilis JPG    
Archaea Halobacterium cutirubrum JPG    
Archaea Halococcus morrhua JPG    
Archaea Haloferax volcanii JPG JPG JPG
Archaea Methanobacterium formicium JPG    
Archaea Methanococcus vannielli JPG JPG JPG
Archaea Methanospirullum JPG    
Archaea Pyrodictium JPG    
Archaea Sulfolobus solfataricus JPG JPG JPG
Archaea Thermococcus celer JPG    
Archaea Thermoplasma acidophilum JPG    
Archaea Thermoproteus tenax JPG    
Bacteria Anacystis nidulans   JPG JPG
Bacteria Agribacterium   JPG JPG
Bacteria Bacillus stearothermophilus   JPG JPG
Bacteria Bacillus subtilis   JPG JPG
Bacteria Escherichia coli   JPG JPG
Bacteria MSB8   JPG JPG
Eukaryotic (Nuclear) C. elegans   JPG JPG
Eukaryotic (Nuclear) Dictyostelium discoideum JPG JPG JPG
Eukaryotic (Nuclear) Maize JPG    
Eukaryotic (Nuclear) Mouse   JPG JPG
Eukaryotic (Nuclear) Physarum   JPG JPG
Eukaryotic (Nuclear) Rat liver JPG JPG JPG
Eukaryotic (Nuclear) Rice   JPG JPG
Eukaryotic (Nuclear) Saccharomyces cerevisiae (Yeast) JPG JPG JPG
Eukaryotic (Nuclear) Tetrahymena boreali JPG    
Eukaryotic (Nuclear) Tetrahymena thermophila JPG    
Eukaryotic (Nuclear) Variamorpha necatrix JPG    
Eukaryotic (Nuclear) Xenopus JPG JPG JPG
Eukaryotic (Chloroplast) Chloroplast Maize   JPG JPG
Eukaryotic (Chloroplast) Chloroplast Tabacco   JPG JPG
Eukaryotic (Mitochondrion) Aspergillus JPG JPG JPG
Eukaryotic (Mitochondrion) Cow JPG JPG JPG
Eukaryotic (Mitochondrion) Crithidia     JPG
Eukaryotic (Mitochondrion) Drosophila   JPG JPG
Eukaryotic (Mitochondrion) Homo sapiens JPG JPG JPG
Eukaryotic (Mitochondrion) Maize   JPG JPG
Eukaryotic (Mitochondrion) Mosquito   JPG JPG
Eukaryotic (Mitochondrion) Mouse JPG JPG JPG
Eukaryotic (Mitochondrion) Oenothera   JPG JPG
Eukaryotic (Mitochondrion) Paramecium JPG JPG JPG
Eukaryotic (Mitochondrion) Podospora JPG JPG JPG
Eukaryotic (Mitochondrion) Rat JPG JPG JPG
Eukaryotic (Mitochondrion) Trypanosome JPG JPG JPG
Eukaryotic (Mitochondrion) Xenopus JPG JPG JPG
Eukaryotic (Mitochondrion) Yeast JPG JPG JPG

Intron Secondary Structure Model Diagram:

Intron RNA Molecule Taxonomy/Cell Location Organism Intron RNA
Group I Intron Eukaryotic Nuclear Tetrahymena thermophila JPG