Last modified in August 1996 (PDFs added in April 2008).

Fields, Dana S., and Gutell, Robin R. (1996)
An Analysis of Large rRNA Sequences Folded by a Thermodynamic Method.
Folding and Design 1:419-430.

In this work, 72 "phylogenetically and structurally diverse" 23S rRNA sequences were chosen for study. View Table 1 from the manuscript.

Definitions:

length:
the # of nucleotides in the full-length RNA sequence.
5':
5' half of secondary structure model diagram.
3':
3' half of secondary structure model diagram.
score-1:
the score of the energetically optimal folding.
score-2:
the score of the best scoring energetically sub-optimal folding.
%NC:
the % of the total base pairs that are non-canonical base pairs in the comparatively derived secondary structure. This does not include non-canonical base pairs which are proposed to contribute to tertiary structure.
%G+C:
the % of the bases in the primary sequence which are G or C.
%HSTL:
the % of the hairpin loops in the comparatively derived secondary structure which are stable tetraloops.
TBP:
the total number of base pairs (canonical + non-canonical) in the comparatively derived secondary structure.
NCBP:
the total number of non-canonical base pairs in the comparatively derived secondary structure.

The manuscript has thirteen figures. Figures 1-9 were given in the paper itself and are also given here; Figures A-D were mentioned in the text of the manuscript but are only presented here in this appendix. To see any figure, click on its name below:

Figure 1: PS | PDF Figure 2: PS | PDF Figure 3: PS | PDF Figure 4: PS | PDF Figure 5: PS | PDF Figure 6: PS | PDF Figure 7: PS | PDF
Figure 8: PS | PDF Figure 9: PS | PDF   Figure A: PS | PDF Figure B: PS | PDF Figure C: PS | PDF Figure D: PS | PDF

Notes for the 72 23S rRNA comparatively derived secondary structures:

  • The comparatively derived secondary structures of 23S rRNA listed below are presented as a "5'-half" and a "3'-half."
  • The Watson-Crick base pairs are indicated by a tick mark.
  • The GU or UG base pairs are indicated by a small closed circle.
  • Not all of the non-canonical base pairs have been marked by a circle. This information will be provided shortly when the database is updated.
  • The GA or AG base pairs are indicated by an open circle.
  • The non-canonical base pairs, but which are not GA or AG, are indicated by a large closed circle.
  • The comparatively inferred base pairs that are correctly predicted by the energetically optimal folding of the Zuker-Turner method are indicated by thick tick marks.
  • Accession numbers for each analyzed sequence are displayed on the secondary structure diagram and are also available at our 16S rRNA WWW address.
  • (References for the Comparatively inferred 23S rRNA secondary structures are:
    • (1) Gutell, Gray, and Schnare (1993) Nucl. Acids Res. 21:3055-3074.
    • (2) Schnare, Damberger, Gray, and Gutell (1996) J.Mol.Biol. 256:701-719.)
    • (3) Schnare, Damberger, Gray, and Gutell manuscript in preparation
Archaea:                    
organism name 5' 3' length score-1 score-2 %NC %G+C %HSTL TBP NCBP
Halobacterium marismortui PS | PDF PS | PDF 2945 51 63 4.9 55 19.1 822 40
Halococcus morrhuae PS | PDF PS | PDF 2927 57 60 5.1 58 19.4 839 43
Methanobacterium thermoautotrophicum PS | PDF PS | PDF 3019 54 56 3.6 57 15.7 868 31
Methanococcus vannielii PS | PDF PS | PDF 2958 67 67 3.1 54 19.7 847 26
Sulfolobus solfataricus PS | PDF PS | PDF 3044 57 61 3.6 60 16.7 890 32
Thermococcus celer PS | PDF PS | PDF 3029 74 74 3.3 64 19.7 884 29
Thermoplasma acidophilum PS | PDF PS | PDF 2908 52 66 5.4 53 26.1 838 45
Thermoproteus tenax PS | PDF PS | PDF 3031 58 66 2.9 67 21.1 888 26
mean:     2983 59 64 4.0 59 19.7 860 34
SD:     54 8 5 1.0 5 3.1 26 8
(eu)Bacteria:                    
organism name 5' 3' length score-1 score-2 %NC %G+C %HSTL TBP NCBP
Anacystis nidulans (Synechococcus sp. 6301) PS | PDF PS | PDF 2876 57 61 4.7 54 20.6 822 39
Bacillus subtilis PS | PDF PS | PDF 2927 55 59 3.5 54 18.8 834 29
Borrelia burgdorferi PS | PDF PS | PDF 2926 45 54 3.3 44 17.4 837 28
Campylobacter coli PS | PDF PS | PDF 3057 48 62 5.9 46 16.2 887 52
Escherichia coli PS | PDF PS | PDF 2904 58 62 4.0 53 20.6 834 33
Frankia sp. PS | PDF PS | PDF 3099 45 50 4.1 57 15.5 906 37
Mycobacterium leprae PS | PDF PS | PDF 3122 51 55 4.9 55 12.5 911 45
Pseudomonas aeruginosa PS | PDF PS | PDF 2893 55 60 4.6 52 16.2 830 38
Pseudomonas cepacia PS | PDF PS | PDF 2878 47 53 4.8 53 14.9 834 40
Rhodobacter sphaeroides(A) PS | PDF PS | PDF 2883 56 63 4.0 56 19.7 820 33
Streptomyces ambofaciens PS | PDF PS | PDF 3120 46 50 4.5 57 15.5 914 41
Thermotoga maritima PS | PDF PS | PDF 3023 66 70 3.7 63 20.0 881 33
Thermus thermophilus PS | PDF PS | PDF 2915 58 72 3.4 64 18.6 843 29
mean:     2971 53 59 4.3 54 17.4 858 37
SD:     98 6 7 .7 6 2.5 36 7
Chloroplasts:                    
organism name 5' 3' length score-1 score-2 %NC %G+C %HSTL TBP NCBP
Alnus incana (alder) PS | PDF PS | PDF 2914 34 35 6.3 55 17.9 814 51
Astasia longa PS | PDF PS | PDF 3105 19 28 4.7 34 11.6 831 39
Chlamydomonas eugametos PS | PDF PS | PDF 3204 48 50 4.2 47 14.9 854 36
Chlamydomonas reinhardtii PS | PDF PS | PDF 2902 54 60 4.5 50 14.9 814 37
Chlorella ellipsoidea PS | PDF PS | PDF 3207 40 52 7.5 49 14.5 828 62
Euglena gracilis PS | PDF PS | PDF 2877 40 43 4.6 43 14.7 805 37
Marchantia polymorpha PS | PDF PS | PDF 2914 35 41 6.0 52 14.9 817 49
Nicotiana tabacum PS | PDF PS | PDF 2913 32 35 5.6 54 19.4 817 46
Palmaria palmata PS | PDF PS | PDF 2885 52 58 4.9 48 13.4 813 40
Zea mays PS | PDF PS | PDF 2981 36 39 7.3 54 16.4 847 62
mean:     2990 39 44 5.6 49 15.3 824 46
SD:     131 10 11 1.2 6 2.2 16 10
Mitochondria:                    
organism name 5' 3' length score-1 score-2 %NC %G+C %HSTL TBP NCBP
Acanthamoeba castellanii PS | PDF PS | PDF 2719 40 47 4.8 34 15.6 756 36
Caenorhabditis elegans PS | PDF PS | PDF 953 30 51 9.6 21 9.5 230 22
Chondrus crispus PS | PDF PS | PDF 2583 33 45 6.5 30 9.7 693 45
Crossostoma lacustre PS | PDF PS | PDF 1680 49 52 9.9 45 5.1 364 36
Dictyostelium discoideum PS | PDF PS | PDF 2872 36 39 6.9 35 12.5 721 50
Drosophila melanogaster PS | PDF PS | PDF 1324 36 42 4.3 17 3.2 302 13
Gallus gallus PS | PDF PS | PDF 1621 28 36 9.1 46 7.9 351 32
Homo sapiens PS | PDF PS | PDF 1558 34 45 8.9 43 5.4 349 31
Marchantia polymorpha PS | PDF PS | PDF 2799 41 44 5.3 47 12.9 735 39
Paracentrotus lividus PS | PDF PS | PDF 1551 34 38 7.8 37 8.8 348 27
Paramecium tetraurelia PS | PDF PS | PDF 2568 45 49 5.7 36 10.2 671 38
Penicillium chrysogenum PS | PDF PS | PDF 3416 45 53 6.9 29 7.0 715 49
Prototheca wickerhamii PS | PDF PS | PDF 3004 41 54 5.1 37 12.9 744 38
Saccharomyces cerevisiae PS | PDF PS | PDF 3273 27 43 6.2 22 3.4 731 45
Schizosaccharomyces pombe PS | PDF PS | PDF 2826 57 57 5.0 31 6.5 733 37
Tetrahymena pyriformis(R) PS | PDF PS | PDF 2595 41 53 6.6 27 10.0 702 46
Xenopus laevis PS | PDF PS | PDF 1640 41 43 8.6 39 2.6 362 31
Zea mays PS | PDF PS | PDF 3514 24 32 7.6 52 14.8 708 54
mean:     2361 38 46 6.9 35 8.8 568 37
SD:     787 8 7 1.7 10 4.0 198 10
Eucarya:                    
organism name 5' 3' length score-1 score-2 %NC %G+C %HSTL TBP NCBP
Aedes albopictus PS | PDF PS | PDF 4262 50 51 6.7 51 13.2 982 66
Arabidopsis thaliana PS | PDF PS | PDF 3539 50 51 6.7 55 19.0 998 67
Caenorhabditis elegans PS | PDF PS | PDF 3662 43 54 6.1 49 15.2 1027 63
Chlorella ellipsoidea PS | PDF PS | PDF 3512 49 54 6.5 52 19.0 1003 65
Crithidia fasciculata PS | PDF PS | PDF 4080 33 40 5.5 51 17.1 902 50
Cryptococcus neoformans B (gattii) PS | PDF PS | PDF 3544 46 52 5.7 48 21.5 1025 58
Drosophila melanogaster PS | PDF PS | PDF 4123 60 65 5.4 39 10.5 1010 55
Euglena gracilis PS | PDF PS | PDF 4052 23 26 8.4 57 11.1 1042 88
Giardia intestinalis PS | PDF PS | PDF 2851 24 35 4.7 76 9.7 782 37
Giardia muris PS | PDF PS | PDF 2811 37 41 5.4 57 10.0 772 42
Herdmania momus PS | PDF PS | PDF 3721 37 43 6.1 57 11.7 939 57
Homo sapiens PS | PDF PS | PDF 5184 32 40 5.7 69 10.4 1005 57
Mus musculus PS | PDF PS | PDF 4869 43 50 5.3 66 9.1 1008 53
Oryza sativa PS | PDF PS | PDF 3541 43 49 7.0 59 16.7 1003 70
Physarum polycephalum PS | PDF PS | PDF 3943 35 37 5.8 53 16.5 997 58
Phytophthora megasperma PS | PDF PS | PDF 3860 59 62 5.9 49 23.4 1015 60
Pneumocystis carinii PS | PDF PS | PDF 3503 49 54 5.6 46 16.7 1015 57
Prorocentrum micans PS | PDF PS | PDF 3562 33 39 6.5 48 13.2 923 60
Saccharomyces cerevisiae PS | PDF PS | PDF 3550 42 49 5.5 48 12.8 1028 57
Tetrahymena thermophila PS | PDF PS | PDF 3501 49 54 4.8 45 20.8 977 47
Toxoplasma gondii-P PS | PDF PS | PDF 3627 45 48 6.3 48 14.7 959 60
Trypanosoma brucei PS | PDF PS | PDF 4188 32 35 5.7 52 14.7 897 51
Xenopus laevis PS | PDF PS | PDF 4273 31 43 5.7 65 9.1 1009 58
mean:     3816 41 47 6.0 54 14.6 970 58
SD:     540 10 9 .8 9 4.2 73 10

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