Literature Reference:

Elgavish T., Cannone J.J., Lee J.C., Harvey S.C., and Gutell R.R. (2001).
AA.AG@Helix.Ends: A:A and A:G Base-pairs at the Ends of 16 S and 23 S rRNA Helices.
Journal of Molecular Biology 310:735-753.

Manuscript Data Tables and Figures:

Secondary structure diagrams use Escherichia coli as a reference sequence.
File formats for secondary structure diagrams: PS = PostScript; PDF = Adobe Portable Document Format.
Figure 1: Secondary Structure Diagrams a) 16S rRNA: PS | PDF
b) 23S rRNA, 5' half: PS | PDF
c) 23S rRNA, 3' half: PS | PDF
Figure 2: JPEG ( large | small ) | PDF | Legend.

Online Data Tables and Figures:

Secondary structure diagrams use Escherichia coli as a reference sequence.
File formats for secondary structure diagrams: PS = PostScript; PDF = Adobe Portable Document Format.
Online Table 4: AA.AG@helix.ends Base Pair Frequency Tables: a) 16S rRNA
b) 23S rRNA
Online Table 5: PDB Structures Included in Manuscript Table 2 Online Table 5.
Online Table 6: PDB Structures Included in the Coaxial Stacking Analysis Online Table 6.
Online Table 7: tRNA Comparative Model Base-Pair Frequency Data: Online Table 7
Online Table 8: A-Site Data: Online Table 8
Online Figure 3: Chemical Drawings of A:G and A:A Base-Pair Conformations: JPEG ( large | small ) | PDF | PS | Legend.
Online Figure 4: Base-Pair Stacking JPEG (w/legend) | PDF (no legend) | Legend.
Online Figure 5: "Other Motifs" Secondary Structure Diagrams: a) 16S rRNA: PS | PDF
b) 23S rRNA, 5' half: PS | PDF
c) 23S rRNA, 3' half: PS | PDF
Online Discussion: Full Probability Calculation.

Alignments Used in the AA.AG@helix.ends Analysis:

File formats for alignments: AE2 = AE2 (AKA "Macke Format"); GB = GenBank Format. The number of non-publicly-available sequences that are excluded from these alignments but used in the analyses is shown in bold/square brackets. Approximate file size is shown next (in parentheses).
Phylogenetic Group / Cell Location 16S rRNA 23S rRNA
Bacteria AE2 - GB - [0] (40 MB) AE2 - GB - [14] (2.5 MB)
Archaea AE2 - GB - [0] (1 MB) AE2 - GB - [1] (270 KB)
Eucarya (Nuclear) AE2 - GB - [172] (9 MB) AE2 - GB - [26] (4 MB)
Eucarya (Chloroplast) AE2 - GB - [8] (1 MB) AE2 - GB - [55] (500 KB)
Eucarya (Mitochondria) AE2 - GB - [84] (9 MB) AE2 - GB - [19] (6 MB)