Phylogenetic evidence for tertiary interactions in 16S-like ribosomal RNA

Major efforts are underway to elucidate the spatial distribution of ribosomal RNAs (rRNAs) in the ribosome. An especially informative approach is the identification of likely base-base tertiary interactions within the RNA by phylogenetic comparison. Herein evidence is presented for three heretofore unrecognized candidate tertiary interactions, G506/C525, C779/G803 and A994/U1380 (1) in 16S-like rRNAs. This brings to eight the number of such interactions that are strongly supported by phylogenetic evidence. The three newly identified interactions further define the folding within domains II and III of 16S-like rRNA. No interactions have yet been found that would serve to orient the domains relative to one another.