DNA hybridization electron microscopy: ribosomal RNA nucleotides 1392-1407 are exposed in the cleft of the small subunit.

The ribosomal sequence corresponding to Escherichia coli 16S rRNA nucleotides 1392-1407 (the "1400 region") is phylogenetically conserved and is in a functionally important region of the subunit. Using the technique of DNA hybridization electron microscopy, we have mapped this sequence on the surface of the small ribosomal subunit. In this procedure a synthetic oligodeoxynucleotide probe, complementary to a specific rRNA sequence and carrying an attached marker molecule, is hybridized to ribosomal subunits in order to determine the dimensional site of attachment. In the E. coli ribosome, the 1400 region is located at the level of the neck, near the cleft and most likely on the head of the small subunit. The related sequence in yeast 18S rRNA, nucleotides 1618-1633, is located in the topological equivalent of the E. coli site. The location of this region, which has been crosslinked to the anticodon of a peptidyl-site-bound tRNA, indicates that this part of the cleft of the small subunit has a similar three-dimensional organization in phylogenetically diverse organisms and suggests that it is the site of the codon-anticodon interaction.