Interaction of the 530 ribosomal site with regions of mRNA

We evaluated the energetic stability of all possible 10-base fragments of the small subunit (SS) rRNA with a large ensemble of mRNAs. Results show that the 530 loop is the only conserved region that interacts favorably around the start codon as well as the elongation region of messengers. The interaction profile of the 530 loop around the stop codon showed that base pairing was energetically unfavorable in that region. With these results we constructed a simple scheme for the role of rRNA–mRNA interactions in the protein translation mechanism.