Structure of ribosome-bound messenger RNA as revealed by enzymatic accessibility studies

Digestion with ribonuclease T2 has been used to study the size of poly(U) protected by ribosome binding. Several different preparations of ribosomes all appear to cover 49 nucleotides of message; however, there are two partially accessible internal nuclease cleavage sites, which yield, ultimately, fragments 20, 16 and 13 nucleotides in length. Curiously, the site between fragments of length 20 and 16 is accessible to RNase T2 but not to the several much smaller RNases. Arguments based on the quantitative pattern of cleavage and comparisons with previous studies lead to the conclusion that the 20-mer is the 5' fragment, while 13-mer (which is lost the moment it is cleaved from the 16-mer) is the 3' fragment. Both ribosome-bound tRNAs appear to contact only the 16-mer. The presence of the two internal cleavage sites fits nicely with recent electron microscopic data suggesting that mRNA forms a loop around the 30 S subunit.