Sites of contact of mRNA with 16S rRNA and 23S rRNA in the Escherichia coli ribosome.

The locations of close encounter between ribosomal RNA (rRNA) and messenger RNA (mRNA) were determined by photochemical cross-linking experiments that employ an artificial mRNA, 51 nucleotides long, containing 14 U residues that were randomly substituted by 1-4 5-thiouridine (s 4 U) residues. The mRNA was bound to 70S ribosomes or 30S subunits and then was irradiated at 366 nm to activate cross-linking between the s 4 U residues and rNA. Cross-linking occurred to both 16S rRNA and 23S RNA. The rRNA was then analyzed by a series of reverse transcriptase experiments to determine the locations of cross-linking. Twelve sites in the 16S rRNA and two sites in the 23S rRNA have been detected