Chemical methods for the structural study of the ribosome: Judgment day

The data on RNA-RNA interactions between the components of the E. coli tran slation machinery obtained by X-ray crystallography and chemical methods ar e compared. The approaches to the study of RNA secondary and tertiary struc ture are assessed. The following conclusions are made: comparative sequence analysis and compensatory mutations approach both give reliable data on th e RNA secondary structure. The chemical modification technique provides goo d results. Local cleavage of internucleotide bonds by hydroxyl radicals is reliable in the frame of its 40 Angstrom resolution, in contrast to the app lication of copper-phenanthroline complex as a cleavage reagent, which is u nreliable. Direct UV irradiation and nitrogen mustard treatment are the bes t methods of crosslink generation. In vitro transcription is the only good method for the incorporation of nucleotide analogs in RNA. RNase H hydrolys is and/or nucleotide-specific RNases fingerprints must be applied for the c rosslink site determination in parallel with reverse transcription.