Dynamic structure of transfer RNA in solution monitored by reaction with hydroxyl radicals

The dynamic structure of initiator and elongator tRNAs was analyzed using a very sensitive reaction with hydroxyl radicals. The main target for this reagent is the ribose moieties not buried (accessible) in the tertiary structure of the RNA molecule. At variable time, temperature and magnesium concentrations, some nucleoside residues of lupin initiator tRNA or yeast tRNA(Phe) become accessible or not depending on the actual tRNA conformation. The nucleotides in the thymidine stem of yeast tRNA(Phe) and amino acid stem in both tRNAs do not change their reactivity and conformation. Also the reactivities of the nucleosides of the anticodons are not changing. Our data clearly suggest that hydroxyl radicals can be very useful for the analysis of the tertiary structure of tRNA.