Structure and function of 5S ribosomal ribonucleic acid from Torulopsis utilis. IV. Detection of exposed guanine residues by chemical modification with kethoxal.

The reaction of Torulopsis (Candida) utilis 5S ribosomal RNA with kethoxal (beta-ethoxy-alpha-ketobutyraldehyde) was studied in an attempt to identify the exposed guanine residues. At most 7-8 out of 32 guanine residues in T.utilis 5S RNA were kethoxalated after reaction at 37 degrees C for 4 h in the presence of magnesium ions. Localization of the kethoxalated guanine residues in T.utilis 5S RNA was achieved by sequence analyses of RNase T1 digests of the kethoxalated 5S RNA. These analyses showed that residues G37, G57, G91, and some of the three guanine residues G80, G82, and G85, are the most accessible sites. Residues G30, G41, and G49 also reacted with kethoxal though less strongly. These results are for the most part compatible with our secondary structure model for T.utilis 5S 5S RNA (Nishikawa and Takemura (1974) J. Biochem. 76, 935-947). However, partial formation of some hydrogen bonds within the loop region of the model seems to be necessary to explain the inaccessibility of residue G101 to kethoxal. The results are also discussed in comparison with those of similar studies on E.coli 5S RNA.