Location of accessible bases in Escherichia coli formylmethionine transfer RNA as determined by chemical modification

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Abstract
Chemical modification of E. coli tRNAfMet with 1 M chloroacetaldehyde, pH 5.5-6.0 at 25.degree. C, resulted in alteration of 6 cytidine and 5 adenosine residues in the molecule. The modified cytidine residues are the same as those previously found to be reactive with NaHSO3 at pH 6.0. The accessible adenosine residues are A36 in the anticodon, A58 in the T.PSI.[pseudourine]C loop, and A73, A74 and A77 in the 3'' terminal sequence. No modification of adenosine residues in the dihydrouridine or variable loops or of adenosine residues on the 3'' side of the anticodon loop could be detected. Treatment of fMet-tRNAfMet with chloracetaldehyde gave the same pattern of modification as was observed with deacylated tRNAfMet. Chemical modification of E. coli tRNAfMet with NaHSO3, pH 7.0 at 25.degree. C, resulted in selective modification of exposed uridine residues in the tRNA. Only 3 sites were reactive: U18 in the dihydrouridine loop, U37 in the anticodon and U48 in the variable loop. The overall pattern of chemical modification of tRNAfMet is very similar to that found by others for yeast tRNAPhe, indicating that many of the tertiary interactions in the 2 tRNAs are the same. The adenosine residue at position 58 in the center of the T.PSI.C loop of the initiator tRNA shows unusual reactivity, being modified by chloroacetaldehyde at the same rate as the 3'' terminal adenosine residue. This result is in sharp contrast to the uniform resistance of nucleotides in the T.PSI.C loop of yeast tRNAPhe to chemical modification.

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