Comparison of isotope labeling patterns of purines in three specific transfer RNAs.

Purine C-8 tritium-labeling rates have been measured at specific sites in Escherichia coli tRNAIle and tRNA2Tyr. The results are compared with those obtained for yeast tRNAPhe (preceding paper(Gamble et al., 1976)). The tRNAIle and tRNAPhe fall into the same general class of tRNA structures, while tRNA2Tyr is in a differint class; in particular, the latter is characterized by a large extra loop. In each of the three tRNAs the 3'-terminal A has the same labeling rate and, on a relative basis, appears to be the most rapidly labeled site. Bases in cloverleaf helical sections have markedly retarded labeling rates that collectively fall within an approximately threefold range of time constants. At some of the common purines, believed to be essential for the construction of a general system of tertiary interactions, exchange rates for yeast tRNAPhe are significantly different than those for the two Escherichia coli tRNAs. these differences may arise from variations among the tRNAs in the relative stabilities of specific tertiary interactions, or from other factors as well. In the case of tRNA2Tyr, labeling rates for bases in the large variable region are sufficiently retarded to suggest some structural organization for this part of the molecule. In addition, since exchange rates are similar for some of the bases common to Escherichia coli tRNAIle and tRNA2Tyr, it is likely that the large variable loop of tRNA2Tyr does not interact with or perturb these common sites. Finally, for all three tRNAs, structure formation (e.g., base pairing, base stacking) invariably decreases the labeling rate, even though the variety of base environments in the three-dimensional structures of these tRNAs might be expected to affect the acidity of C-8 and other chemical properties in diverse ways. Although these chemical effects no doubt bear influence, in these studies the dominant influence on exchange may be the effect of structure on the accessibility of solvent molecules, i.e. water.