Kinetic Study of the Three Conformational Transitions of Alanine Specific Transfer RNA from Yeast

The conformational transitions of tRNAAla (yeast) in a solution of 0.01 M sodium-cacodylate and 0.1 M NaCl have been investigated kinetically by temperature-jump techniques specially adapted for temperatures up to 85°. Throughout the investigated range (15–85°) a fast relaxation time (γ > 1 μsec) was observed and assigned to single strand unstacking. In transitions 1 and 3 of tRNAAla (yeast) a single additional slower first order relaxational effect in the 100 μsec range appeared. In each case this effect can be readily interpreted as a double helix-coil transition according to an “all-or-none” model involving the rate-determining formation of a nucleus of 2 to 3 base pairs. In peak 2 of the melting of tRNAAla (yeast) there were found two strongly temperature dependent relaxation times in addition to that of single strand unstacking transitions. The kinetic results for peak 2 can be explained by a reaction scheme involving two coupled “all-or-none” helix-coil transitions which interfere only slightly: it is considered that in this mechanism two branches of the clover leaf melt and that the process of nucleation is similar to those observed in peaks 1 and 3.