Oligonucleotide binding to the native and denatured conformers of yeast transfer RNA₃^Leu

The equilibrium binding patterns of complementary oligonucleotides to the native and denatured conformers of yeast transfer RNA₃^Leu have been determined. The pattern of binding to the native conformer follows that observed previously with other tRNAs. The results indicate that the anticodon loop and 3′ terminus are free in solution, and that all stems of the cloverleaf appear intact, although the dihydrouracil and "extra arm" stems are sufficiently weak to be subject to competitive binding by the probe oligomers. The T ΨC loop is also inaccessible to oligomer binding, while the dihydrouracil loop shows a low level of binding suggestive of oligomer competition with existing RNA structure. By contrast, in the denatured conformer the dihydrouracil loop and stem show strong oligomer binding characteristics of random RNA segments, whereas the anticodon loop no longer binds complementary oligomers. Binding to other regions remains unchanged, suggesting that the three major cloverleaf stems are intact. These observations are used as a basis for consideration of models for the two conformers.