Complementary oligonucleotide binding to yeast tRNA Phe (HCl)

Investigation of the structure of yeast tRNAphe by nuclear magnetic resonance: paramagnetic rare earth ion probes of structure

The binding of paramagnetic rare earth ions to yeast tRNA(Phe) shifts some resonances in the low-field nuclear magnetic resonance spectrum that have been assigned to ring nitrogen protons of specific Watson-Crick base pairs. The changes in the nuclear magnetic resonance spectrum as the tRNA is titrated with Eu(3+) indicate that 4 (or 5) Eu(3+) ions are tightly bound, that the metal binding is in the fast exchange limit, and that the binding to different sites in the molecule is sequential rather than cooperative. The first metal bound simultaneously shifts resonances associated with the dihydrouridine and the -C-C-A stem. This permits us to conclude that the folding of the tRNA(Phe) in solution brings the phosphate backbone of the -C-C-A and the dihydrouridine stems into close proximity. A model of the three-dimensional structure of tRNA(Phe) incorporating this new information appears to be compatible with the results obtained from x-ray diffraction.

Effect of the removal of the Y base on the conformation of yeast tRNA

The effect of removing the Y base from the anticodon loop of yeast tRNA(Phe) has been examined by high-resolution proton nuclear magnetic resonance spectroscopy and optical melting. Analysis of the changes in the nuclear magnetic resonance spectra indicate that the removal of the Y base produces a small conformational change in the anticodon stem in which all the interbase separations are increased by approximately 0.2 A. The temperature dependence of the nuclear magnetic resonance spectra and the optical melting measurements indicate that the high temperature stability of tRNA(Phe) is decreased by removal of the Y base. With the exception of the anticodon stem, the secondary structure of the other helical stems of the molecule appear to be unaltered when the Y base is excised.