High resolution phosphorus NMR spectroscopy of transfer ribonucleic acids

The temperature dependence of the 31P NMR spectra of yeast phenylalanine tRNA, E. coli tyrosine, glutamate (2), and formylmethione tRNA, and bovine liver aspartate (2b) tRNA is presented. The major difference between the 31P NMR spectra of the different acceptor tRNAs is in the main cluster region between -0.5 and -0.3 ppm. This confirms earlier assignment of the main cluster region to the undistorted phosphate diesters in the hair-pin loops and helical stems. In addition the 31P NMR spectra for all tRNAs reveal approximately 16 non-helical diester signals spread over approximately 7 ppm besides the downfield terminal 3'-phosphate monoester. In the presence of 10 mM Mg++, most scattered and main cluster signals do not shift between 22 and 66 degrees C, thus supporting our earlier hypothesis that 31P chemical shifts are sensitive to phosphate ester torsional and bond angles. At greater than 70 degrees, all of the signals merge into a single random coil conformation signal. Measured spin-lattice and spin-spin relaxation times for tRNAPhe reveal another lower temperature transition associated with a conformational change of the anticodon loop besides the thermal denaturation process. A number of the scattered peaks are shifted (0.2--1.7 ppm) and broadened between 22 and 66 degrees C in the presence of Mg++ as a result of this conformational transition. The effects Mg++ and Mn++ ions on the 31P NMR spectra of tRNAPhe have been used to identify some of the scattered signals upfield and downfield from the main cluster signals. The 31P NMR spectrum of the dimer formed between yeast tRNAPhe and E. coli tRNA2Glu is reported. This dimer stimulates codon-anticodon interaction since the anticodon triplets of the two tRNAs are complementary. Evidence is presented that the anticodon-anticodon interaction alters the anticodon conformation and partially disrupts the tertiary structure of the tRNA.