Identification of tertiary base pair resonances in the nuclear magnetic resonance spectra of transfer ribonucleic acid

Abstract

The low-field H-bond ring NH proton (NMR) spectra of several [Escherichia coli] tRNA related to yeast tRNAPhe were examined in detail. Several resonances are sensitive to Mg2+ and temperature, suggesting that they are derived from tertiary base pairs. These same resonances cannot be attributed to cloverleaf base pairs as shown by experimental assignment and ring current shift calculation of the secondary base pair resonances. The crystal structure of yeast tRNAPhe reveals at least 6 tertiary base pairs involving ring NH H- bonds, which are probably responsible for the extra resonances observed in the low-field NMR spectrum. In several tRNA with the same tertiary folding potential and dihydrouridine helix sequence as yeast tRNAPhe, the extra resonances from tertiary base pairs are observed at the same position in the spectrum.