The structure of tRNA in solution was explored by NMR spectroscopy to evaluate the effect of divalent cations, especially zinc, which has a profound effect on the chromatographic behavior of tRNAs in certain systems. The divalent ions Mg2+and Zn2+have specific effects on the imino proton region of the1H NMR spectrum of valine transfer RNA (tRNAVaI) of Escherichia coli and of phenylalanine transfer RNA (tRNAPhe) of yeast. The dependence of the imino proton spectra of the two tRNAs was examined as a function of Zn2+concentration. In both tRNAs the tertiary base pair (G-15).(C-48) was markedly affected by Zn2+(shifted downfield possibly by as much as 0.4 ppm); this is the terminal base pair in the augmented dihydrouridine helix (D-helix). Base pair (U-8).(A-14) in yeast tRNAPheor (s4U-8).(A-14) in tRNA1val, which are stacked on (G-15)-(C-48), was not affected by Zn2+, except when 1–2 Mg2+ions per tRNA were also present. Another imino proton that may be affected by Zn2+in both tRNAs is that of the tertiary base pair (G-19)-(C-46). The assignment of this resonance in yeast tRNAPheis tentative since it is located in the region of highly overlapping resonances between 12.6 and 12.3 ppm. This base pair helps to anchor the D-loop to the TΨC loop. Surprisingly, the imino proton of (G-18)-(Ψ-55) is not similarly affected by Zn2+, indicating that the effect of Zn2+is not on G-57 which is the central non-hydrogen-bonded base in the “guanosine sandwich” created by the stacking of G-19, G-57, and G-20. The solution structure of tRNAPheshows marked correlation to the crystal structure in terms of Zn2+interactions [Rubin, J. R., Wang, J., & Sundaralingam, M. (1983) Biochim. Biophys. Acta 756, 111–118].
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