Effect of Zinc Ions on tRNA Structure: Imino Proton NMR Spectroscopy

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 (tRNA^VaI) of Escherichia coli and of phenylalanine transfer RNA (tRNA^Phe) 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 tRNA^Pheor (s⁴U-8).(A-14) in tRNA₁^val, 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 tRNA^Pheis 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 tRNA^Pheshows 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].