Proton nuclear magnetic resonance study of the effect of pH on tRNA structure.

The low-field 220-MHz proton nuclear magnetic resonance (NMR) spectra of four tRNA molecules, Escherichia coli tRNA^Phe, tRNA₁^Val, and tRNA^fMet₁, and yeast tRNA^Phe, at neutral and mildly acidic pH are compared. We find a net increase in the number of resonances contributing to the -9.9-ppm peak (downfield from sodium 4,4-dimethyl-4-silapentanesulfonate) in three of these tRNAs at pH 6, while tRNA^fMet₁ does not clearly exhibit this behavior. The increase in intensity at this resonance position is half-completed at pH 6.2 in the case of yeast tRNA^Phe. An alteration at the 5′-phosphate terminus is not involved, since removal of the terminal phosphate does not affect the gain in intensity at -9.9 ppm. Based on a survey of the tertiary interactions in the four molecules, assuming that they possess tertiary structures like that of yeast tRNA^Phe at neutral pH, we tentatively attribute this altered resonance in E. coli and yeast tRNA^Phe to the protonation of the N₃ of the adenine residue at position 9 which results in the stabilization of the tertiary triple A₂₃·U₁₂·A₉. This interpretation is supported by model studies on the low-field proton NMR spectrum of A_N oligomers at acid pH, which reveal an exchanging proton resonance at -9.4 ppm if the chain length N ≥ 6.