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

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Abstract
The low-field 220-MHz proton NMR spectra of 4 tRNA molecules, Escherichia coli tRNAPhe, tRNA1Val and tRNAfMet1, and yeast tRNAPhe, at neutral and mildly acidic pH are compared. A net increase is found in the number of resonances contributing to the -9.9-ppm peak (downfield from sodium 4,4-dimethyl-4-silapentanesulfonate) in 3 of these tRNA at pH 6, while tRNAfMet1 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 tRNAPhe. 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 4 molecules, assuming that they possess tertiary structures like that of yeast tRNAPhe at neutral pH, this altered resonance in E. coli and yeast tRNAPhe is tentatively attributed to the protonation of the N3 of the adenine residue at position 9 which results in the stabilization of the tertiary triple A23.cntdot.U12.cntdot.A9. This interpretation is supported by model studies on the low-field proton NMR spectrum of AN oligomers at acid pH, which reveal an exchanging proton resonance at -9.4 ppm if the chain length N .gtoreq. 6.