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

Abstract

The low-field 220-MHz proton nuclear magnetic resonance (NMR) spectra of four tRNA molecules, Escherichia coli tRNAPhe, tRNA1Val, and tRNAfMet1, and yeast tRNAPhe, 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 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 four molecules, assuming that they possess tertiary structures like that of yeast tRNAPhe at neutral pH, we tentatively attribute this altered resonance in E. coli and yeast tRNAPhe 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 intepretation is supported by model studies on the lowfield proton NMR spectrum of AN oligomers at acid pH, which reveal an exchanging proton resonance at -9.4 ppm if the chain length N greater than or equal to 6.

Fluorine-19 nuclear magnetic resonance studies of the structure of 5-fluorouracil-substituted Escherichia coli transfer RNA

“…From the pH range of these changes and the behavior of the chemical shifts, it is probable they are not due to dissociation of the N(3)-H of incorporated FUra, but may be the result of conformation changes in the tRNA. Such changes under mildly acid conditions have been reported for several tRNA species (Bina-Stein & Crothers, 1974Crothers, , 1975, including E. coli tRNA}1*1 (Steinmetz-Kayne et al, 1977).…”

“…Peak C does exhibit an upfield shift as the pH decreases below 5.5 (Figure 3). This may be due to protonation of the FUra base but is more likely a result of the conformational change observed in E.coli tRNA^al at mildly acidic pH (Steinmetz-Kayne et al, 1977).…”

Ordered forms of dianionic guanosine 5'-monophosphate with sodium ion as the structure director. Proton and phosphorus-31 NMR studies of hydrogen bonding and comparisons of stacked tetramer and stacked dimer models

“…For instance, in certain oligonucleotides and in tRNA, the resonances of amino protons H bonded to a ring nitrogen occur in the 9-10-ppm region. [26][27][28][29] It should be noted at this point that since the ordered octamers give rise to three magnetically nonequivalent H(8) environments, we should expect three nonequivalent N(1)H and N(2)H environments for the ordered forms. Indeed, three N(2)H environments are observed (Hc, HD, HE) but there are only two distinguishable N(1)H environments (HA, HB).…”

Biological Magnetic Resonance

“…Some resonances in the region between 9 and 11 ppm have been tentatively assigned to G . U pairs, non-base-paired tertiary interactions and to tertiary base pairs which do not involve N-H-N hydrogen bonds (Reid and Robillard, 1975;Steinmetz-Kayne et at., 1977;Bolton et at., 1976;. The assignment of resonances in this region will extend the usefulness of PMR in the investigation of tRNA structure since the common 10.5 ppm resonance, for example, is very sensitive to the presence of manganese (Chao and Kearns, 1977) and a resonance at 9.9 ppm is sensitive to pH (Steinmetz-Kayne et at., 1977;Bolton, 1976).…”