1H NMR of valine tRNA modified bases. Evidence for multiple conformations

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Abstract
Methyl and methylene protons of dihydrouridine 17 (hU), 6-methyladenosine 37 (m6A), 7-methylguanosine 46 (m7G) and ribothymidine 54 (rT) give clearly resolved peaks (220 MHz) for tRNA1val (coil) solutions in D20, 0.25 m NaCl, at 27° C. Chemical shifts are generally consistent with a solution structure of tRNA1val similar to the crystal structure of tRNAphe (yeast). At least 3 separate transitions are observed as the temperature is raised. The earliest involves disruption of native tertiary structure and formation of intermediate structures in the m7G and rT regions. A second transition results in a change in structure of the anticodon loop, containing m6A. The final step involves unfolding of the m7G and rT intermediates and melting of the TΨC helix. Low salt concentrations produce multiple, partially denatured conformations, rather than a unique form, for tRNA1val. Native structure is almost completely reformed by addition of Na+ but Mg2+ is required for correct conformation in the vicinity of m7G.