Unusual structures in single-stranded ribonucleic acid: Proton nuclear magnetic resonance of AUCCA in deuterium oxide

Abstract

Conformational features of the oligoribonucleic acid (oligo-RNA) A1-U2-C3-C4-A5 are explored by proton nuclear magnetic resonance (NMR). The sequence is a molecular cognate of a portion of the T psi C loop and stem regions of yeast tRNAPhe. The molecule forms at least two classes of flexible yet ordered structures. Class I states are similar in spectral properties to the component oligomers, AU, AUC, and AUCC, and are likely to be standard right-helical structures. Class II states are characterized by a 2'-endo pucker at A1 and unusually large shielding of several C3 and U2 protons. Most of these features are consistent with identifying the class II solution structures with the "arch" conformation for the T psi C region determined by X-ray crystallography of yeast tRNAPhe.