Chemistry and structure of modified uridine dinucleosides are determined by thiolation

Article abstract of DOI:10.1021/ja00047a005

The structural determination of modified nucleosides is important for understanding the chemistry, structure, and functional changes that they introduce to the nucleic acids in which they occur. Thiolation of transfer RNA wobble position uridine produces an energetically stabilized conformation of the nucleoside in solution at ambient temperature that is independent of the nature of the 5-position substituent and is of biological significance to tRNA selection of only those codons ending in adenosine (Sierzputowska-Gracz, H.; Sochacka, E.; Malkiewicz, A.; Kuo, K.; Gehrke, C.; Agris, P. F. J. Am. Chem. Soc. 1987, 109, 7171-7177. Agris, P. F.; Sierzputowska-Gracz, H.; Smith, W.; Malkiewicz, A.; Sochacka, E.; Nawrot, B. J. Am. Chem. Soc., in press). Dinucleoside monophosphates have been synthesized as models for investigating the conformations and structures of wobble position uridine-34 that is thiolated and differently modified at position-5 and that is either 3′-adjacent to the invariant uridine-33 in tRNA or 5′-adjacent to the second anticodon position uridine-35. The structures and conformations of 11 dinucleoside monophosphates were analyzed by ¹H, ¹³C, and ³¹P magnetic resonance (NMR) spectroscopy. Within the dinucleosides, the individual modified uridine structures and conformations were very similar to those of their respective mononucleosides. The 2-position thiolation, and not the 5-position modification, produced a significantly more stable, C(3′) endo, gauche⁺, anti conformer. However, within those dinucleosides in which the 2-thiouridine was 5′ to the unmodified uridine, the nucleic acid backbone torsion angles of the unmodified uridine 5′-phosphate were affected, as determined from the scalar coupling constants J_1H1H, J_1H31P, and J_13C31P. In contrast, uridines that were only 5-position modified did not affect the conformation of the 3′-adjacent unmodified uridine phosphate. The structural data obtained and the nucleoside conformations derived from the data support the "modified wobble hypothesis" (Agris, P. F. Biochimie 1992, 73, 1345-1349); i.e., the tRNA wobble position-34 nucleoside is modified in such a way as to constrain not only its own conformation but also the structural conformation of the anticodon, thereby producing a specific codon selection during protein synthesis.