Chemistry and structure of modified uridine dinucleosides are determined by thiolation

Abstract

7989 essential imidazolium to the unstable tetrahedral intermediates produced from amides where the N is an aliphatic one, the proton transfer is thermodynamically favorable, and in the case of anilides is either thermodynamically neutral or only slightly uphill.The second and less obvious feature of imidazole which makes it unusually suitable for general-acid or -base catalysis relative to an aliphatic amine (ammonium) has to do with the molecular shape. Because the proton transfer in imidazole occurs at the sp2 N, and in the plane of the ring, there is minimal steric hindrance in transfer to sterically congested tetrahedral intermediates.Acknowledgment. The authors gratefully acknowledge the financial support of the University of Alberta and the Natural Sciences and Engineering Research Council of Canada. In addition, J.K. acknowledges NSERC for a Post Graduate Scholarship.Supplementary Material Available: Tables of observed rate constants vs pH for attack of thiols lb, 5 a 4 , and 6a-d on amide 4 and characterization of thiol ester 8b and amide 9a (7 pages). Ordering information is given on any current masthead page. Abstract: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 undine 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 IH, I3C, and 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 JiHiH, JiH"p, and J13~31p. In contrast, uridines that were only 5-position modified did not affect the conformation of the 3'-adjacent unmodified uridine phosphate. The stru...

Reparameterizations of theχTorsion and Lennard-JonesσParameters Improve the Conformational Characteristics of Modified Uridines

“… Calculated from coupling constants ( J 4′5′ / J 4′5″ ) by the formula % γ = [((13.75 − J 4′5′ − J 4′5″ )/10.05) × 100] from the NMR experimental data …”

Free energy calculation of modified base-pair formation in explicit solvent: A predictive model

“…Our results demonstrate that this could be achieved selectivity through thermodynamic stabilization of the wobble base pair by modified bases. The modified nucleotide and its base-pairing affect the stability of the adjacent nucleotide conformation and its base pairs (Smith et al 1992;Testa et al 1999); and, thereby, it affects the overall stability of an entire RNA, or the mini-helix of the anti-codon-codon interaction (Smith et al 1992;Kumar and Davis 1997;Testa et al 1999;Sipa et al 2007). …”

Human tRNALys3UUU Is Pre-Structured by Natural Modifications for Cognate and Wobble Codon Binding through Keto–Enol Tautomerism

“…7,56 The s 2 , and not the 5-position modification, produces the significantly more stable, anti C3'-endo, g + conformation, and transfers a similar restraint to the 3'-neighbor. 57 In studies of ASLs, it has been demonstrated that mcm 5 U 34 has little measurable effect on structure, but that s 2 U 34 increases the amount of stacking between U 34 and U 35 . 41 This is evident when comparing the anticodon structure of the A-site hASL Lys3 UUU -mnm 5 U 34 ;t 6 A 37 with that of the hASL Lys3 UUU -mcm 5 s 2 U 34 ,ms 2 t 6 A 37 ψ 39 (Fig.…”