title: Conformational rigidity of specific pyrimidine residues in tRNA arises from posttranscriptional modifications that enhance steric interaction between the base and the 2'-hydroxyl group.
abstract: In order to elucidate roles of the 2'-O-methylation of pyrimidine nucleotide residues of tRNAs, conformations of 2'-O-methyluridylyl(3'----5')uridine (UmpU), 2'-O-methyluridine 3'-monophosphate (Ump), and 2'-O-methyluridine (Um) in 2H2O solution were analyzed by one- and two-dimensional proton NMR spectroscopy and compared with those of related nucleotides and nucleoside. As for UpU and UmpU, the 2'-O-methylation was found to stabilize the C3'-endo form of the 3'-nucleotidyl unit (Up-/Ump-moiety). This stabilization of the C3'-endo form is primarily due to an intraresidue effect, since the conformation of the 5'-nucleotidyl unit (-pU moiety) was only slightly affected by the 2'-O-methylation of the 3'-nucleotide unit. In fact even for Up and Ump, the 2'-O-methylation significantly stabilizes the C3'-endo form by 0.8 kcal/.mol-1. By contrast, for nucleosides (U and Um), the C3'-endo form is slightly stabilized by 0.1 kcal/.mol-1. Accordingly, the stabilization of the C3'-endo form by the 2'-O-methylation is primarily due to the steric repulsion among the 2-carbonyl group, the 2'-O-methyl group and the 3'-phosphate group in the C2'-endo form. For some tRNA species, 2-thiolation of pyrimidine residues is found in positions where the 2'-O-methylation is found for other tRNA species.(ABSTRACT TRUNCATED AT 250 WORDS)
authors.affiliation: Department of Biophysics and Biochemistry, Faculty of Science, University of Tokyo, Japan.
authors.forename: G
authors.initials: G
authors.lastname: Kawai
authors.forename: Y
authors.initials: Y
authors.lastname: Yamamoto
authors.forename: T
authors.initials: T
authors.lastname: Kamimura
authors.forename: T
authors.initials: T
authors.lastname: Masegi
authors.forename: M
authors.initials: M
authors.lastname: Sekine
authors.forename: T
authors.initials: T
authors.lastname: Hata
authors.forename: T
authors.initials: T
authors.lastname: Iimori
authors.forename: T
authors.initials: T
authors.lastname: Watanabe
authors.forename: T
authors.initials: T
authors.lastname: Miyazawa
authors.forename: S
authors.initials: S
authors.lastname: Yokoyama
mesh_terms: D015226:Dinucleoside Phosphates / Q000737:chemistry; D006878:Hydroxides / Q000737:chemistry*; D009682:Magnetic Resonance Spectroscopy; D008745:Methylation; D009690:Nucleic Acid Conformation; D011522:Protons; D011742:Pyrimidine Nucleotides / Q000737:chemistry*; D012323:RNA Processing, Post-Transcriptional; D012343:RNA, Transfer / Q000737:chemistry*; D013237:Stereoisomerism; D013816:Thermodynamics
chemical_list: D015226:Dinucleoside Phosphates; D006878:Hydroxides; D011522:Protons; D011742:Pyrimidine Nucleotides; D012343:RNA, Transfer