| Literature DB >> 31435890 |
C C He1, L A Hamlow1, Y Zhu1, Y-W Nei1, L Fan1, C P McNary2, P Maître3, V Steinmetz3, B Schindler4, I Compagnon4, P B Armentrout2, M T Rodgers5.
Abstract
The 2'-substituents distinguish DNA from RNA nucleosides. 2'-O-methylation occurs naturally in RNA and plays important roles in biological processes. Such 2'-modifications may alter the hydrogen-bonding interactions of the nucleoside and thus may affect the conformations of the nucleoside in an RNA chain. Structures of the protonated 2'-O-methylated pyrimidine nucleosides were examined by infrared multiple photon dissociation (IRMPD) action spectroscopy, assisted by electronic structure calculations. The glycosidic bond stabilities of the protonated 2'-O-methylated pyrimidine nucleosides, [Nuom+H]+, were also examined and compared to their DNA and RNA nucleoside analogues via energy-resolved collision-induced dissociation (ER-CID). The preferred sites of protonation of the 2'-O-methylated pyrimidine nucleosides parallel their canonical DNA and RNA nucleoside analogues, [dNuo+H]+ and [Nuo+H]+, yet their nucleobase orientation and sugar puckering differ. The glycosidic bond stabilities of the protonated pyrimidine nucleosides follow the order: [dNuo+H]+ < [Nuo+H]+ < [Nuom+H]+. The slightly altered structures help explain the stabilization induced by 2'-O-methylation of the pyrimidine nucleosides.Entities:
Keywords: 2′-O-methyl-5-methyluridine (Thdm); 2′-O-methylation; 2′-O-methylcytidine (Cydm); 2′-O-methyluridine (Urdm); 5-Methyluridine; Cytidine (Cyd); Cytosine (Cyt); Density functional theory (DFT); Electronic structure calculations; Electrospray ionization (ESI); Energy-resolved collision-induced dissociation (ER-CID); Fourier transform ion cyclotron resonance mass spectrometer (FT-ICR MS); Gas-phase conformation; Glycosidic bond stability; Hydrogen-bonding interactions; Hydrogen-stretching region; IR fingerprint region; IR spectrum; IRMPD spectrum; Infrared multiple photon dissociation (IRMPD) action spectroscopy; Nucleobase; Nucleobase orientation; Nucleoside; Nucleoside modification; Protonation; Pyrimidine nucleosides; Quadrupole ion trap mass spectrometer (QIT MS); Simulated annealing; Sugar puckering; Survival yield analysis; Tandem mass spectrometry; Thymidine (Thd); Thymine (Thy); Uracil (Ura); Uridine (Urd)
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Year: 2019 PMID： 31435890 DOI： 10.1007/s13361-019-02300-9
Source DB: PubMed Journal: J Am Soc Mass Spectrom ISSN： 1044-0305 Impact factor: 3.109