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Structural and Energetic Effects of O2′-Ribose Methylation of Protonated Pyrimidine Nucleosides

  • C. C. He
  • L. A. Hamlow
  • Y. Zhu
  • Y.-w. Nei
  • L. Fan
  • C. P. McNary
  • P. Maître
  • V. Steinmetz
  • B. Schindler
  • I. Compagnon
  • P. B. Armentrout
  • M. T. RodgersEmail author
Research Article

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.

Keywords

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 Infrared multiple photon dissociation (IRMPD) action spectroscopy IR fingerprint region IRMPD spectrum IR spectrum 5-Methyluridine Nucleobase Nucleobase orientation Nucleoside Nucleoside modification 2′-O-methylation 2′-O-methylcytidine (Cydm) 2′-O-methyl-5-methyluridine (Thdm) 2′-O-methyluridine (Urdm) 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) 

Notes

Acknowledgements

This work is financially supported by the National Science Foundation, under Grants OISE-0730072 and OISE-1357787 (for international travel expenses), DBI-0922819 (for the Bruker amaZon ETD QITMS employed in this work), and CHE-1709789 and CHE-1664618 (for other research costs). C.C.H., L.A.H., Y.Z., and Y.-w.N. are supported by the Wayne State University Thomas C. Rumble Graduate Fellowships and Summer Dissertation Fellowships. We thank Wayne State University C&IT for excellent computational resources and support. The skillful assistance of the CLIO staff is gratefully acknowledged.

Supplementary material

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© American Society for Mass Spectrometry 2019

Authors and Affiliations

  1. 1.Department of ChemistryWayne State UniversityDetroitUSA
  2. 2.Department of ChemistryUniversity of UtahSalt Lake CityUSA
  3. 3.Laboratoire de Chimie Physique (UMR8000), Université Paris-Sud, CNRSUniversité Paris SaclayOrsayFrance
  4. 4.Univ Lyon, Université Claude Bernard Lyon 1, CNRSInstitut Lumière MatièreVilleurbanneFrance

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