Abstract
Recent studies revealed that the 3′-terminal nucleotides in plant microRNAs were methylated on the ribose at the 2′ or 3′ hydroxyl groups. Here we examined the fragmentation of the electrospray-produced [M+H]+ and [M-H]− ions of 2′- and 3′-O-methylated ribonucleosides. It turned out that the predominant fragmentation pathway for the [M+H]+ ions of ribose-methylated nucleosides was the neutral loss of the methylated ribose, which made it impossible to distinguish 2′-O-methylation from 3′-O-methylation by positive-ion MS/MS. However, characteristic fragment ions, resulting from the cleavage through the ribose rings, were produced for the [M-H]− ions of each pair of ribose-methylated nucleosides. In this respect, the neutral loss of a 90-Da fragment (C3H6O3) was observed for 2′-O-methylated cytidine, guanosine and adenosine, but not for their 3′-O-methylated counterparts. On the other hand, the neutral loss of a 60-Da fragment (C2H4O2) was found for 3′-O-methyluridine, but not for 2′-O-methyluridine.
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References
Bartel, D. P. MicroRNAs Genomics, Biogenesis, Mechanism, and Function. Cell. 2004, 116, 281.
Limbach, P. A.; Crain, P. F.; McCloskey, J. A. Summary: The Modified Nucleosides of RNA. Nucleic Acids Res. 1994, 22, 2183–2196.
Rozenski, J.; Crain, P. F.; McCloskey, J. A. The RNA Modification Database: 1999 Update. Nucleic Acids Res. 1999, 27, 196–197.
Dunin-Horkawicz, S.; Czerwoniec, A.; Gajda, M. J.; Feder, M.; Grosjean, H.; Bujnicki, J. M. MODOMICS: A Database of RNA Modification Pathways. Nucleic Acids Res. 2006, 34, D145-D149.
Boutet, S. V. F.; Liu, J.; Beclin, C.; Fagard, M.; Gratias, A.; Morel, J.; Crete, P.; Chen, X.; Vaucheret, H. Arabidopsis HEN1: A Genetic Link Between Endogenous miRNA Controlling Development and siRNA Controlling Transgene Silencing and Virus Resistance. Curr. Biol. 2003, 13, 843–858.
Yu, B.; Yang, Z.; Li, J.; Minakhina, S.; Yang, M.; Padgett, R. W.; Steward, R.; Chen, X. Methylation as a Crucial Step in Plant microRNA Biogenesis. Science. 2005, 307, 932–935.
Li, J.; Yang, Z.; Yu, B.; Liu, J.; Chen, X. Methylation Protects miRNAs and siRNAs from a 3′-end Uridylation Activity in Arabidopsis. Curr. Biol. 2005, 15, 1501–1507.
Ebhardt, H. A.; Thi, E. P.; Wang, M.-B.; Unrau, P. J. Extensive 3′ Modification of Plant Small RNAs is Modulated by Helper Component-Proteinase Expression. Proc. Natl. Acad. Sci. U.S.A. 2005, 102, 13398–13403.
Kaufmann, G.; Kallenbach, N. R. Determination of Recognition Sites of T4 RNA Ligase on the 3′-OH and 5′-P Termini of Polyribonucleotide Chains. Nature. 1975, 254, 452.
Silber, R.; Malathi, V. G.; Hurwitz, J. Purification and Properties of Bacteriophage T4-Induced RNA Ligase. Proc. Natl. Acad. Sci. U.S.A. 1972, 69, 3009–3013.
Walker, G. C.; Uhlenbeck, O. C.; Bedows, E.; Gumport, R. I. T4-Induced RNA Ligase Joins Single-Stranded Oligoribonucleotides. Proc. Natl. Acad. Sci. U.S.A. 1975, 72, 122–126.
Howlett, H. A.; Johnson, M. W.; Trim, A. R.; Eagles, J.; Self, R. Mass Spectral Analysis of Modified Ribonucleosides Obtained by Degradation of 14 Alkali-Stable Dinucleotides Isolated from Yeast Ribonucleic acid. Anal. Biochem. 1971, 39, 429–440.
McCloskey, J. A. In Basic Principles in Nucleic Acid Chemistry, Vol. 1. Ts’o P.O.P. Ed., New York: Academic Press, 1974, pp 209–309.
Shaw, S. J.; Desiderio, D. M.; Tsuboyama, K.; McCloskey, J. M. Mass Spectrometry of Nucleic Acid Components. Analogs of Adenosine. J. Am. Chem. Soc. 1970, 92, 2510–2522.
Crow, F. W.; Tomer, K. B.; Gross, M. L.; McCloskey, J. A.; Bergstrom, D. E. Fast Atom Bombardment Combined with Tandem Mass Spectrometry for the Determination of Nucleosides. Anal. Biochem. 1984, 139, 243–262.
McCrery, D. A.; Gross, M. L. Laser Desorption/Fourier-Transform Mass Spectrometry for the Study of Nucleosides, Oligosaccharides, and Glycosides. Anal. Chim. Acta. 1985, 178, 91–103.
Nelson, C. C.; McCloskey, J. A. Collision-Induced Dissociation of Uracil and Its Derivatives. J. Am. Soc. Mass Spectrom. 1994, 5, 339–349.
Frelon, S.; Douki, T.; Ravanat, J.-L.; Pouget, J.-P.; Tornabene, C.; Cadet, J. High-Performance Liquid Chromatography-Tandem Mass Spectrometry Measurement of Radiation-Induced Base Damage to Isolated and Cellular DNA. Chem. Res. Toxicol. 2000, 13, 1002–1010.
Hua, Y.; Wainhaus, S. B.; Yang, Y.; Shen, L.; Xiong, Y.; Xu, X.; Zhang, F.; Bolton, J. L.; van Breemen, R. B. Comparison of Negative and Positive Ion Electrospray Tandem Mass Spectrometry for the Liquid Chromatography Tandem Mass Spectrometry Analysis of Oxidized Deoxynucleosides. J. Am. Soc. Mass Spectrom. 2001, 12, 80–87.
Wang, Y.; Vivekananda, S.; Zhang, K. ESI-MS/MS for the Differentiation of Diastereomeric Pyrimidine Glycols in Mononucleosides. Anal. Chem. 2002, 74, 4505–4512.
McCloskey, J. A. Structural Characterization of Natural Nucleosides by Mass Spectrometry. Acc. Chem. Res. 1991, 24, 81–88.
Smith, D. L.; Schram, K. H.; McCloskey, J. A. The Negative Ion Mass Spectra of Selected Nucleosides. Biomed. Mass Spectrom. 1983, 10, 269–275.
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Published online June 5, 2006
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Zhang, Q., Wang, Y. Differentiation of 2′-O- and 3′-O-methylated Ribonucleosides by tandem mass spectrometry. The official journal of The American Society for Mass Spectrometry 17, 1096–1099 (2006). https://doi.org/10.1016/j.jasms.2006.04.023
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DOI: https://doi.org/10.1016/j.jasms.2006.04.023