Analysis of Mononucleotides by Tandem Mass Spectrometry: Investigation of Fragmentation Pathways for Phosphate- and Ribose-modified Nucleotide Analogues

Overview

Journal Sci Rep

Specialty Science

Date 2017 Aug 23

PMID 28827558

Citations 19

Authors

Dominika Strzelecka

Sebastian Chmielinski

Sylwia Bednarek

Jacek Jemielity

Joanna Kowalska

Affiliations

Soon will be listed here.

Abstract

Synthetic nucleotide and nucleic acid analogues are useful research tools and modern therapeutics. Hence, methods for the rapid and unambiguous identification of mononucleotides derived from organic syntheses or biological materials are of broad interest. Here, we analysed over 150 mononucleotides (mostly nucleoside 5'-mono-, 5'-di-, and 5'-triphosphates) and their structurally related nucleobase-, phosphate-, and ribose-modified analogues by electrospray tandem mass spectrometry (ESI/MS/MS), identifying characteristic fragmentation ions that may be helpful in structure determination. While positive-ion mode yielded fragments derived mainly from nucleobases, negative-ion mode provided insight into the structures of phosphoryl and phosphoribosyl moieties, enabling the determination of structural features such as the number of phosphate groups and the presence of ribose or phosphate substitutions. Based on these data, we proposed fragmentation pathways that were confirmed by experiments with [O]-isotopologues. We demonstrated the utility of ESI(-)/MS/MS in the analysis of structurally related compounds by analysing isomeric and isobaric nucleotides and applying ESI(-)/MS/MS to rapid identification of nucleotide synthesis products. We formulated general rules regarding nucleotide structure-fragmentation pattern relationships and indicating characteristic fragmentation ions for the interpretation of ESI(-)/MS/MS spectra of nucleotides and their analogues. The ESI(-)/MS/MS spectra of all nucleotides are available in an on-line database, msTide, at www.msTide-db.com.

Citing Articles

Isolation and Identification of Novel Taste-Modulating -Guanosine 5'-Monophosphate Derivatives Generated by Maillard-Type Reactions.

Hartl D, Frank O, Hanel V, Heigl V, Dawid C, Hofmann T J Agric Food Chem. 2024; 72(25):14284-14293.

PMID: 38869215 PMC: 11212044. DOI: 10.1021/acs.jafc.4c03485.

Mixed-phase weak anion-exchange/reversed-phase LC-MS/MS for analysis of nucleotide sugars in human fibroblasts.

Rahm M, Kwast H, Wessels H, Noga M, Lefeber D Anal Bioanal Chem. 2024; 416(15):3595-3604.

PMID: 38676823 PMC: 11156716. DOI: 10.1007/s00216-024-05313-w.

Dual function of LapB (YciM) in regulating lipopolysaccharide synthesis.

Shu S, Tsutsui Y, Nathawat R, Mi W Proc Natl Acad Sci U S A. 2024; 121(17):e2321510121.

PMID: 38635633 PMC: 11046580. DOI: 10.1073/pnas.2321510121.

Targeted delivery of immune-stimulating bispecific RNA, inducing apoptosis and anti-tumor immunity in cancer cells.

Rady T, Erb S, Deddouche-Grass S, Morales R, Chaubet G, Cianferani S iScience. 2024; 27(3):109068.

PMID: 38380254 PMC: 10877685. DOI: 10.1016/j.isci.2024.109068.

Quantification of mRNA in Lipid Nanoparticles Using Mass Spectrometry.

Lowenthal M, Antonishek A, Phinney K Anal Chem. 2024; 96(3):1214-1222.

PMID: 38189247 PMC: 10809213. DOI: 10.1021/acs.analchem.3c04406.

References

Pabst M, Grass J, Fischl R, Leonard R, Jin C, Hinterkorner G . Nucleotide and nucleotide sugar analysis by liquid chromatography-electrospray ionization-mass spectrometry on surface-conditioned porous graphitic carbon. Anal Chem. 2010; 82(23):9782-8. PMC: 2995335. DOI: 10.1021/ac101975k. View

Veltkamp S, Hillebrand M, Rosing H, Jansen R, Wickremsinhe E, Perkins E . Quantitative analysis of gemcitabine triphosphate in human peripheral blood mononuclear cells using weak anion-exchange liquid chromatography coupled with tandem mass spectrometry. J Mass Spectrom. 2006; 41(12):1633-42. DOI: 10.1002/jms.1133. View

Tuytten R, Lemiere F, van Dongen W, Esmans E, Witters E, Herrebout W . Intriguing mass spectrometric behavior of guanosine under low energy collision-induced dissociation: H2O adduct formation and gas-phase reactions in the collision cell. J Am Soc Mass Spectrom. 2005; 16(8):1291-304. DOI: 10.1016/j.jasms.2005.03.026. View

Banoub J, Newton R, Esmans E, Ewing D, Mackenzie G . Recent developments in mass spectrometry for the characterization of nucleosides, nucleotides, oligonucleotides, and nucleic acids. Chem Rev. 2005; 105(5):1869-915. DOI: 10.1021/cr030040w. View

Zeng H, Qi C, Liu T, Xiao H, Cheng Q, Jiang H . Formation and Determination of Endogenous Methylated Nucleotides in Mammals by Chemical Labeling Coupled with Mass Spectrometry Analysis. Anal Chem. 2017; 89(7):4153-4160. DOI: 10.1021/acs.analchem.7b00052. View

Dudley E, Bond L . Mass spectrometry analysis of nucleosides and nucleotides. Mass Spectrom Rev. 2013; 33(4):302-31. DOI: 10.1002/mas.21388. View

Kammerer B, Frickenschmidt A, Muller C, Laufer S, Gleiter C, Liebich H . Mass spectrometric identification of modified urinary nucleosides used as potential biomedical markers by LC-ITMS coupling. Anal Bioanal Chem. 2005; 382(4):1017-26. DOI: 10.1007/s00216-005-3232-2. View

Amir A, Shmuel E, Zagalsky R, Sayer A, Nadel Y, Fischer B . Nucleoside-5'-phosphorothioate analogues are biocompatible antioxidants dissolving efficiently amyloid beta-metal ion aggregates. Dalton Trans. 2012; 41(28):8539-49. DOI: 10.1039/c2dt30631j. View

Kowalska J, Lewdorowicz M, Zuberek J, Grudzien-Nogalska E, Bojarska E, Stepinski J . Synthesis and characterization of mRNA cap analogs containing phosphorothioate substitutions that bind tightly to eIF4E and are resistant to the decapping pyrophosphatase DcpS. RNA. 2008; 14(6):1119-31. PMC: 2390807. DOI: 10.1261/rna.990208. View

10.

Grigorenko B, Rogov A, Nemukhin A . Mechanism of triphosphate hydrolysis in aqueous solution: QM/MM simulations in water clusters. J Phys Chem B. 2006; 110(9):4407-12. DOI: 10.1021/jp056395w. View

11.

Hofmann U, Heinkele G, Angelberger S, Schaeffeler E, Lichtenberger C, Jaeger S . Simultaneous quantification of eleven thiopurine nucleotides by liquid chromatography-tandem mass spectrometry. Anal Chem. 2012; 84(3):1294-301. DOI: 10.1021/ac2031699. View

12.

Jemielity J, Fowler T, Zuberek J, Stepinski J, Lewdorowicz M, Niedzwiecka A . Novel "anti-reverse" cap analogs with superior translational properties. RNA. 2003; 9(9):1108-22. PMC: 1370475. DOI: 10.1261/rna.5430403. View

13.

Yoshikawa M, Kato T, Takenishi T . A novel method for phosphorylation of nucleosides to 5'-nucleotides. Tetrahedron Lett. 1967; 50:5065-8. DOI: 10.1016/s0040-4039(01)89915-9. View

14.

Ghosh B, Benyumov A, Ghosh P, Jia Y, Avdulov S, Dahlberg P . Nontoxic chemical interdiction of the epithelial-to-mesenchymal transition by targeting cap-dependent translation. ACS Chem Biol. 2009; 4(5):367-77. PMC: 2796976. DOI: 10.1021/cb9000475. View

15.

Baranowski M, Nowicka A, Rydzik A, Warminski M, Kasprzyk R, Wojtczak B . Synthesis of fluorophosphate nucleotide analogues and their characterization as tools for ¹⁹F NMR studies. J Org Chem. 2015; 80(8):3982-97. DOI: 10.1021/acs.joc.5b00337. View

16.

Kim J, Park S, Tretyakova N, Wagner C . A method for quantitating the intracellular metabolism of AZT amino acid phosphoramidate pronucleotides by capillary high-performance liquid chromatography-electrospray ionization mass spectrometry. Mol Pharm. 2005; 2(3):233-41. DOI: 10.1021/mp0500162. View

17.

Frith J, Monkkonen J, Blackburn G, Russell R, Rogers M . Clodronate and liposome-encapsulated clodronate are metabolized to a toxic ATP analog, adenosine 5'-(beta, gamma-dichloromethylene) triphosphate, by mammalian cells in vitro. J Bone Miner Res. 1997; 12(9):1358-67. DOI: 10.1359/jbmr.1997.12.9.1358. View

18.

Khvorova A, Watts J . The chemical evolution of oligonucleotide therapies of clinical utility. Nat Biotechnol. 2017; 35(3):238-248. PMC: 5517098. DOI: 10.1038/nbt.3765. View

19.

Kirschberg T, Mish M, Zhang L, Squires N, Wang K, Cho A . Synthesis and characterization of 1'-C-cyano-2'-fluoro-2'-C-methyl pyrimidine nucleosides as HCV polymerase inhibitors. Bioorg Med Chem Lett. 2015; 25(5):1040-3. DOI: 10.1016/j.bmcl.2015.01.021. View

20.

Lin L, Caton-Williams J, Kaur M, Patino A, Sheng J, Punetha J . Facile synthesis of nucleoside 5'-(α-P-seleno)-triphosphates and phosphoroselenoate RNA transcription. RNA. 2011; 17(10):1932-8. PMC: 3185924. DOI: 10.1261/rna.2719311. View