Impact of the 2′- and 3′-Sugar Hydroxyl Moieties on Gas-Phase Nucleoside Structure

  • L. A. Hamlow
  • Zachary J. Devereaux
  • H. A. Roy
  • N. A. Cunningham
  • G. Berden
  • J. Oomens
  • M. T. RodgersEmail author
Research Article


Modified nucleosides have been an important target for pharmaceutical development for the treatment of cancer, herpes simplex virus, and the human immunodeficiency virus (HIV). Amongst these nucleoside analogues, those based on 2′,3′-dideoxyribose sugars are quite common, particularly in anti-HIV applications. The gas-phase structures of several protonated 2′,3′-dideoxyribose nucleosides are examined in this work and compared with those of the analogous protonated DNA, RNA, and arabinose nucleosides to elucidate the influence of the 2′- and combined 2′,3′-hydroxyl groups on intrinsic structure. Infrared multiple photon dissociation (IRMPD) action spectra are collected for the protonated 2′,3′-dideoxy forms of adenosine, guanosine, cytidine, thymidine and uridine, [ddAdo+H]+, [ddGuo+H]+, [ddCyd+H]+, [ddThd+H]+, and [ddUrd+H]+, in the IR fingerprint and hydrogen-stretching regions. Molecular mechanics conformational searching followed by electronic structure calculations generates low-energy conformers of the protonated 2′,3′-dideoxynucleosides and corresponding predicted linear IR spectra to facilitate interpretation of the measured IRMPD action spectra. These experimental IRMPD spectra and theoretical calculations indicate that the absence of the 2′- and 3′-hydroxyls largely preserves the protonation preferences of the canonical forms. The spectra and calculated structures indicate a slight preference for C3′-endo sugar puckering. The presence of the 3′- and further 2′-hydroxyl increases the available intramolecular hydrogen-bonding opportunities and shifts the sugar puckering modes for all nucleosides but the guanosine analogues to a slight preference for C2′-endo over C3′-endo.

Graphical Abstract


2′,3′-Dideoxyadenosine 2′,3′-Dideoxyguanosine 2′,3′-Dideoxycytidine 2′,3′-Dideoxythymidine 2′,3′-Dideoxyuridine Infrared multiple photon dissociation action spectroscopy IRMPD Computational chemistry 



This work was financially supported by the National Science Foundation, grant numbers OISE-1357887 (for the FEL IRMPD measurements and international travel), DBI-0922819 (for the Bruker amazon ETD quadrupole ion trap mass spectrometer), and CHE-01709789 (for other research costs). The authors gratefully acknowledge the financial support of the FELIX facility by the Nederlandse Organisatie voor Wetenschappelijk Onderzoek (NWO). L.A.H and Z.J.D. gratefully acknowledge support from Wayne State University Thomas C. Rumble Graduate Fellowships and Z.J.D. also acknowledges support from the Joseph Jasper Scholarship for Graduate Students in Chemistry. Computational resources for this work were provided by Wayne State University C&IT. The assistance of the skilled FELIX staff is immensely appreciated.

Supplementary material

13361_2019_2155_MOESM1_ESM.pdf (15.8 mb)
ESM 1 (PDF 16208 kb)


  1. 1.
    Dickerson, R.E., Drew, H.R., Conner, B.N., Wing, R.M., Fratini, A.V., Kopka, M.L.: The anatomy of A-DNA, B-DNA, and Z-DNA. Science. 216, 475–485 (1982)CrossRefGoogle Scholar
  2. 2.
    Murray, L.J.W., Arendall, W.B., Richardson, D.C., Richardson, J.S.: RNA backbone is rotameric. P Natl Acad Sci USA. 100, 13904–13909 (2003)CrossRefGoogle Scholar
  3. 3.
    Levitt, M., Warshel, A.: Extreme conformational flexibility of Furanose ring in DNA and RNA. J. Am. Chem. Soc. 100, 2607–2613 (1978)CrossRefGoogle Scholar
  4. 4.
    Altona, C., Sundaralingam, M.: Conformational-analysis of sugar ring in nucleosides and nucleotides: new description using concept of pseudorotation. J. Am. Chem. Soc. 94, 8205–8212 (1972)CrossRefGoogle Scholar
  5. 5.
    De Clercq, E.: Dancing with chemical formulae of antivirals: a personal account. Biochem. Pharmacol. 86, 711–725 (2013)CrossRefGoogle Scholar
  6. 6.
    Sommadossi, J.P.: Nucleoside analogs - similarities and differences. Clin. Infect. Dis. 16, S7–S15 (1993)CrossRefGoogle Scholar
  7. 7.
    Mathews, C.K.: DNA synthesis as a therapeutic target: the first 65 years. FASEB J. 26, 2231–2237 (2012)CrossRefGoogle Scholar
  8. 8.
    Mackey, J.R., Baldwin, S.A., Young, J.D., Cass, C.E.: Nucleoside transport and its significance for anticancer drug resistance. Drug Resist. Updat. 1, 310–324 (1998)CrossRefGoogle Scholar
  9. 9.
    Perry, C.M., Noble, S.: Didanosine - an updated review of its use in HIV infection. Drugs. 58, 1099–1135 (1999)CrossRefGoogle Scholar
  10. 10.
    Gray, J.H., Owen, R.P., Giacomini, K.M.: The concentrative nucleoside transporter family, SLC28. Pflugers Arch. - Eur. J. Physiol. 447, 728–734 (2004)CrossRefGoogle Scholar
  11. 11.
    Marquez, V.E., Ezzitouni, A., Russ, P., Siddiqui, M.A., Ford, H., Feldman, R.J., Mitsuya, H., George, C., Barchi, J.J.: HIV-1 reverse transcriptase can discriminate between two conformationally locked carbocyclic AZT triphosphate analogues. J. Am. Chem. Soc. 120, 2780–2789 (1998)CrossRefGoogle Scholar
  12. 12.
    Pastor-Anglada, M., Felipe, A., Casado, F.J.: Transport and mode of action of nucleoside derivatives used in chemical and antiviral therapies. Trends Pharmacol. Sci. 19, 424–430 (1998)CrossRefGoogle Scholar
  13. 13.
    De Clercq, E., Li, G.D.: Approved antiviral drugs over the past 50 years. Clin. Microbiol. Rev. 29, 695–747 (2016)CrossRefGoogle Scholar
  14. 14.
    Cullis, P.A., Cushing, R.: Vidarabine encephalopathy. J Neurol Neurosur Ps. 47, 1351–1354 (1984)CrossRefGoogle Scholar
  15. 15.
    Absalon, M.J., Smith, F.O.: Treatment strategies for pediatric acute myeloid leukemia. Expert. Opin. Pharmacother. 10, 57–79 (2009)CrossRefGoogle Scholar
  16. 16.
    Veal, G.J., Barry, M.G., Back, D.J.: Zalcitabine (ddC) phosphorylation and drug-interactions. Antivir. Chem. Chemother. 6, 379–384 (1995)CrossRefGoogle Scholar
  17. 17.
    Everaert, D.H., Peeters, O.M., Deranter, C.J., Blaton, N.M., Vanaerschot, A., Herdewijn, P.: Conformational-analysis of substituent effects on the sugar puckering mode and the anti-HIV activity of 2′,3′-dideoxypyrimidine nucleosides. Antivir. Chem. Chemother. 4, 289–299 (1993)CrossRefGoogle Scholar
  18. 18.
    Nasr, M., Litterst, C., Mcgowan, J.: Computer-assisted structure-activity correlations of dideoxynucleoside analogs as potential anti-HIV drugs. Antivir. Res. 14, 125–148 (1990)CrossRefGoogle Scholar
  19. 19.
    Plavec, J., Koole, L.H., Chattopadhyaya, J.: Structural-analysis of 2′,3′-dideoxyinosine, 2′,3′-dideoxyadenosine, 2′,3′-dideoxyguanosine and 2′,3′-dideoxycytidine by 500-MHz H-1-NMR spectroscopy and ab-initio molecular-orbital calculations. J. Biochem. Biophys. Methods. 25, 253–272 (1992)CrossRefGoogle Scholar
  20. 20.
    Taylor, E.W., Van Roey, P., Schinazi, R.F., Chu, C.K.: A stereochemical rationale for the activity of anti-HIV nucleosides. Antivir. Chem. Chemother. 1, 163–173 (1990)CrossRefGoogle Scholar
  21. 21.
    Vanroey, P., Salerno, J.M., Chu, C.K., Schinazi, R.F.: Correlation between preferred sugar ring conformation and activity of nucleoside analogs against human immunodeficiency virus. P Natl Acad Sci USA. 86, 3929–3933 (1989)CrossRefGoogle Scholar
  22. 22.
    Wu, R.R., Yang, B., Berden, G., Oomens, J., Rodgers, M.T.: Gas-phase conformations and energetics of protonated 2′-deoxyguanosine and guanosine: IRMPD action spectroscopy and theoretical studies. J. Phys. Chem. B. 118, 14774–14784 (2014)CrossRefGoogle Scholar
  23. 23.
    Wu, R.R., Yang, B., Berden, G., Oomens, J., Rodgers, M.T.: Gas-phase conformations and energetics of protonated 2′-deoxyadenosine and adenosine: IRMPD action spectroscopy and theoretical studies. J. Phys. Chem. B. 119, 2795–2805 (2015)CrossRefGoogle Scholar
  24. 24.
    Wu, R.R., Yang, B., Frieler, C.E., Berden, G., Oomens, J., Rodgers, M.T.: Diverse mixtures of 2,4-dihydroxy tautomers and O4 protonated conformers of uridine and 2′-deoxyuridine coexist in the gas phase. Phys. Chem. Chem. Phys. 17, 25978–25988 (2015)CrossRefGoogle Scholar
  25. 25.
    Wu, R.R., Yang, B., Frieler, C.E., Berden, G., Oomens, J., Rodgers, M.T.: N3 and O2 protonated tautomeric conformations of 2′-deoxycytidine and cytidine coexist in the gas phase. J. Phys. Chem. B. 119, 5773–5784 (2015)CrossRefGoogle Scholar
  26. 26.
    Wu, R.R., Yang, B., Frieler, C.E., Berden, G., Oomens, J., Rodgers, M.T.: 2,4-Dihydroxy and O2 protonated tautomers of dThd and Thd coexist in the gas phase: methylation alters protonation preferences versus dUrd and Urd. J. Am. Soc. Mass Spectrom. 27, 410–421 (2016)CrossRefGoogle Scholar
  27. 27.
    Filippi, Antonello, Fraschetti, Caterina, Rondino, Flaminia, Piccirillo, Susanna, Steinmetz, Vincent, Guidoni, Leonardo, Speranza, Maurizio: Protonated Pyrimidine Nucleosides Probed by IRMPD Spectroscopy. Int. J. Mass Spectrom. 354-355, 54–61 (2013)Google Scholar
  28. 28.
    Salpin, J.-Y., Scuderi, D.: Structure of protonated thymidine characterized by infrared multiple photon dissociation and quantum calculations. Rapid Commun. Mass Spectrom. 29, 1898–1904 (2015)CrossRefGoogle Scholar
  29. 29.
    Ung, H.U., Huynh, K.T., Poutsma, J.C., Oomens, J., Berden, G., Morton, T.H.: Investigation of proton affinities and gas phase vibrational spectra of protonated nucleosides, deoxynucleosides, and their analogs. Int. J. Mass Spectrom. 378, 294–302 (2015)CrossRefGoogle Scholar
  30. 30.
    Hamlow, L. A., He, C. C., Devereaux, Zachary J., Roy, H. A., Cunningham, N. A., Soley, Erik O., Berden, G., Oomens, J., Rodgers, M. T.: Gas-phase structures of protonated arabino nucleosides. Int. J. Mass Spectrom. 438, 124–134 (2019)Google Scholar
  31. 31.
    Polfer, N.C., Oomens, J., Moore, D.T., von Helden, G., Meijer, G., Dunbar, R.C.: Infrared spectroscopy of phenylalanine Ag(I) and Zn (II) complexes in the gas phase. J. Am. Chem. Soc. 128, 517–525 (2006)CrossRefGoogle Scholar
  32. 32.
    Polfer, N.C., Oomens, J.: Reaction products in mass spectrometry elucidated with infrared spectroscopy. Phys. Chem. Chem. Phys. 9, 3804–3817 (2007)CrossRefGoogle Scholar
  33. 33.
    Oepts, D., van der Meer, A.F.G., van Amersfoort, P.W.: The Free-Electron-Laser user facility Felix. Infrared Phys. Technol. 36, 297–308 (1995)CrossRefGoogle Scholar
  34. 34.
    Hamlow, L.A., Zhu, Y., Devereaux, Z.J., Cunningham, N.A., Berden, G., Oomens, J., Rodgers, M.T.: Modified quadrupole ion trap mass spectrometer for infrared ion spectroscopy: application to protonated thiated uridines. J. Am. Soc. Mass Spectrom. 29, 2125–2137 (2018)CrossRefGoogle Scholar
  35. 35.
    Pearlman, D.A., Case, D.A., Caldwell, J.W., Ross, W.R., Cheatham, T.E., DeBolt, S., Ferguson, D., Seibel, G., Kollman, P.: AMBER, a computer program for applying molecular mechanics, normal mode analysis, molecular dynamics and free energy calculations to elucidate the structures and energies of molecules. Comput. Phys. Commun. 91, 1–41 (1995)CrossRefGoogle Scholar
  36. 36.
    Wang, J.M., Wang, W., Kollman, P.A., Case, D.A.: Automatic atom type and bond type perception in molecular mechanical calculations. J Mol Graph Model. 25, 247–260 (2006)CrossRefGoogle Scholar
  37. 37.
    Maier, J.A., Martinez, C., Kasavajhala, K., Wickstrom, L., Hauser, K.E., Simmerling, C.: ff14SB: improving the accuracy of protein side chain and backbone parameters from ff99SB. J. Chem. Theory Comput. 11, 3696–3713 (2015)CrossRefGoogle Scholar
  38. 38.
    Wang, J.M., Wolf, R.M., Caldwell, J.W., Kollman, P.A., Case, D.A.: Development and testing of a general Amber force field. J. Comput. Chem. 25, 1157–1174 (2004)CrossRefGoogle Scholar
  39. 39.
    Frisch, M. J., Trucks, G. W. , Schlegel, H. B. , Scuseria, G. E. , Robb, M. A. , Cheeseman, J. R. , Scalmani, G., Barone, V., Mennucci, B., Petersson, G. A. , Nakatsuji, H., Caricato, M., Li, X., Hratchian, H. P., Izmaylov, A. F., Bloino, J., Zheng, G., Sonnenberg, J. L., Hada, M., Ehara, M., Toyota, K., Fukuda, R., Hasegawa, J., Ishida, M., Nakajima, T., Honda, Y., Kitao, O., Nakai, H., Vreven, T., Montgomery, Jr., J. A. , Peralta, J. E., Ogliaro, F., Bearpark, M., Heyd, J. J., Brothers, E., Kudin, K. N., Staroverov, V. N., Kobayashi, R., Normand, J., Raghavachari, K., Rendell, A. , Burant, J. C. , Millam, J. M. , Iyengar, S. S. , Tomasi, J. , Cossi, M., Rega, N., Millam, J. M., Klene, M., Knox, J. E. , Cross, J. B. , Bakken, V., Adamo, C., Jaramillo, J., Gomperts, R., Stratmann, R. E. , Yazyev, O., Austin, A. J. , Cammi, R., Pomelli, C., Ochterski, J. W. , Martin, R. L. , Morokuma, K., Zakrzewski, V. G. , Voth, G. A. , Salvador, P., Dannenberg, J. J. , Dapprich, S., Daniels, A. D. , Farkas, O., Foresman, J. B. , Ortiz, J. V., Cioslowski, J., Fox, D. J. , Gaussian 09, Revision A.02. (2009), Gaussian Inc.: Pittsburgh, PAGoogle Scholar
  40. 40.
    He, C.C., Hamlow, L.A., Devereaux, Z.J., Zhu, Y., Nei, Y.W., Fan, L., McNary, C.P., Maitre, P., Steinmetz, V., Schindler, B., Compagnon, I., Armentrout, P.B., Rodgers, M.T.: Structural and energetic effects of O2′-ribose methylation of protonated purine nucleosides. J. Phys. Chem. B. 122, 9147–9160 (2018)CrossRefGoogle Scholar

Copyright information

© American Society for Mass Spectrometry 2019

Authors and Affiliations

  1. 1.Department of ChemistryWayne State UniversityDetroitUSA
  2. 2.Institute for Molecules and Materials, FELIX LaboratoryRadboud UniversityNijmegenThe Netherlands

Personalised recommendations