Advertisement

Native Ion Mobility Mass Spectrometry: When Gas-Phase Ion Structures Depend on the Electrospray Charging Process

  • Nina Khristenko
  • Jussara Amato
  • Sandrine Livet
  • Bruno Pagano
  • Antonio Randazzo
  • Valérie GabelicaEmail author
Focus: Ion Mobility Spectrometry (IMS): Research Article

Abstract

Ion mobility spectrometry (IMS) has become popular to characterize biomolecule folding. Numerous studies have shown that proteins that are folded in solution remain folded in the gas phase, whereas proteins that are unfolded in solution adopt more extended conformations in the gas phase. Here, we discuss how general this tenet is. We studied single-stranded DNAs (human telomeric cytosine-rich sequences with CCCTAA repeats), which fold into an intercalated motif (i-motif) structure in a pH-dependent manner, thanks to the formation of C–H+–C base pairs. As i-motif formation is favored at low ionic strength, we could investigate the ESI-IMS-MS behavior of i-motif structures at pH ~ 5.5 over a wide range of ammonium acetate concentrations (15 to 100 mM). The control experiments consisted of either the same sequence at pH ~ 7.5, wherein the sequence is unfolded, or sequence variants that cannot form i-motifs (CTCTAA repeats). The surprising results came from the control experiments. We found that the ionic strength of the solution had a greater effect on the compactness of the gas-phase structures than the solution folding state. This means that electrosprayed ions keep a memory of the charging process, which is influenced by the electrolyte concentration. We discuss these results in light of the analyte partitioning between the droplet interior and the droplet surface, which in turn influences the probability of being ionized via a charged residue-type pathway or a chain extrusion-type pathway.

Keywords

Ion mobility Electrospray mechanisms Native MS Nucleic acids Fundamentals 

Notes

Acknowledgements

This work was supported by the European Research Council under the European Union’s Seventh Framework Program (ERC grant 616551 to VG) and by the Italian Association for Cancer Research (AIRC) (IG-18695 to AR).

Supplementary material

13361_2019_2152_MOESM1_ESM.pdf (1.4 mb)
ESM 1 (PDF 1468 kb)

References

  1. 1.
    Gehring, K., Leroy, J.L., Gueron, M.: A tetrameric DNA structure with protonated cytosine. Cytosine base pairs. Nature. 363, 561–565 (1993)CrossRefGoogle Scholar
  2. 2.
    Leroy, J.L., Gueron, M., Mergny, J.L., Helene, C.: Intramolecular folding of a fragment of the cytosine-rich strand of telomeric DNA into an i-motif. Nucleic Acids Res. 22, 1600–1606 (1994)CrossRefGoogle Scholar
  3. 3.
    Gueron, M., Leroy, J.L.: The i-motif in nucleic acids. Curr. Opin. Struct. Biol. 10, 326–331 (2000)CrossRefGoogle Scholar
  4. 4.
    Abou Assi, H., Garavis, M., Gonzalez, C., Damha, M.J.: i-Motif DNA: structural features and significance to cell biology. Nucleic Acids Res. 46, 8038–8056 (2018)CrossRefGoogle Scholar
  5. 5.
    Phan, A.T., Gueron, M., Leroy, J.L.: The solution structure and internal motions of a fragment of the cytidine-rich strand of the human telomere. J. Mol. Biol. 299, 123–144 (2000)CrossRefGoogle Scholar
  6. 6.
    Wright, E.P., Huppert, J.L., Waller, Z.A.E.: Identification of multiple genomic DNA sequences which form i-motif structures at neutral pH. Nucleic Acids Res. 45, 2951–2959 (2017)CrossRefGoogle Scholar
  7. 7.
    Zeraati, M., Langley, D.B., Schofield, P., Moye, A.L., Rouet, R., Hughes, W.E., Bryan, T.M., Dinger, M.E., Christ, D.: I-motif DNA structures are formed in the nuclei of human cells. Nat. Chem. 10, 631–637 (2018)CrossRefGoogle Scholar
  8. 8.
    Dzatko, S., Krafcikova, M., Hansel-Hertsch, R., Fessl, T., Fiala, R., Loja, T., Krafcik, D., Mergny, J.L., Foldynova-Trantirkova, S., Trantirek, L.: Evaluation of the stability of DNA i-motifs in the nuclei of living mammalian cells. Angew. Chem. Int. Ed. 57, 2165–2169 (2018)CrossRefGoogle Scholar
  9. 9.
    Mergny, J.L., Lacroix, L.: Analysis of thermal melting curves. Oligonucleotides. 13, 515–537 (2003)CrossRefGoogle Scholar
  10. 10.
    Kypr, J., Kejnovska, I., Renciuk, D., Vorlickova, M.: Circular dichroism and conformational polymorphism of DNA. Nucleic Acids Res. 37, 1713–1725 (2009)CrossRefGoogle Scholar
  11. 11.
    Bowers, M.T., Kemper, P.R., Von Helden, G., Van Koppen, P.A.M.: Gas-phase ion chromatography: transition metal state selection and carbon cluster formation. Science. 260, 1446–1451 (1993)CrossRefGoogle Scholar
  12. 12.
    Clemmer, D.E., Hudgins, R.R., Jarrold, M.F.: Naked protein conformations: cytochrome c in the gas phase. J. Am. Chem. Soc. 117, 10141–10142 (1995)CrossRefGoogle Scholar
  13. 13.
    Wyttenbach, T., Von Helden, G., Bowers, M.T.: Gas-phase conformation of biological molecules: bradykinin. J. Am. Chem. Soc. 118, 8355–8364 (1996)CrossRefGoogle Scholar
  14. 14.
    Clemmer, D.E., Jarrold, M.F.: Ion mobility measurements and their applications to clusters of biomolecules. J. Mass Spectrom. 32, 577–592 (1997)CrossRefGoogle Scholar
  15. 15.
    Fenn, J.B., Mann, M., Meng, C.K., Wong, S.F., Whitehouse, C.M.: Electrospray ionization for mass spectrometry. Science. 246, 64–71 (1989)CrossRefGoogle Scholar
  16. 16.
    Yamashita, M., Fenn, J.B.: Electrospray ion source. Another variation on the free-jet theme. J. Phys. Chem. 88, 4451–4459 (1984)CrossRefGoogle Scholar
  17. 17.
    Fenn, J.B., Mann, M., Meng, C.K., Wong, S.F.: Electrospray ionization-principles and practice. Mass Spectrom. Rev. 9, 37–70 (1990)CrossRefGoogle Scholar
  18. 18.
    Chowdhury, S.K., Katta, V., Chait, B.T.: Probing conformational changes in proteins by mass spectrometry. J. Am. Chem. Soc. 112, 9012–9013 (1990)CrossRefGoogle Scholar
  19. 19.
    Smith, R.D., Light-Wahl, K.J., Winger, B.E., Loo, J.A.: Preservation of non-covalent associations in electrospray ionization mass spectrometry: multiply charged polypeptide and protein dimers. Org. Mass Spectrom. 27, 811–821 (1992)CrossRefGoogle Scholar
  20. 20.
    Leney, A.C., Heck, A.J.R.: Native mass spectrometry: what is in the name? J. Am. Soc. Mass Spectrom. 28, 5–13 (2017)CrossRefGoogle Scholar
  21. 21.
    Li, J., Taraszka, J.A., Counterman, A.E., Clemmer, D.E.: Influence of solvent composition and capillary temperature on the conformations of electrosprayed ions: unfolding of compact ubiquitin colformers from pseudonative and denatured solutions. Int. J. Mass Spectrom. 185/186/187, 37–47 (1999)CrossRefGoogle Scholar
  22. 22.
    El-Baba, T.J., Woodall, D.W., Raab, S.A., Fuller, D.R., Laganowsky, A., Russell, D.H., Clemmer, D.E.: Melting proteins: evidence for multiple stable structures upon thermal denaturation of native ubiquitin from ion mobility spectrometry-mass spectrometry measurements. J. Am. Chem. Soc. 139, 6306–6309 (2017)CrossRefGoogle Scholar
  23. 23.
    Beveridge, R., Covill, S., Pacholarz, K.J., Kalapothakis, J.M., MacPhee, C.E., Barran, P.E.: A mass-spectrometry-based framework to define the extent of disorder in proteins. Anal. Chem. 86, 10979–10991 (2014)CrossRefGoogle Scholar
  24. 24.
    Loo, J.A., Ogorzalek Loo, R.R.: In: Cole, R.B. (ed.) Electrospray ionization mass spectrometry of peptides and proteins. Wiley, New York (1997)Google Scholar
  25. 25.
    Gumerov, D.R., Dobo, A., Kaltashov, I.A.: Protein-ion charge-state distributions in electrospray ionization mass spectrometry: distinguishing conformational distributions from masking effects. Eur. J. Mass Spectrom. 8, 123–129 (2002)CrossRefGoogle Scholar
  26. 26.
    Li, J., Santambrogio, C., Brocca, S., Rossetti, G., Carloni, P., Grandori, R.: Conformational effects in protein electrospray-ionization mass spectrometry. Mass Spectrom. Rev. 105, 111–122 (2016)CrossRefGoogle Scholar
  27. 27.
    Grandori, R.: Origin of the conformation dependence of protein charge-state distributions in electrospray ionization mass spectrometry. J. Mass Spectrom. 38, 11–15 (2003)CrossRefGoogle Scholar
  28. 28.
    Laszlo, K.J., Munger, E.B., Bush, M.F.: Folding of protein ions in the gas phase after cation-to-anion proton-transfer reactions. J. Am. Chem. Soc. 138, 9581–9588 (2016)CrossRefGoogle Scholar
  29. 29.
    Laszlo, K.J., Bush, M.F.: Interpreting the collision cross sections of native-like protein ions: insights from cation-to-anion proton-transfer reactions. Anal. Chem. 89, 7607–7614 (2017)CrossRefGoogle Scholar
  30. 30.
    Pacholarz, K.J., Porrini, M., Garlish, R.A., Burnley, R.J., Taylor, R.J., Henry, A.J., Barran, P.E.: Dynamics of intact immunoglobulin G explored by drift-tube ion-mobility mass spectrometry and molecular modeling. Angew. Chem. Int. Ed. 53, 7765–7769 (2014)CrossRefGoogle Scholar
  31. 31.
    Hansen, K., Lau, A.M., Giles, K., McDonnell, J.M., Struwe, W.B., Sutton, B.J., Politis, A.: A mass-spectrometry-based modelling workflow for accurate prediction of IgG antibody conformations in the gas phase. Angew. Chem. Int. Ed. 57, 17194–17199 (2018)Google Scholar
  32. 32.
    Porrini, M., Rosu, F., Rabin, C., Darre, L., Gomez, H., Orozco, M., Gabelica, V.: Compaction of duplex nucleic acids upon native electrospray mass spectrometry. ACS Cent. Sci. 3, 454–461 (2017)CrossRefGoogle Scholar
  33. 33.
    Rosu, F., Gabelica, V., Joly, L., Gregoire, G., De Pauw, E.: Zwitterionic i-motif structures are preserved in DNA negatively charged ions produced by electrospray mass spectrometry. Phys. Chem. Chem. Phys. 12, 13448–13454 (2010)CrossRefGoogle Scholar
  34. 34.
    Garabedian, A., Butcher, D., Lippens, J.L., Miksovska, J., Chapagain, P.P., Fabris, D., Ridgeway, M.E., Park, M.A., Fernandez-Lima, F.: Structures of the kinetically trapped i-motif DNA intermediates. Phys. Chem. Chem. Phys. 18, 26691–26702 (2016)CrossRefGoogle Scholar
  35. 35.
    Cavaluzzi, M.J., Borer, P.N.: Revised UV extinction coefÆcients for nucleoside-5′-monophosphates and unpaired DNA and RNA. Nucleic Acids Res. 32, e13 (2004)CrossRefGoogle Scholar
  36. 36.
    Marchand, A., Livet, S., Rosu, F., Gabelica, V.: Drift tube ion mobility: how to reconstruct collision cross section distributions from arrival time distributions? Anal. Chem. 89, 12674–12681 (2017)CrossRefGoogle Scholar
  37. 37.
    D'Atri, V., Porrini, M., Rosu, F., Gabelica, V.: Linking molecular models with ion mobility experiments. Illustration with a rigid nucleic acid structure. J. Mass Spectrom. 50, 711–726 (2015)CrossRefGoogle Scholar
  38. 38.
    Gabelica, V., Livet, S., Rosu, F.: Optimizing native ion mobility Q-TOF in helium and nitrogen for very fragile noncovalent structures. J. Am. Soc. Mass Spectrom. 29, 2189–2198 (2018)CrossRefGoogle Scholar
  39. 39.
    Lannes, L., Halder, S., Krishnan, Y., Schwalbe, H.: Tuning the pH response of i-motif DNA oligonucleotides. ChemBioChem. 16, 1647–1656 (2015)CrossRefGoogle Scholar
  40. 40.
    Mergny, J.L., Lacroix, L., Han, X., Leroy, J.L., Hélène, C.: Intramolecular folding of pyrimidine oligodeoxynucleotides into an i-DNA motif. J. Am. Chem. Soc. 117, 8887–8898 (1995)CrossRefGoogle Scholar
  41. 41.
    Pagano, A., Iaccarino, N., Abdelhamid, M.A.S., Brancaccio, D., Garzarella, E.U., Di Porzio, A., Novellino, E., Waller, Z.A.E., Pagano, B., Amato, J., Randazzo, A.: Common G-quadruplex binding agents found to interact with i-motif-forming DNA: unexpected multi-target-directed compounds. Front. Chem. 6, 281 (2018)Google Scholar
  42. 42.
    Markham, N.R., Zuker, M.: DINAMelt web server for nucleic acid melting prediction. Nucleic Acids Res. 33, W577–W581 (2005)CrossRefGoogle Scholar
  43. 43.
    Clore, G.M., Gronenborn, A.M.: An investigation into the solution structure of the single-stranded DNA undecamer S’d AAGTGTGATAT by means of nuclear Overhauser enhancement measurements. Eur. Biophys. J. 11, 95–102 (1984)CrossRefGoogle Scholar
  44. 44.
    Griffey, R.H., Sasmor, H., Greig, M.J.: Oligonucleotide charge states in negative ionization electrospray - mass spectrometry are a function of solution ammonium ion concentration. J. Am. Soc. Mass Spectrom. 8, 155–160 (1997)CrossRefGoogle Scholar
  45. 45.
    Xu, N., Chingin, K., Chen, H.: Ionic strength of electrospray droplets affects charging of DNA oligonucleotides. J. Mass Spectrom. 49, 103–107 (2014)CrossRefGoogle Scholar
  46. 46.
    Ren, W., Zheng, K., Liao, C., Yang, J., Zhao, J.: Charge evolution during the unfolding of a single DNA i-motif. Phys. Chem. Chem. Phys. 20, 916–924 (2018)CrossRefGoogle Scholar
  47. 47.
    Zhou, S., Prebyl, B.S., Cook, K.D.: Profiling pH changes in the electrospray plume. Anal. Chem. 74, 4885–4888 (2002)CrossRefGoogle Scholar
  48. 48.
    Girod, M., Dagany, X., Antoine, R., Dugourd, P.: Relation between charge state distributions of peptide anions and pH changes in the electrospray plume. A mass spectrometry and optical spectroscopy investigation. Int. J. Mass Spectrom. 308, 41–48 (2011)CrossRefGoogle Scholar
  49. 49.
    Gabelica, V., Baker, E.S., Teulade-Fichou, M.P., De Pauw, E., Bowers, M.T.: Stabilization and structure of telomeric and c-myc region intramolecular G-quadruplexes: the role of central cations and small planar ligands. J. Am. Chem. Soc. 129, 895–904 (2007)CrossRefGoogle Scholar
  50. 50.
    Ickert, S., Hofmann, J., Riedel, J., Beck, S., Pagel, K., Linscheid, M.W.: Charge induced geometrical reorganization of DNA oligonucleotides studied by tandem mass spectrometry and ion mobility. Eur. J. Mass Spectrom. 24, 225–230 (2018)CrossRefGoogle Scholar
  51. 51.
    Ogorzalek Loo, R.R., Lakshmanan, R., Loo, J.A.: What protein charging (and supercharging) reveal about the mechanism of electrospray ionization. J. Am. Soc. Mass Spectrom. 25, 1675–1693 (2014)CrossRefGoogle Scholar
  52. 52.
    Lipfert, J., Doniach, S., Das, R., Herschlag, D.: Understanding nucleic acid-ion interactions. Annu. Rev. Biochem. 83, 813–841 (2014)CrossRefGoogle Scholar
  53. 53.
    Enke, C.G.: A predictive model for matrix and analyte effects in electrospray ionization of singly-charged ionic analytes. Anal. Chem. 69, 4885–4893 (1997)CrossRefGoogle Scholar
  54. 54.
    Constantopoulos, T.L., Jackson, G.S., Enke, C.G.: Effects of salt concentration on analyte response using electrospray ionization mass spectrometry. J. Am. Soc. Mass Spectrom. 10, 625–634 (1999)CrossRefGoogle Scholar
  55. 55.
    Konermann, L., Ahadi, E., Rodriguez, A.D., Vahidi, S.: Unraveling the mechanism of electrospray ionization. Anal. Chem. 85, 2–9 (2013)CrossRefGoogle Scholar
  56. 56.
    Lin, H., Kitova, E.N., Johnson, M.A., Eugenio, L., Ng, K.K., Klassen, J.S.: Electrospray ionization-induced protein unfolding. J. Am. Soc. Mass Spectrom. 23, 2122–2131 (2012)CrossRefGoogle Scholar

Copyright information

© American Society for Mass Spectrometry 2019

Authors and Affiliations

  1. 1.Laboratoire Acides Nucléiques: Régulations Naturelle et Artificielle, Université de Bordeaux, Inserm & CNRS (ARNA, U1212, UMR5320), IECBPessacFrance
  2. 2.Department of PharmacyUniversity of Naples Federico IINaplesItaly

Personalised recommendations