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Application of deuterium–hydrogen exchange to study the secondary structure of oligonucleotide ions in a gas phase

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Abstract

At present, the secondary structure of oligonucleotide ions in a gas phase is almost not understood. One of the main points is the retention of a hairpin secondary structure during ionization. In this work, we used a deuterium–hydrogen exchange reaction in a gas phase at atmospheric pressure for studying the conformational dynamics of oligonucleotide ions formed as a result of electrospray ionization. The exchange reactions of two oligonucleotides, which consisted of the identical sets of nucleotides but differed in their sequence, have been studied. One of these oligonucleotides formed a hairpin secondary structure, but the other did not. It has been found that both of the oligonucleotides demonstrate similar reaction dynamics of deuterium/hydrogen exchange in the gas phase; thereby indicating that the secondary structure has been completely destroyed during ionization.

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References

  1. Katta, V. and Chait, B.T., J. Am. Chem. Soc., 1993, vol. 115, no. 14, p. 6317.

    Article  CAS  Google Scholar 

  2. Wales, T.E. and Engen, J.R., Mass Spectrom. Rev., 2006, vol. 25, no. 1, p. 158.

    Article  CAS  Google Scholar 

  3. Gard, E., Green, M.K., Bregar, J., and Lebrilla, C.B., J. Am. Soc. Mass Spectrom., 1994, vol. 5, no. 7, p. 623.

    Article  CAS  Google Scholar 

  4. McLafferty, F.W., Guan, Z.Q., Haupts, U., Wood, T.D., and Kelleher, N.L., J. Am. Chem. Soc., 1998, vol. 120, no. 19, p. 4732.

    Article  CAS  Google Scholar 

  5. Freitas, M.A., Hendrickson, C.L., Emmett, M.R., and Marshall, A.G., Int. J. Mass Spectrom., 1999, vol. 185, p. 565.

    Article  Google Scholar 

  6. Price, N.P.J., Anal. Chem., 2006, vol. 78, no. 15, p. 5302.

    Article  CAS  Google Scholar 

  7. Green-Church, K.B., Limbach, P.A., Freitas, M.A., and Marshall, A.G., J. Am. Soc. Mass Spectrom., 2001, vol. 12, no. 3, p. 268.

    Article  CAS  Google Scholar 

  8. Balbeur, D., Widart, J., Leyh, B., Cravello, L., and De Pauw, E., J. Am. Soc. Mass Spectrom., 2008, vol. 19, no. 7, p. 938.

    Article  CAS  Google Scholar 

  9. Solouki, T., Freitas, M.A., and Alomary, A., Anal. Chem., 1999, vol. 71, no. 20, p. 4719.

    Article  CAS  Google Scholar 

  10. Kostyukevich, Y., Kononikhin, A., Popov, I., and Nikolaev, E.N., Anal. Chem., 2013, vol. 85, no. 11, p. 5330.

    Article  CAS  Google Scholar 

  11. Hemling, M.E., Conboy, J.J., Bean, M.F., Mentzer, M., and Carr, S.A., J. Am. Soc. Mass Spectrom., 1994, vol. 5, no. 5, p. 434.

    Article  CAS  Google Scholar 

  12. Kostyukevich, Y., Kononikhin, A., Popov, I., and Nikolaev, E.N., Eur. J. Mass Spectrom., 2015, vol. 21, no. 2, p. 109.

    Article  CAS  Google Scholar 

  13. Takats, Z., Nanita, S.C., Schlosser, G., Vekey, K., and Cooks, R.G., Anal. Chem., 2003, vol. 75, no. 22, p. 6147.

    Article  CAS  Google Scholar 

  14. Kostyukevich, Y., Kononikhin, A., Popov, I., Indeykina, M., Kozin, S.A., Makarov, A.A., and Nikolaev, E.N., J. Mass Spectrom., 2015, vol. 50, no. 9, p. 1079.

    Article  CAS  Google Scholar 

  15. Perminova, I.V., Dubinenkov, I.V., Kononikhin, A.S., Konstantinov, A.I., Zherebker, A.Y., Andzhushev, M.A., Lebedev, V.A., Bulygina, E., Holmes, R.M., Kostyukevich, Y.I., Popov, I.A., and Nikolaev, E.N., Environ. Sci. Technol., 2014, vol. 48, no. 13, p. 7461.

    Article  CAS  Google Scholar 

  16. Kostyukevich, Y., Kononikhin, A., Popov, I., Spasskiy, A., and Nikolaev, E.N., J. Mass Spectrom., 2015, vol. 50, no. 1, p. 49.

    Article  CAS  Google Scholar 

  17. Kostyukevich, Y., Kononikhin, A., and Popov, I., Nikolaev, Anal. Chem., 2014, vol. 86, no. 5, p. 2595.

    Article  CAS  Google Scholar 

  18. Kostyukevich, Y., Kononikhin, A., Popov, I., and Nikolaev, E., J. Mass Spectrom., 2015, vol. 50, no. 10, p. 1150.

    Article  CAS  Google Scholar 

  19. Kononikhin, A., Huang, M.Z., Popov, I., Kostyukevich, Y., Kukaev, E., Boldyrev, A., Spasskiy, A., Leypunskiy, I., Shiea, J., and Nikolaev, E., Eur. J. Mass Spectrom., 2013, vol. 19, no. 4, p. 247.

    Article  CAS  Google Scholar 

  20. Kostyukevich, Y., Kononikhin, A., Popov, I., Starodubtseva, N., Kukaev, E., and Nikolaev, E., Eur. J. Mass Spectrom., 2014, vol. 20, no. 4, p. 345.

    Article  CAS  Google Scholar 

  21. Kostyukevich, Y., Kononikhin, A., Popov, I., and Nikolaev, E., J. Mass Spectrom., 2014, vol. 49, no. 10, p. 989.

    Article  CAS  Google Scholar 

  22. Ahmed, A. and Kim, S., J. Am. Soc. Mass Spectrom., 2013, vol. 24, no. 12, p. 1900.

    Article  CAS  Google Scholar 

  23. Cho, Y., Ahmed, A., and Kim, S., Anal. Chem., 2013, vol. 85, no. 20, p. 9758.

    Article  CAS  Google Scholar 

  24. Zherebker, A.Y., Airapetyan, D., Konstantinov, A.I., Kostyukevich, Y.I., Kononikhin, A.S., Popov, I.A., Zaitsev, K.V., Nikolaev, E.N., and Perminova, I.V., Analyst, 2015, vol. 140, no. 13, p. 4708.

    Article  CAS  Google Scholar 

  25. Zherebker, A., Kostyukevich, Y., Kononikhin, A., Roznyatovsky, V.A., Popov, I., Grishin, Y.K., Perminova, I.V., and Nikolaev, E., Analyst, 2016, vol. 141, no. 8, p. 2426.

    Article  CAS  Google Scholar 

  26. Kostyukevich, Y., Kononikhin, A., Zherebker, A., Popov, I., Perminova, I., and Nikolaev, E., Anal. Bioanal. Chem., 2014, vol. 406, no. 26, p. 6655.

    Article  CAS  Google Scholar 

  27. Kostyukevich, Y., Kononikhin, A., Popov, I., Starodubtzeva, N., Pekov, S., Kukaev, E., Indeykina, M., and Nikolaev, E., Eur. J. Mass Spectrom., 2015, vol. 21, no. 1, p. 59.

    Article  CAS  Google Scholar 

  28. Abi-Ghanem, J. and Gabelica, V., Phys. Chem. Chem. Phys., 2014, vol. 16, no. 39, p. 21204.

    Article  CAS  Google Scholar 

  29. Mo, J.J.E., Todd, G.C., and Hakansson, K., Biopolymers, 2009, vol. 91, no. 4, p. 256.

    Article  CAS  Google Scholar 

  30. Arcella, A., Dreyer, J., Ippoliti, E., Ivani, I., Portella, G., Gabelica, V., Carloni, P., and Orozco, M., Angew. Chem. Int. Ed., 2015, vol. 54, no. 2, p. 467.

    CAS  Google Scholar 

  31. Gidden, J., Bushnell, J.E., and Bowers, M.T., J. Am. Chem. Soc., 2001, vol. 123, no. 23, p. 5610.

    Article  CAS  Google Scholar 

  32. Bohrer, B.C., Atlasevich, N., and Clemmer, D.E., J. Phys. Chem. B, 2011, vol. 115, no. 15, p. 4509.

    Article  CAS  Google Scholar 

  33. Nousiainen, M., Vainiotalo, P., Derrick, P.J., Cooper, H.J., Hoxha, A., Fati, D., Trayer, H.R., Ward, D.G., and Trayer, I.P., Eur. J. Mass Spectrom., 2002, vol. 8, no. 6, p. 471.

    Article  CAS  Google Scholar 

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Authors and Affiliations

  1. Skolkovo Institute of Science and Technology, Skolkovo, Moscow oblast, 143025, Russia

    Yu. I. Kostyukevich & E. N. Nikolaev

  2. Talrose Institute of Energy Problems of Chemical Physics, Russian Academy of Sciences, Moscow, 119334, Russia

    Yu. I. Kostyukevich, A. S. Kononikhin & E. N. Nikolaev

  3. Emanuel Institute of Biochemical Physics, Russian Academy of Sciences, Moscow, 119334, Russia

    I. A. Popov & A. E. Bugrova

  4. Moscow Institute of Physics and Technology (State University), Dolgoprudnyi, Moscow oblast, 141700, Russia

    Yu. I. Kostyukevich, A. S. Kononikhin, I. A. Popov, N. L. Starodubtseva & E. N. Nikolaev

  5. Kulakov Research Center for Obstetrics, Gynecology, and Perinatology, Ministry of Public Health of the Russian Federation, Moscow, 117997, Russia

    A. S. Kononikhin, A. E. Bugrova & N. L. Starodubtseva

Authors
  1. Yu. I. Kostyukevich
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  2. A. S. Kononikhin
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  3. I. A. Popov
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  4. A. E. Bugrova
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  5. N. L. Starodubtseva
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  6. E. N. Nikolaev
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Correspondence to Yu. I. Kostyukevich.

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Original Russian Text © Yu.I. Kostyukevich, A.S. Kononikhin, I.A. Popov, A.E. Bugrova, N.L. Starodubtseva, E.N. Nikolaev, 2016, published in Khimiya Vysokikh Energii, 2016, Vol. 50, No. 6, pp. 453–457.

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Kostyukevich, Y.I., Kononikhin, A.S., Popov, I.A. et al. Application of deuterium–hydrogen exchange to study the secondary structure of oligonucleotide ions in a gas phase. High Energy Chem 50, 427–432 (2016). https://doi.org/10.1134/S0018143916060096

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  • DOI: https://doi.org/10.1134/S0018143916060096

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