Abstract
Data on intermolecular noncovalent interactions of nitrogen base components of nucleic acid with organic polyethers are of interest both for fundamental molecular biophysics and for applications in the production of pharmaceutical organic nanoparticles. In the present work, systems composed of pyrimidine nitrogen base cytosine (Cyt) or its methyl derivatives and polyethylene glycol PEG-400 oligomers M n have been examined by electrospray ionization (ESI) and fast atom bombardment mass spectrometry. Detection of a set of associates of the M n · Cyt · H+ type (n = 3–17) in ESI mass spectra evidences the formation of protonated complexes of the base with oligomers of different chain lengths in all of the studied systems. Computer modeling by molecular dynamics gave answers to the questions concerning the stability and structure of these complexes under different conditions. It has been shown that M n · Cyt · H+ clusters in the gas phase (vacuum) adopt a compact structure with a quasi-cyclic or quasi-helical self-organization of the polymer chain around the protonated base. It has been found that the compact structure of the M8 · Cyt · H+ complex characteristic for its state in the gas phase is preserved in a liquid medium of methanol (used as a solvent in ESI). The results of simulation of the evolution of a methanol droplet in vacuum, which mimics the droplet disintegration under ESI conditions, have shown that the M8 · Cyt · H+ complex initially present in the droplet does not disintegrate in the course of droplet evaporation. After the completion of desolvation, the complex returns to the conformation characteristic for the gas phase. Thus, the evidence has been found confirming that the M8 · Cyt · H+ clusters recorded in ESI mass spectra adequately reflect the presence of corresponding noncovalent complexes in the analyzed liquid solution.
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Wyttenbach, Th. and Bowers, M.T., Ann. Rev. Phys. Chem., 2007, vol. 58, no. 1, p. 511.
Loo, J.A., Int. J. Mass Spectrom. Ion Processes, 2000, vol. 200, nos. 1–3, p. 175.
McCullough, B.J. and Gaskell, S.J., Comb. Chem. High Throughput Screening, 2009, vol. 12, no. 2, p. 203.
Schalley, C.A. and Springer, A., Mass Spectrometry of Non-Covalent Complexes: Supramolecular Chemistry in the Gas Phase, Hoboken: Wiley, 2009.
Kaltashov, I.A. and Eyles, S.J., Mass spectrometry in Biophysics: Conformation and Dynamics of Biomolecules, Hoboken: Wiley, 2005.
Zhong, W.-H., Li, B., Maguire, R.G., Dang, V.T., Shatkin, J.A., Gross, G.M., and Richey, M.C., in Nanoscience and Nanomaterials: Synthesis, Manufacturing, and Industry Impacts, Lancaster: DEStech Publications, 2012, p. 303.
Suzdalev, I.P., Nanotekhnologiya: fiziko-khimiya nanoklasterov, nanostruktur i nanomaterialov (Nanotechnology: Physics and Chemistry of Nanoclusters, Nanostructures, and Nanomaterials), Moscow: KomKniga, 2006.
Zobnina, V.G., Kosevich, M.V., Chagovets, V.V., and Boryak, O.A., in Nanomaterials Imaging Techniques, Surface Studies, and Applications, Fesenko, O., Yatsenko, L., and Brodin, M., Eds., London: Springer, 2013, p. 327.
Zobnina, V.G., Kosevich, M.V., Chagovets, V.V., Boryak, O.A., Vékey, K., Gömöry, Á., and Kulyk, A.N., Rapid Commun. Mass Spectrom., 2012, vol. 26, no. 5, p. 532.
Kosevich, M.V., Zobnina, V.G., Boryak, O.A., Chagovets, V.V., and Zinchenko, A.V., Probl. Kriobiol., 2012, vol. 22, no. 3, p. 327.
Zobnina, V.G., Kosevich, M.V., Boryak, O.A., and Chagovets, V.V., Vestnik Sevastopolsk. Nats. Tech. Univ., Ser.: Fiz. Biol. Syst. Mol., 2011, no. 113, p. 88.
Zobnina, V.G., Boryak, O.A., Kosevich, M.V., Chagovets, V.V., Orlov, V.V., Snegir’, V.V., Pokrovskii, V.A., Zhivotova, E.N., Zinchenko, A.V., and Gomory, A., Visn. Kharkovsk. Nats. Univ. Biofiz. Visn., 2009, no. 1, p. 103.
Electrospray and MALDI Mass Spectrometry: Fundamentals, Instrumentation, Practicalities, and Biological Applications, Cole, R., Ed., Hoboken: Wiley, 2010, 2nd ed.
Veronese, F.M. and Pasut, G., Drug Discovery Today, 2005, vol. 10, no. 21, p. 1451.
Van Vlerken, L.E., Vyas, T.K., and Amiji, M.M., Pharm. Res., 2007, vol. 24, no. 8, p. 1405.
Kleemann, E., Neu, M., Jekel, N., Fink, L., Schmehl, T., Gessler, T., Seeger, W., and Kissel, T., J. Controlled Release, 2005, vol. 109, nos. 1–3, p. 299.
Harris, J.M. and Zalipsky, S., Poly(Ethylene Glycol): Chemistry and Biological Applications, Washington, DC: Am. Chem. Soc., 1997.
Wyttenbach, T., Helden, G., and Bowers, M.T., Int. J. Mass Spectrom. Ion Processes, 1997, vols. 165–166, p. 377.
Gidden, J., Wyttenbach, T., Jackson, A.T., Scrivens, J.H., and Bowers, M.T., J. Am. Chem. Soc., 2000, vol. 122, no. 19, p. 4692.
Jackson, A.T., Scrivens, J.H., Williams, J.P., Baker, E.S., Gidden, J., and Bowers, M.T., Int. J. Mass Spectrom. Ion Processes, 2004, vol. 238, no. 3, p. 287.
Belan, V.I., Belous, L.F., Grechnev, G.E., Zarudnev, E.S., Zobnina, V.G., Ivanov, A.Yu., Karachevtsev, M.V., Kosevich, M.V., Rubin, Yu.V., Slavin, V.V., Smirnov, S.N., Stepanian, S.G., and Chagovets, V.V., in Parallel and Distributed Computing Systems: Collection of Scientific Papers, Cherepynets, V., Ed., Kharkov: ISMA House, 2013, p. 32
Znamenskiy, V., Marginean, I., and Vertes, A., J. Phys. Chem. A, 2003, vol. 107, no. 38, p. 7406.
Konermann, L., Ahadi, E., Rodriguez, A.D., and Vahidi, S., Anal. Chem., 2013, vol. 85, no. 1, p. 2.
Ahadi, E. and Konermann, L., J. Am. Chem. Soc., 2011, vol. 133, no. 24, p. 9354.
Daub, C.D. and Cann, N.M., Anal. Chem., 2011, vol. 83, no. 22, p. 8372.
Ahadi, E. and Konermann, L., J. Phys. Chem. B, 2012, vol. 116, no. 1, p. 104.
Skurat, V.E., Itogi Nauki Tekh., Ser.: Radiats. Khim. Fotokhim., vol. 5: Poluchenie i issledovanie ionov neletuchikh organicheskikh veshchestv v gazovoi faze i v vakuume (Preparation and Study of Ions of Nonvolatile Organic Compounds in the Gas Phase and in Vacuum), Moscow: VINITI, 1988.
Kebarle, P. and Verkerk, U.H., Mass Spectrom. Rev., 2009, vol. 28, no. 6, p. 898.
Breuker, K. and McLafferty, F.W., Proc. Natl. Acad. Sci. USA, 2008, vol. 105, no. 47, p. 18145.
Phillips, J.C., Braun, R., Wang, W., Gumbart, J., Tajkhorshid, E., Villa, E., Chipot, C., Skeel, R.D., Kale, L., and Schulten, K., J. Comput. Chem., 2005, vol. 26, no. 16, p. 1781.
Brooks, B.R., Brooks, C.L.III., Mackerell, A.D., Jr., Nilsson, L., Petrella, R.J., Roux, B., Won, Y., Archontis, G., Bartels, C., Boresch, S., Caflisch, A., Caves, L., Cui, Q., Dinner, A.R., Feig, M., Fischer, S., Gao, J., Hodoscek, M., Im, W., Kuczera, K., Lazaridis, T., Ma, J., Ovchinnikov, V., Paci, E., Pastor, R.W., Post, C.B., Pu, J.Z., Schaefer, M., Tidor, B., Venable, R.M., Woodcock, H.L., Wu, X., Yang, W., York, D.M., and Karplus, M., J. Comput. Chem., 2009, vol. 30, no. 10, p. 1545.
ChemCraft. http://www.chemcraftprog.com. Cited March 27, 2014.
Visual Molecular Dynamics (VMD). http://www.ks.uiuc.edu/Research/vmd/. Cited March 27, 2014.
GRID-cluster of the Institute for Low Temperature Physics and Engineering of the National Academy of Sciences of Ukraine. http://www.ilt.kharkov.ua/cluster/. Cited March 27, 2014.
Montaudo, G. and Lattimer, R.P., Mass Spectrometry of Polymers, Boca Raton: CRC Press, 2002.
Zaikin, V.G., Mass-spektrometriya sinteticheskikh polimerov (Mass Spectrometry of Synthetic Polymers), Moscow: All-Russ. Mass-Spectrom. Soc., 2009.
Varray, S., Aubagnac, J.-L., Lamaty, F., Lazaro, R., Martinez, J., and Enjalbal, C., Analysis, 2000, vol. 28, no. 4, p. 263.
Kosevich, M.V., Zobnina, V.G., Zhivotova, E.N., Shmigol’, I.V., Boryak, O.A., Chagovets, V.V., Chekanova, V.V., Zinchenko, A.V., Pokrovskii, V.A., and Gomory, A., Mass-Spektrometria, 2009, vol. 6, no. 1, p. 7.
Zobnina, V.G., Kosevich, M.V., Chagovets, V.V., Boryak, O.A., Kulik, A.N., and Gomory, A., MassSpektrometria, 2010, vol. 7, no. 3, p. 225.
Kosevich, M.V., Zobnina, V.G., Chagovets, V.V., and Boryak, O.A., Rapid Commun. Mass Spectrom., 2011, vol. 25, no. 6, p. 713.
Zobnina, V.G., Kosevich, M.V., Boryak, O.A., Orlov, V.V., Gomory, A., and Vekey, K., in Materialy I Mezhdunar. nauchno-tekhnich. konf. FizKhimBio-2012 (Proc. 1st Int. Sci.-Tech. Conf. PhysKhimBio-2012), Sevastopol, 2012, p. 67.
NIST Chemistry WebBook, NIST Standard Ref. Database no. 69, Linstrom, P.J. and Mallard, W.G., Eds., Natl. Inst. Standards Technol., 2014. http://webbook.nist.gov/chemistry/. Cited March 27, 2014.
Hunter, E.P. and Lias, S.G., J. Phys. Chem. Ref. Data, 1998, vol. 27, no. 3, p. 413.
Lin, H.Y., Rockwood, A., Munson, M.S.B., and Ridge, D.P., Anal. Chem., 1993, vol. 65, no. 15, p. 2119.
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Original Russian Text © V.G. Zobnina, V.V. Chagovets, O.A. Boryak, M.V. Kosevich, 2014, published in Mass-spektrometriya, 2014, Vol. 11, No. 2, pp. 97–106.
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Zobnina, V.G., Chagovets, V.V., Boryak, O.A. et al. A mass spectrometric study and computer modeling of noncovalent interactions of cytosine with polyethylene glycol oligomers. J Anal Chem 70, 1533–1541 (2015). https://doi.org/10.1134/S1061934815130110
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DOI: https://doi.org/10.1134/S1061934815130110