%0 Journal Article %T Ammonium ion binding to DNA G-quadruplexes: do electrospray mass spectra faithfully reflect the solution-phase species? %+ Physical Chemistry and Mass Spectrometry Laboratory %+ Slovenian NMR Centre %+ Faculty of Chemistry and Chemical Technology %+ Centre of Excelence EN-FIST [Ljubljana] %A Balthasart, Françoise %A Plavec, Janez %A Gabelica, Valérie %Z This work was supported by the Fonds de la Recherche Scientifique-FNRS (research associate position and FRFC Grant 2.4528.11 to VG),the EU COST action MP0802, the Slovenian research agency [ARRS, P1-0242 and J1-4020], EU FP7 projects with acronyms EAST-NMR [228461] and Bio-NMR [261863],and the Cooperation Agreement between Wallonia-Brussels and the Republic of Slovenia. %< avec comité de lecture %@ 1044-0305 %J Journal of The American Society for Mass Spectrometry %I American Chemical Society %V 24 %N 1 %P 1-8 %8 2013-01 %D 2013 %R 10.1007/s13361-012-0499-3 %M 23132414 %Z Life Sciences [q-bio]/Biochemistry, Molecular Biology %Z Chemical Sciences/Analytical chemistryJournal articles %X G-quadruplex nucleic acids can bind ammonium ions in solution, and these complexes can be detected by electrospray mass spectrometry (ESI-MS). However, because ammonium ions are volatile, the extent to which ESI-MS quantitatively could provide an accurate reflection of such solution-phase equilibria is unclear. Here we studied five G-quadruplexes having known solution-phase structure and ammonium ion binding constants: the bimolecular G-quadruplexes (dG(4)T(4)G(4))(2), (dG(4)T(3)G(4))(2), and (dG(3)T(4)G(4))(2), and the intramolecular G-quadruplexes dG(4)(T(4)G(4))(3) and dG(2)T(2)G(2)TGTG(2)T(2)G(2) (thrombin binding aptamer). We found that not all mass spectrometers are equally suited to reflect the solution phase species. Ion activation can occur in the electrospray source, or in a high-pressure traveling wave ion mobility cell. When the softest instrumental conditions are used, ammonium ions bound between G-quartets, but also additional ammonium ions bound at specific sites outside the external G-quartets, can be observed. However, even specifically bound ammonium ions are in some instances too labile to be fully retained in the gas phase structures, and although the ammonium ion distribution observed by ESI-MS shows biases at specific stoichiometries, the relative abundances in solution are not always faithfully reflected. Ion mobility spectrometry results show that all inter-quartet ammonium ions are necessary to preserve the G-quadruplex fold in the gas phase. Ion mobility experiments, therefore, help assign the number of inner ammonium ions in the solution phase structure. %G English %2 https://inserm.hal.science/inserm-00980848/document %2 https://inserm.hal.science/inserm-00980848/file/120904_NH4preservation_R2_final.pdf %L inserm-00980848 %U https://inserm.hal.science/inserm-00980848 %~ INSERM %~ OPENAIRE