Acidity constants and protonation sites of cyclic dinucleotides determined by capillary electrophoresis, quantum chemical calculations, and NMR spectroscopy

0583095 - ÚOCHB 2025 RIV US eng J - Článek v odborném periodiku
Štěpánová, Sille - Andris, Erik - Gutten, Ondrej - Buděšínský, Miloš - Dejmek, Milan - Břehová, Petra - Rulíšek, Lubomír - Kašička, Václav
Acidity constants and protonation sites of cyclic dinucleotides determined by capillary electrophoresis, quantum chemical calculations, and NMR spectroscopy.
Electrophoresis. Roč. 45, 7/8 (2024), s. 687-705. ISSN 0173-0835. E-ISSN 1522-2683
Grant CEP: GA ČR(CZ) GA20-03899S; GA ČR(CZ) GA23-05940S
Institucionální podpora: RVO:61388963
Klíčová slova: acidity constant * capillary electrophoresis * cyclic dinucleotides * DFT calculations * NMR spectroscopy
Impakt faktor: 2.9, rok: 2022
Způsob publikování: Open access
https://doi.org/10.1002/elps.202300232

Cyclic dinucleotides (CDNs) are important second messengers in bacteria and eukaryotes. Detailed characterization of their physicochemical properties is a prerequisite for understanding their biological functions. Herein, we examine acid-base and electromigration properties of selected CDNs employing capillary electrophoresis (CE), density functional theory (DFT), and nuclear magnetic resonance (NMR) spectroscopy to provide benchmark pKa values, as well as to unambiguously determine the protonation sites. Acidity constants (pKa) of the NH+ moieties of adenine and guanine bases and actual and limiting ionic mobilities of CDNs were determined by nonlinear regression analysis of the pH dependence of their effective electrophoretic mobilities measured by CE in aqueous background electrolytes in a wide pH range (0.98-11.48), at constant temperature (25 degrees C), and constant ionic strength (25 mM). The thermodynamic pKa values were found to be in the range 3.31-4.56 for adenine and 2.28-3.61 for guanine bases, whereas the pKa of enol group of guanine base was in the range 10.21-10.40. Except for systematic shifts of similar to 2 pKa, the pKa values calculated by the DFT-D3//COSMO-RS composite protocol that included large-scale conformational sampling and cross-morphing were in a relatively good agreement with the pKas determined by CE and predict N1 atom of adenine and N7 atom of guanine as the protonation sites. The protonation of the N1 atom of adenine and N7 atom of guanine in acidic background electrolytes (BGEs) and the dissociation of the enol group of guanine in alkaline BGEs was confirmed also by NMR spectroscopy.
Trvalý link: https://hdl.handle.net/11104/0351092