SFB 1309
Aldehyde or Hydrate? Investigation into the Oxidation of 5-Formylcytosine Derivatives Using a Computational and Experimental Approach
2025-09-23
Kuangjie Liu, Annika Menke, Fabian L. Zott, Domenic Mayer, Lena J. Daumann, Hendrik Zipse
ChemBioChem 2025, 26, e70085
This study investigates the oxidation of 5-hydroxymethyl and 5-formyl nucleobases using an iron(IV)-oxido complex that mimics the function of TET enzymes. A central question in this context is whether the oxidation of formyl substrates proceeds via the aldehyde or the hydrate form. To investigate the possible different reaction kinetics of these two forms, nucleobases containing a 6-aza-moiety are employed, giving rise to significantly more aldehyde hydrate as compared to the unaltered nucleobase. The concentration changes of substrates and products during oxidation were followed with 1H NMR spectroscopy. To analyze the kinetics of the oxidation reactions, a detailed numerical simulation of the stepwise sequential oxidation process is applied. 5-Hydroxymethyl nucleobases are first oxidized to the respective 5-formyl derivatives, which exist in equilibrium with their hydrate forms, and then further oxidized to the final 5-carboxyl nucleobases. The rate constants for 5-hydroxymethyl nucleobase oxidation show a good correlation with CH bond dissociation values. The influence of hydrate formation on sequential oxidation is most prominent in the 6-aza-derivatives. The results not only deepen our understanding of substrate oxidation by iron-oxido species but also pave the way for future studies on related biological oxidation mechanisms.
