On March 26, 2020, Jeong, Ye Eun Rebecca; Lenz, Stefan A. P.; Wetmore, Stacey D. published an article.Reference of 5-(Hydroxymethyl)pyrimidine-2,4(1H,3H)-dione The title of the article was DFT Study on the Deglycosylation of Methylated, Oxidized, and Canonical Pyrimidine Nucleosides in Water: Implications for Epigenetic Regulation and DNA Repair. And the article contained the following:
D. functional theory (B3LYP) was used to characterize the kinetics and thermodn. of the (nonenzymic) deglycosylation in water for a variety of 2′-deoxycytidine (dC) and 2′-deoxyuridine (dU) nucleoside derivatives that differ in methylation and subsequent oxidation of the C5 substituent. A range of computational models are considered that combine implicit and explicit solvation of the nucleophile and nucleobase. Regardless of the model implemented, our calculations reveal that the glycosidic bond in dC is inherently more stable than that in dU. Furthermore, C5 methylation of either pyrimidine and subsequent oxidation of the Me group yield overall small changes to the Gibbs reaction energy profiles and thereby preserve lower deglycosylation barriers for the dC compared to those for the dU nucleoside derivatives However, hydrolytic deglycosylation becomes significantly more energetically favorable when 5-methyl-dC (5m-dC) undergoes two or three rounds of oxidation, with the Gibbs energy barrier decreasing and the reaction becoming more exergonic by up to 40 kJ/mol. In fact, two or three oxidation reactions from 5m-dC result in a deglycosylation barrier similar to that for dU, as well as those for the associated C5-methylated (2′-deoxythymidine) and oxidized (5-hydroxymethyl-dU) derivatives These predicted trends in the inherent deglycosylation energetics in water directly correlate with the previously reported activity of thymine DNA glycosylase (TDG), which cleaves the glycosidic bond in select dC nucleosides as part of epigenetic regulation and in dU variants as part of DNA repair. Thus, our data suggests that fundamental differences in the intrinsic reactivity of the pyrimidine nucleosides help regulate the function of human enzymes that maintain cellular integrity. The experimental process involved the reaction of 5-(Hydroxymethyl)pyrimidine-2,4(1H,3H)-dione(cas: 4433-40-3).Reference of 5-(Hydroxymethyl)pyrimidine-2,4(1H,3H)-dione
The Article related to methylated oxidized canonical pyrimidine nucleoside hydrolytic deglycosylation dft, epigenetics dna repair pyrimidine nucleoside hydrolytic deglycosylation dft, General Biochemistry: Nucleic Acids and Their Constituents and other aspects.Reference of 5-(Hydroxymethyl)pyrimidine-2,4(1H,3H)-dione
Referemce:
Pyrimidine | C4H4N2 – PubChem,
Pyrimidine – Wikipedia