Reactivity of damaged pyrimidines: formation of a Schiff base intermediate at the glycosidic bond of saturated dihydrouridine

Yajun Jian , Gengjie Lin , Lidia Chomicz , Lei Li


DNA glycosylases catalyze the first step of the base excision repair (BER) pathway. The chemistry used by these enzymes for deglycosylation has been largely considered as the chemistry of the oxocarbenium ion, e.g., direct rupture of the C1′–N1 bond resulting in an oxocarbenium ion intermediate. Here we present mechanistic studies revealing the 2′-deoxyribose isomerization and subsequent deglycosylation processes in two pyrimidine lesions: 5,6-dihydro-2′-deoxyuridine (dHdU) and 5,6-dihydrothymidine (dHT), formed via ionizing radiation damage to 2′-deoxycytidine and thymidine, respectively, under anoxic conditions. Acid or heat treatment of these two lesions leads to the production of two pairs of C1′ epimers containing a pyranose and a furanose, respectively, indicating that both lesions favor the rupture of the C1′–O4′ bond, resulting in a Schiff base intermediate at the N-glycosidic bond. Such a Schiff base intermediate was trapped and characterized by either Pd-catalyzed hydrogenation or thiol-mediated addition reaction. In contrast, in undamaged 2′-deoxyuridine and thymidine, reactions at elevated temperatures lead to the release of nucleobases most likely via the traditional oxocarbenium ion pathway. DFT calculations further support the experimental findings, suggesting that the oxocarbenium ion intermediate is responsible for the deglycosylation process if the integrity of the pyrimidine ring is maintained, while the Schiff base intermediate is preferred if the C5═C6 bond is saturated. Currently, the oxocarbenium ion pathway is indicated to be solely responsible for the deglycosylation in BER enzymes, however our results suggest an alternative Schiff base mechanism which may be responsible for the repair of saturated pyrimidine damages.
Author Yajun Jian
Yajun Jian,,
, Gengjie Lin
Gengjie Lin,,
, Lidia Chomicz (FCh/DPCh/LBS)
Lidia Chomicz,,
- Laboratory of Biological Sensitizers
, Lei Li
Lei Li,,
Journal seriesJournal of the American Chemical Society, ISSN 0002-7863, (A 45 pkt)
Issue year2015
Publication size in sheets0.55
ASJC Classification1505 Colloid and Surface Chemistry; 1303 Biochemistry; 1600 General Chemistry; 1503 Catalysis
Languageen angielski
Score (nominal)45
Score sourcejournalList
ScoreMinisterial score = 40.0, 28-04-2020, ArticleFromJournal
Ministerial score (2013-2016) = 45.0, 28-04-2020, ArticleFromJournal
Publication indicators WoS Citations = 4.000; Scopus SNIP (Source Normalised Impact per Paper): 2015 = 2.600; WoS Impact Factor: 2015 = 13.038 (2) - 2015=12.376 (5)
Citation count*5 (2020-08-06)
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* presented citation count is obtained through Internet information analysis and it is close to the number calculated by the Publish or Perish system.
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