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Repair and DNA Polymerase Bypass of Clickable Pyrimidine Nucleotides.
Endutkin, Anton V; Yudkina, Anna V; Zharkov, Timofey D; Barmatov, Alexander E; Petrova, Daria V; Kim, Daria V; Zharkov, Dmitry O.
Affiliation
  • Endutkin AV; Siberian Branch of the Russian Academy of Sciences Institute of Chemical Biology and Fundamental Medicine, 8 Lavrentieva Ave., 630090 Novosibirsk, Russia.
  • Yudkina AV; Siberian Branch of the Russian Academy of Sciences Institute of Chemical Biology and Fundamental Medicine, 8 Lavrentieva Ave., 630090 Novosibirsk, Russia.
  • Zharkov TD; Siberian Branch of the Russian Academy of Sciences Institute of Chemical Biology and Fundamental Medicine, 8 Lavrentieva Ave., 630090 Novosibirsk, Russia.
  • Barmatov AE; Siberian Branch of the Russian Academy of Sciences Institute of Chemical Biology and Fundamental Medicine, 8 Lavrentieva Ave., 630090 Novosibirsk, Russia.
  • Petrova DV; Siberian Branch of the Russian Academy of Sciences Institute of Chemical Biology and Fundamental Medicine, 8 Lavrentieva Ave., 630090 Novosibirsk, Russia.
  • Kim DV; Siberian Branch of the Russian Academy of Sciences Institute of Chemical Biology and Fundamental Medicine, 8 Lavrentieva Ave., 630090 Novosibirsk, Russia.
  • Zharkov DO; Siberian Branch of the Russian Academy of Sciences Institute of Chemical Biology and Fundamental Medicine, 8 Lavrentieva Ave., 630090 Novosibirsk, Russia.
Biomolecules ; 14(6)2024 Jun 12.
Article de En | MEDLINE | ID: mdl-38927084
ABSTRACT
Clickable nucleosides, most often 5-ethynyl-2'-deoxyuridine (EtU), are widely used in studies of DNA replication in living cells and in DNA functionalization for bionanotechology applications. Although clickable dNTPs are easily incorporated by DNA polymerases into the growing chain, afterwards they might become targets for DNA repair systems or interfere with faithful nucleotide insertion. Little is known about the possibility and mechanisms of these post-synthetic events. Here, we investigated the repair and (mis)coding properties of EtU and two bulkier clickable pyrimidine nucleosides, 5-(octa-1,7-diyn-1-yl)-U (C8-AlkU) and 5-(octa-1,7-diyn-1-yl)-C (C8-AlkC). In vitro, EtU and C8-AlkU, but not C8-AlkC, were excised by SMUG1 and MBD4, two DNA glycosylases from the base excision repair pathway. However, when placed into a plasmid encoding a fluorescent reporter inactivated by repair in human cells, EtU and C8-AlkU persisted for much longer than uracil or its poorly repairable phosphorothioate-flanked derivative. DNA polymerases from four different structural families preferentially bypassed EtU, C8-AlkU and C8-AlkC in an error-free manner, but a certain degree of misincorporation was also observed, especially evident for DNA polymerase ß. Overall, clickable pyrimidine nucleotides could undergo repair and be a source of mutations, but the frequency of such events in the cell is unlikely to be considerable.
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Texte intégral: 1 Collection: 01-internacional Base de données: MEDLINE Sujet principal: Nucléotides pyrimidiques / Réparation de l'ADN / Chimie click Limites: Humans Langue: En Journal: Biomolecules Année: 2024 Type de document: Article Pays d'affiliation: Russie Pays de publication: Suisse

Texte intégral: 1 Collection: 01-internacional Base de données: MEDLINE Sujet principal: Nucléotides pyrimidiques / Réparation de l'ADN / Chimie click Limites: Humans Langue: En Journal: Biomolecules Année: 2024 Type de document: Article Pays d'affiliation: Russie Pays de publication: Suisse