Recognition of a Clickable Abasic Site Analog by DNA Polymerases and DNA Repair Enzymes | Sciact - CRIS-system of Boreskov Institute of Catalysis

Recognition of a Clickable Abasic Site Analog by DNA Polymerases and DNA Repair Enzymes Full article

Journal

International Journal of Molecular Sciences
ISSN: 1422-0067 , E-ISSN: 1661-6596

Output data

Year: 2022, Volume: 23, Number: 21, Article number : 13353, Pages count : 14 DOI: 10.3390/ijms232113353

Tags

click chemistry; AP site; DNA repair; AP endonucleases; DNA glycosylases; translesion synthesis; DNA polymerases

Authors

Endutkin Anton V. ¹ , Yudkina Anna V. ¹ , Zharkov Timofey D. ¹ , Kim Daria V. ^1,2 , Zharkov Dmitry O. ^1,2

Affiliations

1	SB RAS Institute of Chemical Biology and Fundamental Medicine, 8 Lavrentieva Ave., Novosibirsk 630090, Russia
2	Department of Natural Sciences, Novosibirsk State University, 2 Pirogova Street, Novosibirsk 630090, Russia

Azide–alkyne cycloaddition (“click chemistry”) has found wide use in the analysis of molecular interactions in living cells. 5-ethynyl-2-(hydroxymethyl)tetrahydrofuran-3-ol (EAP) is a recently developed apurinic/apyrimidinic (AP) site analog functionalized with an ethynyl moiety, which can be introduced into cells in DNA constructs to perform labeling or cross-linking in situ. However, as a non-natural nucleoside, EAP could be subject to removal by DNA repair and misreading by DNA polymerases. Here, we investigate the interaction of this clickable AP site analog with DNA polymerases and base excision repair enzymes. Similarly to the natural AP site, EAP was non-instructive and followed the “A-rule”, directing residual but easily detectable incorporation of dAMP by E. coli DNA polymerase I Klenow fragment, bacteriophage RB69 DNA polymerase and human DNA polymerase β. On the contrary, EAP was blocking for DNA polymerases κ and λ. EAP was an excellent substrate for the major human AP endonuclease APEX1 and E. coli AP exonucleases Xth and Nfo but was resistant to the AP lyase activity of DNA glycosylases. Overall, our data indicate that EAP, once within a cell, would represent a replication block and would be removed through an AP endonuclease-initiated long-patch base excision repair pathway.

Endutkin A.V. , Yudkina A.V. , Zharkov T.D. , Kim D.V. , Zharkov D.O.
Recognition of a Clickable Abasic Site Analog by DNA Polymerases and DNA Repair Enzymes
International Journal of Molecular Sciences. 2022. V.23. N21. 13353 :1-14. DOI: 10.3390/ijms232113353 WOS Scopus AN PMID OpenAlex

Submitted:	Oct 8, 2022
Accepted:	Oct 30, 2022
Published print:	Nov 1, 2022
Published online:	Nov 1, 2022

Web of science:	WOS:000883913000001
Scopus:	2-s2.0-85141605485
Chemical Abstracts:	2022:2897837
PMID:	36362137
OpenAlex:	W4308118433

DB	Citing
OpenAlex	10
Scopus	7
Web of science	7