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Molecules 2018, 23(9), 2101; https://doi.org/10.3390/molecules23092101

Kinetic Features of 3′-5′ Exonuclease Activity of Human AP-Endonuclease APE1

1
Institute of Chemical Biology and Fundamental Medicine (ICBFM), Siberian Branch of Russian Academy of Sciences, Novosibirsk 630090, Russia
2
Department of Natural Sciences, Novosibirsk State University, 2 Pirogova St., Novosibirsk 630090, Russia
*
Authors to whom correspondence should be addressed.
Received: 19 July 2018 / Revised: 2 August 2018 / Accepted: 16 August 2018 / Published: 21 August 2018
(This article belongs to the Special Issue Protein-DNA Interactions: From Biophysics to Genomics)
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Abstract

Human apurinic/apyrimidinic (AP)-endonuclease APE1 is one of the key enzymes taking part in the repair of damage to DNA. The primary role of APE1 is the initiation of the repair of AP-sites by catalyzing the hydrolytic incision of the phosphodiester bond immediately 5′ to the damage. In addition to the AP-endonuclease activity, APE1 possesses 3′-5′ exonuclease activity, which presumably is responsible for cleaning up nonconventional 3′ ends that were generated as a result of DNA damage or as transition intermediates in DNA repair pathways. In this study, the kinetic mechanism of 3′-end nucleotide removal in the 3′-5′ exonuclease process catalyzed by APE1 was investigated under pre-steady-state conditions. DNA substrates were duplexes of deoxyribonucleotides with one 5′ dangling end and it contained a fluorescent 2-aminopurine residue at the 1st, 2nd, 4th, or 6th position from the 3′ end of the short oligonucleotide. The impact of the 3′-end nucleotide, which contained mismatched, undamaged bases or modified bases as well as an abasic site or phosphate group, on the efficiency of 3′-5′ exonuclease activity was determined. Kinetic data revealed that the rate-limiting step of 3′ nucleotide removal by APE1 in the 3′-5′ exonuclease process is the release of the detached nucleotide from the enzyme’s active site. View Full-Text
Keywords: AP-endonuclease; DNA repair; exonuclease activity; pre-steady-state kinetics AP-endonuclease; DNA repair; exonuclease activity; pre-steady-state kinetics
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Kuznetsova, A.A.; Fedorova, O.S.; Kuznetsov, N.A. Kinetic Features of 3′-5′ Exonuclease Activity of Human AP-Endonuclease APE1. Molecules 2018, 23, 2101.

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