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Quantitative parameters of the 3′–5′ exonuclease reaction of human apurinic/apyrimidinic endonuclease 1 with nicked DNA containing dYMP or a modified dCMP analogue

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Abstract

Human apurinic/apyrimidinic (AP) endonuclease 1 (APE1) is a multifunctional enzyme. In addition to its main AP endonuclease activity, that incises DNA 5′ to the AP-site, it possesses other weak enzymatic activities. One of them is 3′–5′ exonuclease activity, which is most effectively exhibited for DNA duplexes containing modified or mismatched nucleotides at the 3′-end of the primer chain. There is a presumption that APE1 can correct the DNA synthesis catalyzed by DNA polymerase β through the base excision repair process. We determined the quantitative parameters of the 3′–5′ exonuclease reaction in dependence on the reaction conditions to reveal the detailed mechanism of this process. The kinetic parameters of APE1 exonuclease excision of mismatched dCMP and dTMP from the 3′ terminus of single-strand DNA and of photoreactive dCMP analogues applied for photoaffinity modification of proteins and DNA in recombinant systems and cell/nuclear extracts were determined.

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Abbreviations

AP site:

apurinic/apyrimidinic site

APE1:

human apurinic/apyrimidinic (AP) endonuclease 1 (EC 3.1.22.3)

BER:

DNA base excision reparation

NIR:

DNA nucleotide incision repair

F:

3-hydroxy-2-hydroxymethyltetrahydrofuran

5′-pF:

a group at the 5′-terminus of oligonucleotide in the nicked singlestrand DNA with a residue of 3-hydroxy-2-hydroxymethyltetrahydrofuran 2-phosphate.

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Authors and Affiliations

  1. Institute of Chemical Biology and Fundamental Medicine, Siberian Branch, Russian Academy of Sciences, pr. Akademika Lavrent’eva 8, Novosibirsk, 630090, Russia

    N. S. Dyrkheeva, S. N. Khodyreva & O. I. Lavrik

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  1. N. S. Dyrkheeva
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  2. S. N. Khodyreva
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  3. O. I. Lavrik
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Correspondence to O. I. Lavrik.

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Original Russian Text © N.S. Dyrkheeva, S.N. Khodyreva, O.I. Lavrik, 2008, published in Bioorganicheskaya Khimiya, 2008, Vol. 34, No. 2, pp. 210–219.

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Dyrkheeva, N.S., Khodyreva, S.N. & Lavrik, O.I. Quantitative parameters of the 3′–5′ exonuclease reaction of human apurinic/apyrimidinic endonuclease 1 with nicked DNA containing dYMP or a modified dCMP analogue. Russ J Bioorg Chem 34, 192–200 (2008). https://doi.org/10.1134/S1068162008020088

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  • DOI: https://doi.org/10.1134/S1068162008020088

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