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bioRxiv · 10.1101/2021.11.28.470279

Processing of oxidatively damaged DNA dirty ends by APE1

Whitaker, A. M.·Stark, W. J.·Freudenthal, B. D.
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Abstract

Reactive oxygen species attack the structure of DNA, thus altering its base-pairing properties. Consequently, oxidative stress-associated DNA lesions are a major source of the mutation load that gives rise to cancer and other diseases. Base excision repair (BER) is the pathway primarily tasked with repairing DNA base damage, with apurinic/apyrimidinic endonuclease (APE1) having both AP-endonuclease and 3 to 5 exonuclease (exo) DNA cleavage functions. The lesion 8-oxo-7,8-dihydroguanine (8-oxoG) can enter the genome as either a product of direct damage to the DNA, or through polymerase insertion at the 3-end of a DNA strand during replication or repair. Importantly, 3-8-oxoG impairs the ligation step of BER and therefore must be removed by the exo activity of a surrogate enzyme to prevent double stranded breaks and cell death. In the present study, we characterize the exo activity of APE1 on 3-8-oxoG substrates. These structures demonstrate that APE1 uses a unified mechanism for its exo activities that differs from its more canonical AP-endonuclease activity. In addition, through complementation of the structural data with enzyme kinetics and binding studies employing both wild-type and rationally designed APE1 mutants, we were able to identify and characterize unique protein:DNA contacts that specifically mediate 8-oxoG removal by APE1.

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Whitaker, A. M., Stark, W. J., Freudenthal, B. D.. 2021-11-29. Processing of oxidatively damaged DNA dirty ends by APE1. https://doi.org/10.1101/2021.11.28.470279

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