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APE1 Activity is Controlled by Non-G-Quadruplex Conformations in Single- and Double-Stranded G-Quadruplex Constructs.

Brianna L Trabucco1, Aaron M Fleming1, Cynthia J Burrows1

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Chemistry (Weinheim an Der Bergstrasse, Germany)
|December 17, 2025
PubMed
Summary
This summary is machine-generated.

Apurinic/apyrimidinic endonuclease-1 (APE1) efficiently cleaves noncanonical DNA structures, not just standard duplexes. Its activity decreases with increased G-quadruplex folding, showing structure controls repair enzyme function.

Keywords:
APE1Abasic sitesDNA damageG‐quadruplexesendonucleases

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Area of Science:

  • Biochemistry
  • Molecular Biology
  • DNA Repair

Background:

  • Apurinic/apyrimidinic endonuclease-1 (APE1) is a key DNA repair enzyme.
  • APE1 typically cleaves abasic (AP) sites in duplex DNA.
  • Previous studies indicated reduced APE1 activity on single-stranded G-quadruplexes (ssG4).

Purpose of the Study:

  • To investigate the in vitro activity of APE1 on noncanonical DNA structures, specifically G-quadruplexes.
  • To determine how G-quadruplex folding affects APE1 endonuclease activity.
  • To clarify the cleavage efficiency of APE1 on non-G4 conformations within G4-like structures.

Main Methods:

  • Circular dichroism (CD) spectroscopy to analyze DNA structure.
  • In vitro activity assays to measure APE1 cleavage rates.
  • Studies on various scaffolds including AP-containing ssG4 and duplex-embedded G4 (DGD).

Main Results:

  • APE1 efficiently cleaves AP sites in noncanonical, non-G4 conformations of G4-like structures.
  • Cleavage yields were comparable to those on duplex DNA substrates.
  • APE1 activity significantly decreased with increasing G-quadruplex folding in both ssG4 and DGD systems.
  • A positional dependency of cleavage yield was observed in non-G4 DGD scaffolds.

Conclusions:

  • APE1 demonstrates efficient cleavage of noncanonical DNA conformations.
  • The secondary structure of DNA, particularly G-quadruplex folding, critically controls APE1 endonuclease activity.
  • This highlights the enzyme's ability to act on structurally diverse DNA substrates beyond canonical duplexes.