{"doi":"10.1002/chem.202503023","title":"APE1 Activity is Controlled by Non‐G‐Quadruplex Conformations in Single‐ and Double‐Stranded G‐Quadruplex Constructs","abstract":"Apurinic/apyrimidinic endonuclease-1 (APE1) is a repair enzyme that efficiently cleaves abasic (AP) site damage in duplex DNA. Reports of in vitro activity assays between APE1 and single-stranded G-quadruplex (ssG4) reveal significant decreases in the endonuclease activity. Here, we identify that the low yields observed represent cleavage of the noncanonical folds that did not adopt a complete G4 fold. This conclusion is supported through circular dichroism analysis and activity assays analyzing the cleavage rate, folding impact on cleavage, and product inhibition. Studies were performed on AP-containing ssG4 and duplex-embedded G4 scaffolds. The CD spectra of a non-G4 containing potential quadruplex sequence reveal a noncanonical structure. APE1 can cleave an AP in these non-G4 conformation(s) in high yields comparable to the preferred duplex substrate. There is direct evidence of decreasing APE1 activity with increasing G4 folding in ssG4 and duplex-G-quadruplex-duplex (DGD) systems. Also observed is a positional dependency on yield in the non-G4 DGD scaffolds, but not in the non-G4 ssG4 scaffolds. In conclusion, our studies provide evidence that APE1 efficiently cleaves noncanonical conformations in G4-like structures, highlighting the control of secondary structure on APE1 endonuclease activity.","journal":"Chemistry - A European Journal","year":2025,"id":585530,"datarank":0.0,"base_score":0.0,"endowment":0.0,"self_citation_contribution":0.0,"citation_network_contribution":0.0,"self_endowment_contribution":0.0,"citer_contribution":0.0,"corpus_percentile":null,"corpus_rank":null,"citation_count":0,"citer_count":0,"citers_with_citation_signal":0,"citers_with_endowment":0,"datacite_reuse_total":0,"is_dataset":false,"is_dataset_confidence":0.9566,"is_data_producer":false,"deposit_databanks":null,"is_oa":true,"file_count":0,"downloads":0,"has_version_chain":false,"published_date":"2025-01-01","fair_score":null,"fair_percentile":null,"algorithm_id":"datarank_citation_only_1hop_v6","ranking_scope":"data_only","authors":[{"id":765972,"name":"Aaron M. Fleming","orcid":"0000-0002-2000-0310","position":1,"is_corresponding":false},{"id":765973,"name":"Cynthia J. Burrows","orcid":"0000-0001-7253-8529","position":2,"is_corresponding":false},{"id":1498870,"name":"Brianna L. Trabucco","orcid":"0009-0005-5135-2801","position":0,"is_corresponding":true}],"reference_count":44,"raw_metadata":null,"created_at":"2026-07-19T02:59:20.067334Z","pmid":"41405288","pmcid":null,"fwci":null,"citation_percentile":null,"influential_citations":0,"oa_status":null,"license":null,"views":0,"total_file_size_bytes":0,"version_count":0,"fair_f":null,"fair_a":null,"fair_i":null,"fair_r":null,"fair_zscore":null,"fair_rationale":null,"fair_model":null,"fair_agent_version":null,"fair_fulltext_source":null,"fair_has_llm":null,"fair_computed_at":null,"clinical_trials":[],"software_tools":[],"db_accessions":[],"linked_datasets":[],"topics":[]}