{"doi":"10.1101/2020.01.16.909549","title":"Impact of DNA sequences in the DNA duplex opening by the Rad4/XPC nucleotide excision repair complex","abstract":"ABSTRACT Rad4/XPC is a key DNA damage sensor for nucleotide excision repair (NER) in eukaryotes. Rad4/XPC recognizes diverse bulky lesions by flipping out two lesion-containing nucleotide pairs and inserting a β-hairpin from the BHD3 domain (β-hairpin3) into the DNA duplex. We have previously observed that Rad4 can form the same ‘open’ structure when covalently tethered to a normal DNA sequence containing consecutive C/G’s (CCC/GGG) and that a similar open-like structure can be formed even when the β-hairpin3 is lacking. Here, we report a crystal structure of the Δβ-hairpin3 mutant tethered to a sequence containing alternating C/G’s (CGC/GCG). In contrast to the previous structures, Rad4 bound to CGC/GCG in a 180°-reversed manner, capping the end of the duplex without flipping out the nucleotides. MD simulations showed that CGC/GCG was inherently less ‘openable’ than CCC/GGG and that Rad4 failed to engage with its minor groove, a hallmark of productive binding towards ‘opening’. These results reveal that DNA sequences significantly influence the thermodynamic barrier for DNA opening by Rad4, which may render certain DNA structures/sequences resistant to ‘opening’ despite a long residence time of Rad4. The reverse- mode may indicate unproductive binding for NER whereas the DNA end-binding may hint at Rad4/XPC’s functions beyond NER.","journal":"bioRxiv (Cold Spring Harbor Laboratory)","year":2020,"id":126164,"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":1,"citer_count":0,"citers_with_citation_signal":0,"citers_with_endowment":0,"datacite_reuse_total":0,"is_dataset":false,"is_dataset_confidence":0.9525,"is_data_producer":false,"deposit_databanks":null,"is_oa":true,"file_count":0,"downloads":0,"has_version_chain":false,"published_date":"2020-01-01","fair_score":null,"fair_percentile":null,"algorithm_id":"datarank_citation_only_1hop_v6","ranking_scope":"data_only","authors":[{"id":415072,"name":"Hong Mu","orcid":null,"position":1,"is_corresponding":false},{"id":233670,"name":"Qing Dai","orcid":"0000-0002-8578-1568","position":2,"is_corresponding":false},{"id":414269,"name":"Amirrasoul Tavakoli","orcid":"0000-0002-7991-9858","position":3,"is_corresponding":false},{"id":21408,"name":"Chuan He","orcid":"0000-0003-4319-7424","position":4,"is_corresponding":false},{"id":414272,"name":"Suse Broyde","orcid":"0000-0002-3802-7511","position":5,"is_corresponding":false},{"id":573565,"name":"Jung Min","orcid":"0000-0002-4925-3880","position":6,"is_corresponding":false},{"id":414268,"name":"Debamita Paul","orcid":"0000-0003-4535-9642","position":0,"is_corresponding":true}],"reference_count":69,"raw_metadata":null,"created_at":"2026-07-18T23:15:23.509897Z","pmid":null,"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":[]}