{"doi":"10.1101/2021.01.05.425498","title":"Kinetic and structural mechanism for DNA unwinding by a non-hexameric helicase","abstract":"Abstract UvrD, a model for non-hexameric Superfamily 1 helicases, utilizes ATP hydrolysis to translocate stepwise along single-stranded DNA and unwind the duplex. To dissect the mechanism underlying DNA unwinding, we use optical tweezers to measure directly the stepping behavior of UvrD as it processes a DNA hairpin and show that UvrD exhibits a variable step size averaging ~3 base pairs. Analyzing stepping kinetics across ATP reveals the type and number of catalytic events that occur with different step sizes. These single-molecule data reveal a mechanism in which UvrD moves one base pair at a time but sequesters the nascent single strands, releasing them non-uniformly after a variable number of catalytic cycles. Molecular dynamics simulations point to a structural basis for this behavior, identifying the protein-DNA interactions responsible for strand sequestration. Based on structural and sequence alignment data, we propose that this stepping mechanism may be conserved among other non-hexameric helicases.","journal":"bioRxiv (Cold Spring Harbor Laboratory)","year":2021,"id":222915,"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":0.954,"is_data_producer":false,"deposit_databanks":null,"is_oa":true,"file_count":0,"downloads":0,"has_version_chain":false,"published_date":"2021-01-01","fair_score":null,"fair_percentile":null,"algorithm_id":"datarank_citation_only_1hop_v6","ranking_scope":"data_only","authors":[{"id":484369,"name":"Wen Ma","orcid":"0000-0002-1123-5273","position":1,"is_corresponding":false},{"id":744741,"name":"Kevin D. Whitley","orcid":"0000-0001-9719-6916","position":2,"is_corresponding":false},{"id":744742,"name":"Haifeng Jia","orcid":"0000-0002-8092-9033","position":3,"is_corresponding":false},{"id":418459,"name":"Timothy M. Lohman","orcid":"0000-0001-6616-2967","position":4,"is_corresponding":false},{"id":254091,"name":"Zaida Luthey‐Schulten","orcid":"0000-0001-9749-8367","position":5,"is_corresponding":false},{"id":284454,"name":"Yann R. Chemla","orcid":"0000-0001-9167-0234","position":6,"is_corresponding":false},{"id":745406,"name":"Sean P. Carney","orcid":null,"position":0,"is_corresponding":true}],"reference_count":65,"raw_metadata":null,"created_at":"2026-07-18T23:54:07.287704Z","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":[]}