{"doi":"10.1093/nar/gkae874","title":"A compact stem-loop DNA aptamer targets a uracil-binding pocket in the SARS-CoV-2 nucleocapsid RNA-binding domain","abstract":"SARS-CoV-2 nucleocapsid (N) protein is a structural component of the virus with essential roles in the replication and packaging of the viral RNA genome. The N protein is also an important target of COVID-19 antigen tests and a promising vaccine candidate along with the spike protein. Here, we report a compact stem-loop DNA aptamer that binds tightly to the N-terminal RNA-binding domain of SARS-CoV-2 N protein. Crystallographic analysis shows that a hexanucleotide DNA motif (5'-TCGGAT-3') of the aptamer fits into a positively charged concave surface of N-NTD and engages essential RNA-binding residues including Tyr109, which mediates a sequence-specific interaction in a uracil-binding pocket. Avid binding of the DNA aptamer allows isolation and sensitive detection of full-length N protein from crude cell lysates, demonstrating its selectivity and utility in biochemical applications. We further designed a chemically modified DNA aptamer and used it as a probe to examine the interaction of N-NTD with various RNA motifs, which revealed a strong preference for uridine-rich sequences. Our studies provide a high-affinity chemical probe for the SARS-CoV-2 N protein RNA-binding domain, which may be useful for diagnostic applications and investigating novel antiviral agents.","journal":"Nucleic Acids Research","year":2024,"id":426194,"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":18,"citer_count":0,"citers_with_citation_signal":0,"citers_with_endowment":0,"datacite_reuse_total":0,"is_dataset":false,"is_dataset_confidence":0.9569,"is_data_producer":false,"deposit_databanks":null,"is_oa":true,"file_count":0,"downloads":0,"has_version_chain":false,"published_date":"2024-01-01","fair_score":null,"fair_percentile":null,"algorithm_id":"datarank_citation_only_1hop_v6","ranking_scope":"data_only","authors":[{"id":805260,"name":"Christopher Belica","orcid":"0000-0001-8492-4427","position":1,"is_corresponding":false},{"id":1225602,"name":"Joseph A. Rollie","orcid":null,"position":2,"is_corresponding":false},{"id":940196,"name":"William L. Brown","orcid":"0000-0002-3398-2042","position":3,"is_corresponding":false},{"id":879896,"name":"Seyed Arad Moghadasi","orcid":"0000-0001-6598-8994","position":4,"is_corresponding":false},{"id":103757,"name":"Ke Shi","orcid":"0000-0003-4175-3714","position":5,"is_corresponding":false},{"id":458585,"name":"Daniel A. Harki","orcid":"0000-0001-5950-931X","position":6,"is_corresponding":false},{"id":257763,"name":"Reuben S. Harris","orcid":"0000-0002-9034-9112","position":7,"is_corresponding":false},{"id":103759,"name":"Hideki Aihara","orcid":"0000-0001-7508-6230","position":8,"is_corresponding":false},{"id":882410,"name":"Morgan A. Esler","orcid":"0000-0002-5570-385X","position":0,"is_corresponding":true}],"reference_count":49,"raw_metadata":null,"created_at":"2026-07-19T01:58:37.924718Z","pmid":"39380503","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":[]}