{"doi":"10.1093/nar/gkae493","title":"Symmetry breaking of fluorophore binding to a G-quadruplex generates an RNA aptamer with picomolar <i>KD</i>","abstract":"Fluorogenic RNA aptamer tags with high affinity enable RNA purification and imaging. The G-quadruplex (G4) based Mango (M) series of aptamers were selected to bind a thiazole orange based (TO1-Biotin) ligand. Using a chemical biology and reselection approach, we have produced a MII.2 aptamer-ligand complex with a remarkable set of properties: Its unprecedented KD of 45 pM, formaldehyde resistance (8% v/v), temperature stability and ligand photo-recycling properties are all unusual to find simultaneously within a small RNA tag. Crystal structures demonstrate how MII.2, which differs from MII by a single A23U mutation, and modification of the TO1-Biotin ligand to TO1-6A-Biotin achieves these results. MII binds TO1-Biotin heterogeneously via a G4 surface that is surrounded by a stadium of five adenosines. Breaking this pseudo-rotational symmetry results in a highly cooperative and homogeneous ligand binding pocket: A22 of the G4 stadium stacks on the G4 binding surface while the TO1-6A-Biotin ligand completely fills the remaining three quadrants of the G4 ligand binding face. Similar optimization attempts with MIII.1, which already binds TO1-Biotin in a homogeneous manner, did not produce such marked improvements. We use the novel features of the MII.2 complex to demonstrate a powerful optically-based RNA purification system.","journal":"Nucleic Acids Research","year":2024,"id":440678,"datarank":0.4733097453141614,"base_score":2.302585092994046,"endowment":2.302585092994046,"self_citation_contribution":0.3453877639491069,"citation_network_contribution":0.1279219813650545,"self_endowment_contribution":0.3453877639491069,"citer_contribution":0.1279219813650545,"corpus_percentile":null,"corpus_rank":null,"citation_count":9,"citer_count":8,"citers_with_citation_signal":5,"citers_with_endowment":5,"datacite_reuse_total":0,"is_dataset":false,"is_dataset_confidence":0.9597,"is_data_producer":true,"deposit_databanks":{"PDB":["8U5J","8U5K","8U5P","8U5R","8U5T","8U5Z","8U60"]},"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":496034,"name":"Luiz F. M. Passalacqua","orcid":"0000-0002-5490-2427","position":1,"is_corresponding":false},{"id":1253116,"name":"Matthew B. Nodwell","orcid":null,"position":2,"is_corresponding":false},{"id":1252620,"name":"Kristen Y. S. Kong","orcid":"0000-0001-5647-9565","position":3,"is_corresponding":false},{"id":1252621,"name":"Guillermo Caballero‐García","orcid":"0000-0002-5776-0591","position":4,"is_corresponding":false},{"id":1252622,"name":"Elena V. Dolgosheina","orcid":"0000-0001-8262-9299","position":5,"is_corresponding":false},{"id":321054,"name":"A.R. Ferré-D′Amaré","orcid":"0000-0003-4549-1619","position":6,"is_corresponding":false},{"id":392239,"name":"Robert Britton","orcid":"0000-0002-9335-0047","position":7,"is_corresponding":false},{"id":478455,"name":"Peter J. Unrau","orcid":"0000-0003-1392-6948","position":8,"is_corresponding":false},{"id":1252619,"name":"Xiaocen Lu","orcid":"0000-0002-8269-3837","position":0,"is_corresponding":true}],"reference_count":43,"raw_metadata":null,"created_at":"2026-07-19T02:01:01.842286Z","pmid":"38945550","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":[]}