{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,8,1]],"date-time":"2026-08-01T11:48:50Z","timestamp":1785584930977,"version":"3.56.0"},"reference-count":40,"publisher":"Oxford University Press (OUP)","issue":"14","license":[{"start":{"date-parts":[[2024,7,1]],"date-time":"2024-07-01T00:00:00Z","timestamp":1719792000000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by-nc\/4.0\/"}],"funder":[{"DOI":"10.13039\/100000002","name":"NIH","doi-asserted-by":"publisher","award":["NIH P30 GM124165"],"award-info":[{"award-number":["NIH P30 GM124165"]}],"id":[{"id":"10.13039\/100000002","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100000038","name":"Natural Sciences and Engineering Research Council of Canada","doi-asserted-by":"publisher","award":["2019-06368"],"award-info":[{"award-number":["2019-06368"]}],"id":[{"id":"10.13039\/501100000038","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100000038","name":"Natural Sciences and Engineering Research Council of Canada","doi-asserted-by":"publisher","award":["2022-03628"],"award-info":[{"award-number":["2022-03628"]}],"id":[{"id":"10.13039\/501100000038","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100016958","name":"NIH-ORIP","doi-asserted-by":"publisher","award":["S10 RR029205"],"award-info":[{"award-number":["S10 RR029205"]}],"id":[{"id":"10.13039\/100016958","id-type":"DOI","asserted-by":"publisher"}]},{"name":"Unrau's NSERC"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2024,8,12]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>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\u2013ligand 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.<\/jats:p>","DOI":"10.1093\/nar\/gkae493","type":"journal-article","created":{"date-parts":[[2024,7,1]],"date-time":"2024-07-01T00:02:43Z","timestamp":1719792163000},"page":"8039-8051","source":"Crossref","is-referenced-by-count":11,"title":["Symmetry breaking of fluorophore binding to a G-quadruplex generates an RNA aptamer with picomolar <i>KD<\/i>"],"prefix":"10.1093","volume":"52","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-8269-3837","authenticated-orcid":false,"given":"Xiaocen","family":"Lu","sequence":"first","affiliation":[{"name":"Department of Molecular Biology and Biochemistry, Simon Fraser University , Burnaby, British Columbia V5A 1S6, Canada"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-5490-2427","authenticated-orcid":false,"given":"Luiz\u00a0F M","family":"Passalacqua","sequence":"additional","affiliation":[{"name":"Laboratory of Nucleic Acids, National Heart, Lung and Blood Institute , Bethesda , MD\u00a020892 , USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Matthew","family":"Nodwell","sequence":"additional","affiliation":[{"name":"Department of Chemistry, Simon Fraser University , Burnaby, British Columbia V5A 1S6, Canada"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-5647-9565","authenticated-orcid":false,"given":"Kristen\u00a0Y S","family":"Kong","sequence":"additional","affiliation":[{"name":"Department of Molecular Biology and Biochemistry, Simon Fraser University , Burnaby, British Columbia V5A 1S6, Canada"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-5776-0591","authenticated-orcid":false,"given":"Guillermo","family":"Caballero-Garc\u00eda","sequence":"additional","affiliation":[{"name":"Department of Chemistry, Simon Fraser University , Burnaby, British Columbia V5A 1S6, Canada"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-8262-9299","authenticated-orcid":false,"given":"Elena\u00a0V","family":"Dolgosheina","sequence":"additional","affiliation":[{"name":"Department of Molecular Biology and Biochemistry, Simon Fraser University , Burnaby, British Columbia V5A 1S6, Canada"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-4549-1619","authenticated-orcid":false,"given":"Adrian\u00a0R","family":"Ferr\u00e9-D\u2019Amar\u00e9","sequence":"additional","affiliation":[{"name":"Laboratory of Nucleic Acids, National Heart, Lung and Blood Institute , Bethesda , MD\u00a020892 , USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-9335-0047","authenticated-orcid":false,"given":"Robert","family":"Britton","sequence":"additional","affiliation":[{"name":"Department of Chemistry, Simon Fraser University , Burnaby, British Columbia V5A 1S6, Canada"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-1392-6948","authenticated-orcid":false,"given":"Peter\u00a0J","family":"Unrau","sequence":"additional","affiliation":[{"name":"Department of Molecular Biology and Biochemistry, Simon Fraser University , Burnaby, British Columbia V5A 1S6, Canada"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"286","published-online":{"date-parts":[[2024,7,1]]},"reference":[{"key":"2024081123565794400_B1","doi-asserted-by":"crossref","first-page":"820","DOI":"10.1126\/science.287.5454.820","article-title":"Adaptive recognition by nucleic acid aptamers","volume":"287","author":"Hermann","year":"2000","journal-title":"Science"},{"key":"2024081123565794400_B2","doi-asserted-by":"crossref","first-page":"4071","DOI":"10.1039\/D3CS00030C","article-title":"Harmonizing the growing fluorogenic RNA aptamer toolbox for RNA detection and imaging","volume":"52","author":"Lu","year":"2023","journal-title":"Chem. 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