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The Chili RNA aptamer mimics large Stokes shift fluorescent proteins and exhibits high affinity for 3,5-dimethoxy-4-hydroxybenzylidene imidazolone (DMHBI) derivatives to elicit green or red fluorescence emission. Here, we elucidate the structural and mechanistic basis of fluorescence activation by crystallography and time-resolved optical spectroscopy. Two co-crystal structures of the Chili RNA with positively charged DMHBO\n                    <jats:sup>+<\/jats:sup>\n                    and DMHBI\n                    <jats:sup>+<\/jats:sup>\n                    ligands revealed a G-quadruplex and a\n                    <jats:italic>trans<\/jats:italic>\n                    -sugar-sugar edge G:G base pair that immobilize the ligand by \u03c0-\u03c0 stacking. A Watson-Crick G:C base pair in the fluorophore binding site establishes a short hydrogen bond between the N7 of guanine and the phenolic OH of the ligand. Ultrafast excited state proton transfer (ESPT) from the neutral chromophore to the RNA was found with a time constant of 130\u2009fs and revealed the mode of action of the large Stokes shift fluorogenic RNA aptamer.\n                  <\/jats:p>","DOI":"10.1038\/s41467-021-23932-0","type":"journal-article","created":{"date-parts":[[2021,6,10]],"date-time":"2021-06-10T06:04:33Z","timestamp":1623305073000},"update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":58,"title":["Large Stokes shift fluorescence activation in an RNA aptamer by intermolecular proton transfer to guanine"],"prefix":"10.1038","volume":"12","author":[{"given":"Mateusz","family":"Mieczkowski","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Christian","family":"Steinmetzger","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Irene","family":"Bessi","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Ann-Kathrin","family":"Lenz","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Alexander","family":"Schmiedel","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Marco","family":"Holzapfel","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-9652-9165","authenticated-orcid":false,"given":"Christoph","family":"Lambert","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Vladimir","family":"Pena","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-4548-2299","authenticated-orcid":false,"given":"Claudia","family":"H\u00f6bartner","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"297","published-online":{"date-parts":[[2021,6,10]]},"reference":[{"key":"23932_CR1","doi-asserted-by":"publisher","first-page":"e8","DOI":"10.1017\/S0033583519000064","volume":"52","author":"RJ Trachman","year":"2019","unstructured":"Trachman, R. 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