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The chemical probing and MS data for the free riboswitch show high exposure to solvent of the uridine nucleobases <jats:styled-content>U<\/jats:styled-content>7, <jats:styled-content>U<\/jats:styled-content>8, <jats:styled-content>U<\/jats:styled-content>13, <jats:styled-content>U<\/jats:styled-content>14, <jats:styled-content>U<\/jats:styled-content>18 as part of the proposed internal and apical loops, but those of <jats:styled-content>U<\/jats:styled-content>10 and <jats:styled-content>U<\/jats:styled-content>21 as part of the proposed internal loop were found to be far less exposed than expected. Thus, our data are in better agreement with the proposed secondary structure of the riboswitch in complexes with aminoglycosides than with that of free RNA. For the riboswitch in complexes with neomycin B, ribostamycin, and paromomycin, we found highly similar CMC<jats:sup>+<\/jats:sup>\u2010modification patterns and excellent agreement with previous NMR studies. Differences between the chemical probing and MS data in the absence and presence of the aminoglycoside ligands were quantitative rather than qualitative (i.\u2009e., the same nucleobases were labeled, but to different extents) and can be rationalized by stabilization of both the proposed bulge and the apical loop by aminoglycoside binding. Our study shows that chemical probing and mass spectrometry can provide important structural information and complement other techniques such as NMR spectroscopy.<\/jats:p>","DOI":"10.1002\/cplu.202200256","type":"journal-article","created":{"date-parts":[[2022,10,11]],"date-time":"2022-10-11T21:14:29Z","timestamp":1665522869000},"update-policy":"https:\/\/doi.org\/10.1002\/crossmark_policy","source":"Crossref","is-referenced-by-count":6,"title":["RNA Chemical Labeling with Site\u2010Specific, Relative Quantification by Mass Spectrometry for the Structural Study of a Neomycin\u2010Sensing Riboswitch Aptamer Domain"],"prefix":"10.1002","volume":"87","author":[{"given":"Michael","family":"Palasser","sequence":"first","affiliation":[{"name":"Institut of Organic Chemistry and Center for Molecular Biosciences Innsbruck (CMBI) University of Innsbruck  Innrain 80\/82 6020 Innsbruck Austria"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-4978-0883","authenticated-orcid":false,"given":"Kathrin","family":"Breuker","sequence":"additional","affiliation":[{"name":"Institut of Organic Chemistry and Center for Molecular Biosciences Innsbruck (CMBI) University of Innsbruck  Innrain 80\/82 6020 Innsbruck Austria"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"311","published-online":{"date-parts":[[2022,10,11]]},"reference":[{"key":"e_1_2_8_1_1","doi-asserted-by":"publisher","DOI":"10.1021\/acs.chemrev.1c00386"},{"key":"e_1_2_8_2_1","author":"Liu R. 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