{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,7,10]],"date-time":"2026-07-10T23:06:39Z","timestamp":1783724799900,"version":"3.55.0"},"reference-count":65,"publisher":"Oxford University Press (OUP)","issue":"22","license":[{"start":{"date-parts":[[2016,11,10]],"date-time":"2016-11-10T00:00:00Z","timestamp":1478736000000},"content-version":"vor","delay-in-days":1164,"URL":"http:\/\/creativecommons.org\/licenses\/by\/3.0\/"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2013,12,1]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>Riboswitches are structural elements in the 5\u2032 untranslated regions of many bacterial messenger RNAs that regulate gene expression in response to changing metabolite concentrations by inhibition of either transcription or translation initiation. The preQ1 (7-aminomethyl-7-deazaguanine) riboswitch family comprises some of the smallest metabolite sensing RNAs found in nature. Once ligand-bound, the transcriptional Bacillus subtilis and translational Thermoanaerobacter tengcongensis preQ1 riboswitch aptamers are structurally similar RNA pseudoknots; yet, prior structural studies have characterized their ligand-free conformations as largely unfolded and folded, respectively. In contrast, through single molecule observation, we now show that, at near-physiological Mg2+ concentration and pH, both ligand-free aptamers adopt similar pre-folded state ensembles that differ in their ligand-mediated folding. Structure-based G\u014d-model simulations of the two aptamers suggest that the ligand binds late (Bacillus subtilis) and early (Thermoanaerobacter tengcongensis) relative to pseudoknot folding, leading to the proposal that the principal distinction between the two riboswitches lies in their relative tendencies to fold via mechanisms of conformational selection and induced fit, respectively. These mechanistic insights are put to the test by rationally designing a single nucleotide swap distal from the ligand binding pocket that we find to predictably control the aptamers\u2032 pre-folded states and their ligand binding affinities.<\/jats:p>","DOI":"10.1093\/nar\/gkt798","type":"journal-article","created":{"date-parts":[[2013,9,4]],"date-time":"2013-09-04T01:55:17Z","timestamp":1378259717000},"page":"10462-10475","source":"Crossref","is-referenced-by-count":91,"title":["Single transcriptional and translational preQ1 riboswitches adopt similar pre-folded ensembles that follow distinct folding pathways into the same ligand-bound structure"],"prefix":"10.1093","volume":"41","author":[{"given":"Krishna C.","family":"Suddala","sequence":"first","affiliation":[{"name":"1 Biophysics, University of Michigan, Ann Arbor, MI 48109, USA, 2Single Molecule Analysis Group, University of Michigan, Ann Arbor, MI 48109, USA, 3Department of Chemistry, University of Michigan, Ann Arbor, MI 48109, USA, 4Program in Chemical Biology, University of Michigan, Ann Arbor, MI 48109, USA, 5Department of Biochemistry and Biophysics, Center for RNA Biology, University of Rochester School of Medicine and Dentistry, Rochester, NY 14642, USA and 6Center for Theoretical Biological Physics, University of California San Diego, San Diego, CA 92037, USA"},{"name":"1 Biophysics, University of Michigan, Ann Arbor, MI 48109, USA, 2Single Molecule Analysis Group, University of Michigan, Ann Arbor, MI 48109, USA, 3Department of Chemistry, University of Michigan, Ann Arbor, MI 48109, USA, 4Program in Chemical Biology, University of Michigan, Ann Arbor, MI 48109, USA, 5Department of Biochemistry and Biophysics, Center for RNA Biology, University of Rochester School of Medicine and Dentistry, Rochester, NY 14642, USA and 6Center for Theoretical Biological Physics, University of California San Diego, San Diego, CA 92037, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Arlie J.","family":"Rinaldi","sequence":"additional","affiliation":[{"name":"1 Biophysics, University of Michigan, Ann Arbor, MI 48109, USA, 2Single Molecule Analysis Group, University of Michigan, Ann Arbor, MI 48109, USA, 3Department of Chemistry, University of Michigan, Ann Arbor, MI 48109, USA, 4Program in Chemical Biology, University of Michigan, Ann Arbor, MI 48109, USA, 5Department of Biochemistry and Biophysics, Center for RNA Biology, University of Rochester School of Medicine and Dentistry, Rochester, NY 14642, USA and 6Center for Theoretical Biological Physics, University of California San Diego, San Diego, CA 92037, USA"},{"name":"1 Biophysics, University of Michigan, Ann Arbor, MI 48109, USA, 2Single Molecule Analysis Group, University of Michigan, Ann Arbor, MI 48109, USA, 3Department of Chemistry, University of Michigan, Ann Arbor, MI 48109, USA, 4Program in Chemical Biology, University of Michigan, Ann Arbor, MI 48109, USA, 5Department of Biochemistry and Biophysics, Center for RNA Biology, University of Rochester School of Medicine and Dentistry, Rochester, NY 14642, USA and 6Center for Theoretical Biological Physics, University of California San Diego, San Diego, CA 92037, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jun","family":"Feng","sequence":"additional","affiliation":[{"name":"1 Biophysics, University of Michigan, Ann Arbor, MI 48109, USA, 2Single Molecule Analysis Group, University of Michigan, Ann Arbor, MI 48109, USA, 3Department of Chemistry, University of Michigan, Ann Arbor, MI 48109, USA, 4Program in Chemical Biology, University of Michigan, Ann Arbor, MI 48109, USA, 5Department of Biochemistry and Biophysics, Center for RNA Biology, University of Rochester School of Medicine and Dentistry, Rochester, NY 14642, USA and 6Center for Theoretical Biological Physics, University of California San Diego, San Diego, CA 92037, USA"},{"name":"1 Biophysics, University of Michigan, Ann Arbor, MI 48109, USA, 2Single Molecule Analysis Group, University of Michigan, Ann Arbor, MI 48109, USA, 3Department of Chemistry, University of Michigan, Ann Arbor, MI 48109, USA, 4Program in Chemical Biology, University of Michigan, Ann Arbor, MI 48109, USA, 5Department of Biochemistry and Biophysics, Center for RNA Biology, University of Rochester School of Medicine and Dentistry, Rochester, NY 14642, USA and 6Center for Theoretical Biological Physics, University of California San Diego, San Diego, CA 92037, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Anthony M.","family":"Mustoe","sequence":"additional","affiliation":[{"name":"1 Biophysics, University of Michigan, Ann Arbor, MI 48109, USA, 2Single Molecule Analysis Group, University of Michigan, Ann Arbor, MI 48109, USA, 3Department of Chemistry, University of Michigan, Ann Arbor, MI 48109, USA, 4Program in Chemical Biology, University of Michigan, Ann Arbor, MI 48109, USA, 5Department of Biochemistry and Biophysics, Center for RNA Biology, University of Rochester School of Medicine and Dentistry, Rochester, NY 14642, USA and 6Center for Theoretical Biological Physics, University of California San Diego, San Diego, CA 92037, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Catherine D.","family":"Eichhorn","sequence":"additional","affiliation":[{"name":"1 Biophysics, University of Michigan, Ann Arbor, MI 48109, USA, 2Single Molecule Analysis Group, University of Michigan, Ann Arbor, MI 48109, USA, 3Department of Chemistry, University of Michigan, Ann Arbor, MI 48109, USA, 4Program in Chemical Biology, University of Michigan, Ann Arbor, MI 48109, USA, 5Department of Biochemistry and Biophysics, Center for RNA Biology, University of Rochester School of Medicine and Dentistry, Rochester, NY 14642, USA and 6Center for Theoretical Biological Physics, University of California San Diego, San Diego, CA 92037, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Joseph A.","family":"Liberman","sequence":"additional","affiliation":[{"name":"1 Biophysics, University of Michigan, Ann Arbor, MI 48109, USA, 2Single Molecule Analysis Group, University of Michigan, Ann Arbor, MI 48109, USA, 3Department of Chemistry, University of Michigan, Ann Arbor, MI 48109, USA, 4Program in Chemical Biology, University of Michigan, Ann Arbor, MI 48109, USA, 5Department of Biochemistry and Biophysics, Center for RNA Biology, University of Rochester School of Medicine and Dentistry, Rochester, NY 14642, USA and 6Center for Theoretical Biological Physics, University of California San Diego, San Diego, CA 92037, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Joseph E.","family":"Wedekind","sequence":"additional","affiliation":[{"name":"1 Biophysics, University of Michigan, Ann Arbor, MI 48109, USA, 2Single Molecule Analysis Group, University of Michigan, Ann Arbor, MI 48109, USA, 3Department of Chemistry, University of Michigan, Ann Arbor, MI 48109, USA, 4Program in Chemical Biology, University of Michigan, Ann Arbor, MI 48109, USA, 5Department of Biochemistry and Biophysics, Center for RNA Biology, University of Rochester School of Medicine and Dentistry, Rochester, NY 14642, USA and 6Center for Theoretical Biological Physics, University of California San Diego, San Diego, CA 92037, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Hashim M.","family":"Al-Hashimi","sequence":"additional","affiliation":[{"name":"1 Biophysics, University of Michigan, Ann Arbor, MI 48109, USA, 2Single Molecule Analysis Group, University of Michigan, Ann Arbor, MI 48109, USA, 3Department of Chemistry, University of Michigan, Ann Arbor, MI 48109, USA, 4Program in Chemical Biology, University of Michigan, Ann Arbor, MI 48109, USA, 5Department of Biochemistry and Biophysics, Center for RNA Biology, University of Rochester School of Medicine and Dentistry, Rochester, NY 14642, USA and 6Center for Theoretical Biological Physics, University of California San Diego, San Diego, CA 92037, USA"},{"name":"1 Biophysics, University of Michigan, Ann Arbor, MI 48109, USA, 2Single Molecule Analysis Group, University of Michigan, Ann Arbor, MI 48109, USA, 3Department of Chemistry, University of Michigan, Ann Arbor, MI 48109, USA, 4Program in Chemical Biology, University of Michigan, Ann Arbor, MI 48109, USA, 5Department of Biochemistry and Biophysics, Center for RNA Biology, University of Rochester School of Medicine and Dentistry, Rochester, NY 14642, USA and 6Center for Theoretical Biological Physics, University of California San Diego, San Diego, CA 92037, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"suffix":"III","given":"Charles L.","family":"Brooks","sequence":"additional","affiliation":[{"name":"1 Biophysics, University of Michigan, Ann Arbor, MI 48109, USA, 2Single Molecule Analysis Group, University of Michigan, Ann Arbor, MI 48109, USA, 3Department of Chemistry, University of Michigan, Ann Arbor, MI 48109, USA, 4Program in Chemical Biology, University of Michigan, Ann Arbor, MI 48109, USA, 5Department of Biochemistry and Biophysics, Center for RNA Biology, University of Rochester School of Medicine and Dentistry, Rochester, NY 14642, USA and 6Center for Theoretical Biological Physics, University of California San Diego, San Diego, CA 92037, USA"},{"name":"1 Biophysics, University of Michigan, Ann Arbor, MI 48109, USA, 2Single Molecule Analysis Group, University of Michigan, Ann Arbor, MI 48109, USA, 3Department of Chemistry, University of Michigan, Ann Arbor, MI 48109, USA, 4Program in Chemical Biology, University of Michigan, Ann Arbor, MI 48109, USA, 5Department of Biochemistry and Biophysics, Center for RNA Biology, University of Rochester School of Medicine and Dentistry, Rochester, NY 14642, USA and 6Center for Theoretical Biological Physics, University of California San Diego, San Diego, CA 92037, USA"},{"name":"1 Biophysics, University of Michigan, Ann Arbor, MI 48109, 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for RNA Biology, University of Rochester School of Medicine and Dentistry, Rochester, NY 14642, USA and 6Center for Theoretical Biological Physics, University of California San Diego, San Diego, CA 92037, USA"},{"name":"1 Biophysics, University of Michigan, Ann Arbor, MI 48109, USA, 2Single Molecule Analysis Group, University of Michigan, Ann Arbor, MI 48109, USA, 3Department of Chemistry, University of Michigan, Ann Arbor, MI 48109, USA, 4Program in Chemical Biology, University of Michigan, Ann Arbor, MI 48109, USA, 5Department of Biochemistry and Biophysics, Center for RNA Biology, University of Rochester School of Medicine and Dentistry, Rochester, NY 14642, USA and 6Center for Theoretical Biological Physics, University of California San Diego, San Diego, CA 92037, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"286","published-online":{"date-parts":[[2013,9,3]]},"reference":[{"key":"2024100116383630800_gkt798-B1","doi-asserted-by":"crossref","first-page":"281","DOI":"10.1038\/nature02362","article-title":"Control of gene expression by a natural metabolite-responsive ribozyme","volume":"428","author":"Winkler","year":"2004","journal-title":"Nature"},{"key":"2024100116383630800_gkt798-B2","doi-asserted-by":"crossref","first-page":"11","DOI":"10.1016\/j.tibs.2003.11.004","article-title":"The riboswitch control of bacterial metabolism","volume":"29","author":"Nudler","year":"2004","journal-title":"Trends Biochem. 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