{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,10,24]],"date-time":"2026-10-24T08:03:26Z","timestamp":1792829006163,"version":"4.5.0"},"reference-count":117,"publisher":"Oxford University Press (OUP)","issue":"22","license":[{"start":{"date-parts":[[2024,11,30]],"date-time":"2024-11-30T00:00:00Z","timestamp":1732924800000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/100000897","name":"Cystic Fibrosis Foundation","doi-asserted-by":"publisher","award":["PORTER20F0"],"award-info":[{"award-number":["PORTER20F0"]}],"id":[{"id":"10.13039\/100000897","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000897","name":"Cystic Fibrosis Foundation","doi-asserted-by":"publisher","award":["LUECK20GO"],"award-info":[{"award-number":["LUECK20GO"]}],"id":[{"id":"10.13039\/100000897","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000002","name":"NIH","doi-asserted-by":"publisher","award":["R01 HL153988"],"award-info":[{"award-number":["R01 HL153988"]}],"id":[{"id":"10.13039\/100000002","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2024,12,11]]},"abstract":"<jats:title>Abstract<\/jats:title>\n                  <jats:p>Nonsense suppressor transfer RNAs (tRNAs) or AntiCodon-Edited tRNAs (ACE-tRNAs) have long been envisioned as a therapeutic approach to overcome genetic diseases resulting from the introduction of premature termination codons (PTCs). The ACE-tRNA approach for the rescue of PTCs has been hampered by ineffective delivery through available modalities for gene therapy. Here we have screened a series of ACE-tRNA expression cassette sequence libraries containing\u00a0&amp;gt;1800 members in an effort to optimize ACE-tRNA function and provide a roadmap for optimization in the future. By optimizing PTC suppression efficiency of ACE-tRNAs, we have decreased the amount of ACE-tRNA required by \u223c16-fold for the most common cystic fibrosis-causing PTCs.<\/jats:p>","DOI":"10.1093\/nar\/gkae1112","type":"journal-article","created":{"date-parts":[[2024,10,28]],"date-time":"2024-10-28T16:15:35Z","timestamp":1730132135000},"page":"14112-14132","source":"Crossref","is-referenced-by-count":27,"title":["Optimization of ACE-tRNAs function in translation for suppression of nonsense mutations"],"prefix":"10.1093","volume":"52","author":[{"given":"Joseph\u00a0J","family":"Porter","sequence":"first","affiliation":[{"name":"Department of Pharmacology and Physiology, University of Rochester School of Medicine and Dentistry , 601 Elmwood Ave.,\u00a0 Rochester , NY\u00a0 14642 ,","place":["USA"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Wooree","family":"Ko","sequence":"additional","affiliation":[{"name":"Department of Pharmacology and Physiology, University of Rochester School of Medicine and Dentistry , 601 Elmwood Ave.,\u00a0 Rochester , NY\u00a0 14642 ,","place":["USA"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Emily\u00a0G","family":"Sorensen","sequence":"additional","affiliation":[{"name":"Department of Pharmacology and Physiology, University of Rochester School of Medicine and Dentistry , 601 Elmwood Ave.,\u00a0 Rochester , NY\u00a0 14642 ,","place":["USA"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-1820-711X","authenticated-orcid":false,"given":"John\u00a0D","family":"Lueck","sequence":"additional","affiliation":[{"name":"Department of Pharmacology and Physiology, University of Rochester School of Medicine and Dentistry , 601 Elmwood Ave.,\u00a0 Rochester , NY\u00a0 14642 ,","place":["USA"]},{"name":"Department of Neurology, University of Rochester School of Medicine and Dentistry , 601 Elmwood Ave.,\u00a0 Rochester , NY\u00a0 14642 ,","place":["USA"]},{"name":"Center for RNA Biology, University of Rochester School of Medicine and Dentistry , 601 Elmwood Ave.,\u00a0 Rochester , NY\u00a0 14642 ,","place":["USA"]}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"286","published-online":{"date-parts":[[2024,11,30]]},"reference":[{"key":"2024122115573602400_B1","doi-asserted-by":"crossref","first-page":"406","DOI":"10.1038\/s41580-019-0126-2","article-title":"Quality and quantity control of gene expression by nonsense-mediated mRNA decay","volume":"20","author":"Kurosaki","year":"2019","journal-title":"Nat. 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Biol."},{"key":"2024122115573602400_B85","doi-asserted-by":"crossref","first-page":"W542","DOI":"10.1093\/nar\/gkz438","article-title":"tRNAviz: explore and visualize tRNA sequence features","volume":"47","author":"Lin","year":"2019","journal-title":"Nucleic Acids Res."},{"key":"2024122115573602400_B86","doi-asserted-by":"crossref","first-page":"547","DOI":"10.1097\/01.mcp.0000141247.22078.46","article-title":"Pharmacologic therapy for stop mutations: how much CFTR activity is enough?","volume":"10","author":"Kerem","year":"2004","journal-title":"Curr. Opin. Pulm. Med."},{"key":"2024122115573602400_B87","doi-asserted-by":"crossref","first-page":"12508","DOI":"10.1073\/pnas.1605336113","article-title":"Ataluren stimulates ribosomal selection of near-cognate tRNAs to promote nonsense suppression","volume":"113","author":"Roy","year":"2016","journal-title":"Proc. Natl Acad. Sci. 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Commun."},{"key":"2024122115573602400_B102","doi-asserted-by":"crossref","first-page":"1528","DOI":"10.1093\/nar\/gkad007","article-title":"The tRNA identity landscape for aminoacylation and beyond","volume":"51","author":"Giege","year":"2023","journal-title":"Nucleic Acids Res."},{"key":"2024122115573602400_B103","doi-asserted-by":"crossref","first-page":"366","DOI":"10.1186\/s12864-016-2692-4","article-title":"Selective forces and mutational biases drive stop codon usage in the human genome: a comparison with sense codon usage","volume":"17","author":"Trotta","year":"2016","journal-title":"BMC Genomics"},{"key":"2024122115573602400_B104","doi-asserted-by":"crossref","first-page":"9260","DOI":"10.1038\/s41598-018-27570-3","article-title":"Purifying and positive selection in the evolution of stop codons","volume":"8","author":"Belinky","year":"2018","journal-title":"Sci. Rep."},{"key":"2024122115573602400_B105","doi-asserted-by":"crossref","first-page":"1167","DOI":"10.1021\/acs.biochem.8b01280","article-title":"Interrogation of eukaryotic stop codon readthrough signals by in vitro RNA selection","volume":"58","author":"Anzalone","year":"2019","journal-title":"Biochemistry"},{"key":"2024122115573602400_B106","doi-asserted-by":"crossref","first-page":"334","DOI":"10.1006\/jmbi.1995.0438","article-title":"The efficiency of translation termination is determined by a synergistic interplay between upstream and downstream sequences in Saccharomyces cerevisiae","volume":"251","author":"Bonetti","year":"1995","journal-title":"J. Mol. Biol."},{"key":"2024122115573602400_B107","doi-asserted-by":"crossref","first-page":"1927","DOI":"10.1093\/nar\/gkx1315","article-title":"Eukaryotic translational termination efficiency is influenced by the 3' nucleotides within the ribosomal mRNA channel","volume":"46","author":"Cridge","year":"2018","journal-title":"Nucleic Acids Res."},{"key":"2024122115573602400_B108","doi-asserted-by":"crossref","first-page":"787","DOI":"10.1093\/embo-reports\/kve176","article-title":"Impact of the six nucleotides downstream of the stop codon on translation termination","volume":"2","author":"Namy","year":"2001","journal-title":"EMBO Rep."},{"key":"2024122115573602400_B109","doi-asserted-by":"crossref","first-page":"e03640","DOI":"10.7554\/eLife.03640","article-title":"Peroxisomal lactate dehydrogenase is generated by translational readthrough in mammals","volume":"3","author":"Schueren","year":"2014","journal-title":"eLife"},{"key":"2024122115573602400_B110","doi-asserted-by":"crossref","first-page":"6679","DOI":"10.1093\/nar\/gkr224","article-title":"Stimulation of stop codon readthrough: frequent presence of an extended 3' RNA structural element","volume":"39","author":"Firth","year":"2011","journal-title":"Nucleic Acids Res."},{"key":"2024122115573602400_B111","doi-asserted-by":"crossref","first-page":"1605","DOI":"10.1016\/j.cell.2014.04.033","article-title":"Programmed translational readthrough generates antiangiogenic VEGF-ax","volume":"157","author":"Eswarappa","year":"2014","journal-title":"Cell"},{"key":"2024122115573602400_B112","doi-asserted-by":"crossref","first-page":"e1739","DOI":"10.1002\/wrna.1739","article-title":"Mammalian proteome expansion by stop codon readthrough","volume":"14","author":"Manjunath","year":"2023","journal-title":"Wiley Interdiscip. Rev. 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