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A comprehensive structural and functional characterization of single-nucleotide variations in the 5\u2032-untranslated region (UTR) of SARS-CoV-2 has remained elusive. The co-evolution of 5\u2032-UTR stem-loop 1 (SL1) and non-structural protein (nsp) 1 mutants are of particular importance, as both are key in directing the translation of the viral genome. Here, we investigate the structure and function of the most frequently emerging mutations in SL1 and nsp1. Mutation C21U in the apical loop of SL1 shows changed loop dynamics and reduced escape from repression by nsp1 mutants. Mutation analyses of the pyrimidine loop and the apical helix of SL1 identify preferred sequence motifs for escape from nsp1 repression. Importantly, sequence preferences are governed by the structural features, with suboptimal pyrimidine sequences escaping repression when presented in the SL1 context. Compared to the nsp1 wild type (wt), the currently circulating nsp1 linker variant S135R is much more sensitive toward sequence and structure variations of the apical loop of SL1. Thus, our study provides new insights into the structure\u2013function relationship and co-evolution between viral RNA structures and viral proteins.<\/jats:p>","DOI":"10.1093\/nar\/gkag364","type":"journal-article","created":{"date-parts":[[2026,4,10]],"date-time":"2026-04-10T11:40:57Z","timestamp":1775821257000},"source":"Crossref","is-referenced-by-count":2,"title":["Structure and sequence characteristics of 5\u2032-stem-loop 1 modulate the escape from nsp1-mediated repression in SARS-CoV-2 variants"],"prefix":"10.1093","volume":"54","author":[{"ORCID":"https:\/\/orcid.org\/0009-0004-7313-7320","authenticated-orcid":false,"given":"Julian B","family":"Schoth","sequence":"first","affiliation":[{"name":"Department of Pharmacy, Institute of Pharmaceutical Chemistry, Marburg University , Marburg 35037 ,","place":["Germany"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Inge","family":"Schwedt","sequence":"additional","affiliation":[{"name":"Department of Pharmacy, Institute of Pharmaceutical Chemistry, Marburg University , Marburg 35037 ,","place":["Germany"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-9396-0750","authenticated-orcid":false,"given":"Susanne","family":"Philipp","sequence":"additional","affiliation":[{"name":"Department of Pharmacy, Institute of Pharmaceutical Chemistry, Marburg University , Marburg 35037 ,","place":["Germany"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0009-0008-5501-6276","authenticated-orcid":false,"given":"Sabrina","family":"Toews","sequence":"additional","affiliation":[{"name":"Institute for Organic Chemistry and Chemical Biology, Center for Biomolecular Magnetic Resonance (BMRZ), Goethe University Frankfurt am Main , Frankfurt\/Main 60438 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for Organic Chemistry and Chemical Biology, Center for Biomolecular Magnetic Resonance (BMRZ), Goethe University Frankfurt am Main , Frankfurt\/Main 60438 ,","place":["Germany"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-4247-1348","authenticated-orcid":false,"given":"Julia E","family":"Weigand","sequence":"additional","affiliation":[{"name":"Department of Pharmacy, Institute of Pharmaceutical Chemistry, Marburg University , Marburg 35037 ,","place":["Germany"]},{"name":"Center for Synthetic Microbiology (SYNMIKRO), Marburg University , Marburg 35043 ,","place":["Germany"]}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"286","published-online":{"date-parts":[[2026,4,28]]},"reference":[{"key":"2026042805151537500_B1","doi-asserted-by":"publisher","first-page":"125","DOI":"10.1038\/s41586-020-2739-1","article-title":"The coding capacity of 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