{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"institution":[{"name":"bioRxiv"}],"indexed":{"date-parts":[[2026,6,24]],"date-time":"2026-06-24T06:05:16Z","timestamp":1782281116537,"version":"3.54.5"},"posted":{"date-parts":[[2026,4,2]]},"group-title":"Biochemistry","reference-count":74,"publisher":"openRxiv","license":[{"start":{"date-parts":[[2026,4,2]],"date-time":"2026-04-02T00:00:00Z","timestamp":1775088000000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by-nc\/4.0\/"}],"funder":[{"DOI":"10.13039\/100000060","name":"National Institute of Allergy and Infectious Diseases","doi-asserted-by":"crossref","award":["R01-AI144067"],"award-info":[{"award-number":["R01-AI144067"]}],"id":[{"id":"10.13039\/100000060","id-type":"DOI","asserted-by":"crossref"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"accepted":{"date-parts":[[2026,5,8]]},"abstract":"<jats:title>Abstract<\/jats:title>\n                <jats:p>The innate immune system relies on pathogen recognition receptors, such as the 2\u2019,5\u2019-oligoadenylate synthetase (OAS) proteins, to detect pathogen-associated molecular patterns like viral double-stranded (ds)RNA. A specific splicing variant of OAS1 (OAS1-p46) has been implicated in initiating an immune response that leads to decreased disease severity during SARS-CoV-2 infection. OAS1-p46 has a C-terminal lipid modification motif that allows for anchoring of the protein to intracellular membranes and thus potential colocalization with immunogenic viral RNA regions such as the SARS-CoV-2 5\u2019-untranslated region (5\u2019-UTR). Here, we show that OAS proteins can detect the 5\u2019-structured elements (5\u2019-SE)\u2013comprising the 5\u2019-UTR and three additional stem-loop structures\u2013and activate the cellular RNase L pathway. Through systematic 3\u2019-end truncations of the 5\u2019-SE, we show that the smallest 5\u2019-SE fragment capable of potently activating OAS1 is the conserved and highly structured SL1-4b region, containing the first four stem-loop structures and their intervening linking sequences (SL1-4), as well as an unstructured region (\u201cSL4b\u201d) to the 3\u2019-side of SL4. Analyses of OAS1 activation and RNA secondary structure probing using selective 2\u2019-hydroxyl acylation analyzed by primer extension and mutational profiling (SHAPE-MaP) of additional SL1-4b RNA variants suggests a model in which SL4 acts as the primary OAS1 interaction site, while the unstructured SL4b region and two other stem-loops (SL1 and SL3) are necessary for optimal presentation of this region for OAS1 activation. Our findings reveal a structurally complex viral RNA region that potently activates OAS1, underscoring the potential complexity of RNAs that can strongly activate this innate immune sensor.<\/jats:p>","DOI":"10.64898\/2026.04.01.715984","type":"posted-content","created":{"date-parts":[[2026,4,3]],"date-time":"2026-04-03T02:10:36Z","timestamp":1775182236000},"source":"Crossref","is-referenced-by-count":0,"title":["SARS-CoV-2 5\u2019-UTR stem-loops activate the antiviral protein oligoadenylate synthetase 1 (OAS1)"],"prefix":"10.64898","author":[{"ORCID":"https:\/\/orcid.org\/0000-0003-2787-6945","authenticated-orcid":false,"given":"Alejandro","family":"Oviedo","sequence":"first","affiliation":[{"name":"Department of Biochemistry, Emory University School of Medicine, 1510 Clifton Road NE, Atlanta, GA 30322, USA"},{"name":"Graduate Program in Biochemistry, Cell and Developmental Biology, Emory University, Atlanta, GA 30322, 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Atlanta, GA 30322, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-1933-8103","authenticated-orcid":false,"given":"David","family":"Vanlnsberghe","sequence":"additional","affiliation":[{"name":"Department of Microbiology and Immunology, Emory University School of Medicine, 1510 Clifton Road NE, Atlanta, GA 30322, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-9829-112X","authenticated-orcid":false,"given":"Anice C.","family":"Lowen","sequence":"additional","affiliation":[{"name":"Department of Microbiology and Immunology, Emory University School of Medicine, 1510 Clifton Road NE, Atlanta, GA 30322, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-2419-380X","authenticated-orcid":false,"given":"Graeme L.","family":"Conn","sequence":"additional","affiliation":[{"name":"Department of Biochemistry, Emory University School of Medicine, 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