{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,8,25]],"date-time":"2026-08-25T10:35:32Z","timestamp":1787654132047,"version":"build-2736575974"},"reference-count":35,"publisher":"Oxford University Press (OUP)","issue":"15","license":[{"start":{"date-parts":[[2025,8,11]],"date-time":"2025-08-11T00:00:00Z","timestamp":1754870400000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by-nc\/4.0\/"}],"funder":[{"DOI":"10.13039\/501100001809","name":"National Natural Science Foundation of China","doi-asserted-by":"publisher","award":["32325029"],"award-info":[{"award-number":["32325029"]}],"id":[{"id":"10.13039\/501100001809","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100001809","name":"National Natural Science Foundation of China","doi-asserted-by":"publisher","award":["91940302"],"award-info":[{"award-number":["91940302"]}],"id":[{"id":"10.13039\/501100001809","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100001809","name":"National Natural Science Foundation of China","doi-asserted-by":"publisher","award":["91640104"],"award-info":[{"award-number":["91640104"]}],"id":[{"id":"10.13039\/501100001809","id-type":"DOI","asserted-by":"publisher"}]},{"name":"Zhejiang Provincial Natural Science Foundationof China","award":["LD25C050002"],"award-info":[{"award-number":["LD25C050002"]}]},{"name":"National Key Research and Development Project of China","award":["2023YFC2604300"],"award-info":[{"award-number":["2023YFC2604300"]}]},{"name":"National Key Research and Development Project of China","award":["2021YFC2300300"],"award-info":[{"award-number":["2021YFC2300300"]}]},{"DOI":"10.13039\/501100004835","name":"Zhejiang University","doi-asserted-by":"publisher","id":[{"id":"10.13039\/501100004835","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2025,8,11]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>Riboswitches are conserved non-coding RNA domains predominantly located at the 5\u2032-end of the bacterial mRNAs, serving as gene expression regulators.\u00a0Recently, a third class of 2\u2032-deoxyguanosine riboswitch (2\u2032-dG-III) has been identified from guanine riboswitch family, exhibiting comparable binding affinity toward\u00a02\u2032-dG, guanine, and guanosine. To elucidate the unique ligand recognition mechanism of this riboswitch, we solved its crystal structures in complex with different purine derivatives, including 2\u2032-dG, guanine, and guanosine. The tertiary structure reveals a typical tuning-fork-like architecture, with three stems converging at a central three-way junction. The bound ligand, 2\u2032-dG, is anchored within the junctional core through specific molecular interactions involving certain critical nucleotides. Through systemic comparative analysis of the binding pocket across different ligand-bound states, as well as related guanine family riboswitches, including 2\u2032-dG-I, 2\u2032-dG-II, and Guanine-I riboswitches, we identified subtle yet significant structural variations that modulate binding affinity and specificity. Leveraging these findings, we further engineered RNA biosensors by fusing the 2\u2032-dG-III riboswitch with Pepper fluorogenic RNA aptamer, which exhibits\u00a0a robust, positive correlation between fluorescence intensity and 2\u2032-dG levels in vitro. Together, this work not only advances our understanding of the ligand recognition mechanisms underlying the 2\u2032-dG-III riboswitch and related guanine riboswitch family but also lays the groundwork for fine-tuning riboswitch specificity, paving the way for the development of highly specific RNA-based biosensors.<\/jats:p>","DOI":"10.1093\/nar\/gkaf773","type":"journal-article","created":{"date-parts":[[2025,7,25]],"date-time":"2025-07-25T11:45:55Z","timestamp":1753443955000},"source":"Crossref","is-referenced-by-count":4,"title":["Structure-based insights into the ligand specificity tuning of 2\u2032-dG-III riboswitch"],"prefix":"10.1093","volume":"53","author":[{"given":"Xin","family":"Shen","sequence":"first","affiliation":[{"name":"Zhejiang University Department of Cardiology of The Second Affiliated Hospital and Life Sciences Institute and School of Medicine, , Hangzhou 310058 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Medicine, , Hangzhou 310058 ,","place":["China"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Xiaoqing","family":"Tai","sequence":"additional","affiliation":[{"name":"Zhejiang University Department of Cardiology of The Second Affiliated Hospital and Life Sciences Institute and School of Medicine, , Hangzhou 310058 ,","place":["China"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Mengqi","family":"He","sequence":"additional","affiliation":[{"name":"Zhejiang University Department of Cardiology of The Second Affiliated Hospital and Life Sciences Institute and School of Medicine, , Hangzhou 310058 ,","place":["China"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-5420-4899","authenticated-orcid":false,"given":"Aiming","family":"Ren","sequence":"additional","affiliation":[{"name":"Zhejiang University Department of Cardiology of The Second Affiliated Hospital and Life Sciences Institute and School of 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