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Although G-quadruplexes (G4s) have previously been reported in coding regions of DENV, their presence within the 3\u2032 untranslated region (3\u2032 UTR) has not been experimentally characterized. Here, we focused on selected guanine-rich motifs within the 3\u2032 UTRs of DENV-1 to DENV-4 and investigated their ability to form RNA G4 structures. Using bioinformatic analysis, we identified comparable G-rich regions in the 3\u2032 UTRs of the four serotypes, with serotype-dependent differences in conservation. We then examined the propensity of the selected putative quadruplex-forming sequences (PQSs) to adopt G4 structures using circular dichroism spectroscopy, UV melting analysis, 1H NMR spectroscopy, ligand-binding analysis, and reverse transcription stop (RT-stop) assays. Our results provided in vitro evidence that the 3\u2032 UTR oligonucleotides from DENV-1 to DENV-4 are capable of forming ligand-responsive G4 structures, with serotype-dependent differences in conservation, stability, and conformational homogeneity. In addition, reverse transcription (RT)-stop analysis revealed ligand-dependent arrest at the corresponding PQS sites in the presence of the G4 ligand 6OTD, which stabilizes G4 structures. These findings suggest the DENV 3\u2032 UTR as an additional source of ligand-responsive RNA G4-forming elements and support future studies on their possible roles in DENV RNA regulation.<\/jats:p>","DOI":"10.3390\/biom16070946","type":"journal-article","created":{"date-parts":[[2026,7,1]],"date-time":"2026-07-01T03:06:34Z","timestamp":1782875194000},"page":"946","update-policy":"https:\/\/doi.org\/10.3390\/mdpi_crossmark_policy","source":"Crossref","is-referenced-by-count":0,"title":["Identification of Ligand-Responsive RNA G-Quadruplexes in the 3\u2032 UTRs of Dengue Virus Serotypes"],"prefix":"10.3390","volume":"16","author":[{"given":"Mohammad Jafar","family":"Sheikhi","sequence":"first","affiliation":[{"name":"Department of Biotechnology and Life Science, Faculty of Engineering, Tokyo University of Agriculture and Technology, 2-24-16, Naka-cho, Tokyo 184-8588, Japan"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Ayuka","family":"Onuma","sequence":"additional","affiliation":[{"name":"Department of Biotechnology and Life Science, Faculty of Engineering, Tokyo University of Agriculture and Technology, 2-24-16, Naka-cho, Tokyo 184-8588, Japan"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Yutaro","family":"Imachi","sequence":"additional","affiliation":[{"name":"Department of Biotechnology and Life Science, Faculty of Engineering, Tokyo University of Agriculture and Technology, 2-24-16, Naka-cho, Tokyo 184-8588, Japan"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-3456-3074","authenticated-orcid":false,"given":"Akira","family":"Shiraishi","sequence":"additional","affiliation":[{"name":"Bioorganic Research Institute, Suntory Foundation for Life Sciences, 8-1-1 Seikadai, Seika-cho, Soraku-gun, Kyoto 619-0284, Japan"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-9309-8005","authenticated-orcid":false,"given":"Shoko","family":"Mori","sequence":"additional","affiliation":[{"name":"Bioorganic Research Institute, Suntory Foundation for Life Sciences, 8-1-1 Seikadai, Seika-cho, Soraku-gun, Kyoto 619-0284, Japan"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Kohtaro","family":"Sugahara","sequence":"additional","affiliation":[{"name":"Bioorganic Research Institute, Suntory Foundation for Life Sciences, 8-1-1 Seikadai, Seika-cho, Soraku-gun, Kyoto 619-0284, Japan"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-4308-0499","authenticated-orcid":false,"given":"Daisuke","family":"Miyoshi","sequence":"additional","affiliation":[{"name":"Faculty of Frontiers of Innovative Research in Science and Technology (FIRST), Konan University, Kobe 650-0047, Japan"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Yue","family":"Ma","sequence":"additional","affiliation":[{"name":"Laboratory for Biomaterials and Bioengineering, Institute of Science Tokyo, 2-3-10 Kanda-Surugadai, Chiyoda-ku, Tokyo 101-0062, Japan"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Takayuki","family":"Hishiki","sequence":"additional","affiliation":[{"name":"Department of Drug Development, National Institute of Infectious Diseases, Japan Institute for Health Security, Tokyo 162-8655, Japan"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Kazuo","family":"Nagasawa","sequence":"additional","affiliation":[{"name":"Department of Biotechnology and Life Science, Faculty of Engineering, Tokyo University of Agriculture and Technology, 2-24-16, Naka-cho, Tokyo 184-8588, Japan"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-4430-579X","authenticated-orcid":false,"given":"Masayuki","family":"Tera","sequence":"additional","affiliation":[{"name":"Department of Biotechnology and Life Science, Faculty of Engineering, Tokyo University of Agriculture and Technology, 2-24-16, Naka-cho, Tokyo 184-8588, Japan"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"1968","published-online":{"date-parts":[[2026,6,25]]},"reference":[{"key":"ref_1","doi-asserted-by":"crossref","unstructured":"Zhang, Y., Wang, M., Huang, M., and Zhao, J. 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