{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,4,30]],"date-time":"2026-04-30T15:25:52Z","timestamp":1777562752814,"version":"3.51.4"},"reference-count":31,"publisher":"MDPI AG","issue":"9","license":[{"start":{"date-parts":[[2023,5,2]],"date-time":"2023-05-02T00:00:00Z","timestamp":1682985600000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"name":"National Supercomputing Centre","award":["202D800013"],"award-info":[{"award-number":["202D800013"]}]},{"name":"National Supercomputing Centre","award":["PTDC\/SAU-ENB\/117013\/2010"],"award-info":[{"award-number":["PTDC\/SAU-ENB\/117013\/2010"]}]},{"name":"National Supercomputing Centre","award":["2022.02763.PTDC"],"award-info":[{"award-number":["2022.02763.PTDC"]}]},{"name":"National Supercomputing Centre","award":["2022.02763"],"award-info":[{"award-number":["2022.02763"]}]},{"name":"National Supercomputing Centre","award":["IF\/00772\/2013"],"award-info":[{"award-number":["IF\/00772\/2013"]}]},{"name":"National Supercomputing Centre","award":["CEECIND\/01670\/2017"],"award-info":[{"award-number":["CEECIND\/01670\/2017"]}]},{"name":"National Supercomputing Centre","award":["PD\/BD\/113698\/2015"],"award-info":[{"award-number":["PD\/BD\/113698\/2015"]}]},{"name":"National Supercomputing Centre","award":["2022.02763"],"award-info":[{"award-number":["2022.02763"]}]},{"name":"A*STAR","award":["202D800013"],"award-info":[{"award-number":["202D800013"]}]},{"name":"A*STAR","award":["PTDC\/SAU-ENB\/117013\/2010"],"award-info":[{"award-number":["PTDC\/SAU-ENB\/117013\/2010"]}]},{"name":"A*STAR","award":["2022.02763.PTDC"],"award-info":[{"award-number":["2022.02763.PTDC"]}]},{"name":"A*STAR","award":["2022.02763"],"award-info":[{"award-number":["2022.02763"]}]},{"name":"A*STAR","award":["IF\/00772\/2013"],"award-info":[{"award-number":["IF\/00772\/2013"]}]},{"name":"A*STAR","award":["CEECIND\/01670\/2017"],"award-info":[{"award-number":["CEECIND\/01670\/2017"]}]},{"name":"A*STAR","award":["PD\/BD\/113698\/2015"],"award-info":[{"award-number":["PD\/BD\/113698\/2015"]}]},{"name":"A*STAR","award":["2022.02763"],"award-info":[{"award-number":["2022.02763"]}]},{"name":"BII (A*STAR)","award":["202D800013"],"award-info":[{"award-number":["202D800013"]}]},{"name":"BII (A*STAR)","award":["PTDC\/SAU-ENB\/117013\/2010"],"award-info":[{"award-number":["PTDC\/SAU-ENB\/117013\/2010"]}]},{"name":"BII (A*STAR)","award":["2022.02763.PTDC"],"award-info":[{"award-number":["2022.02763.PTDC"]}]},{"name":"BII (A*STAR)","award":["2022.02763"],"award-info":[{"award-number":["2022.02763"]}]},{"name":"BII (A*STAR)","award":["IF\/00772\/2013"],"award-info":[{"award-number":["IF\/00772\/2013"]}]},{"name":"BII (A*STAR)","award":["CEECIND\/01670\/2017"],"award-info":[{"award-number":["CEECIND\/01670\/2017"]}]},{"name":"BII (A*STAR)","award":["PD\/BD\/113698\/2015"],"award-info":[{"award-number":["PD\/BD\/113698\/2015"]}]},{"name":"BII (A*STAR)","award":["2022.02763"],"award-info":[{"award-number":["2022.02763"]}]},{"DOI":"10.13039\/501100001871","name":"Funda\u00e7\u00e3o para a Ci\u00eancia e a Tecnologia\u2014Minist\u00e9rio da Ci\u00eancia, Tecnologia e Ensino Superior (FCT-MCTES, Portugal)","doi-asserted-by":"publisher","award":["202D800013"],"award-info":[{"award-number":["202D800013"]}],"id":[{"id":"10.13039\/501100001871","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100001871","name":"Funda\u00e7\u00e3o para a Ci\u00eancia e a Tecnologia\u2014Minist\u00e9rio da Ci\u00eancia, Tecnologia e Ensino Superior (FCT-MCTES, Portugal)","doi-asserted-by":"publisher","award":["PTDC\/SAU-ENB\/117013\/2010"],"award-info":[{"award-number":["PTDC\/SAU-ENB\/117013\/2010"]}],"id":[{"id":"10.13039\/501100001871","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100001871","name":"Funda\u00e7\u00e3o para a Ci\u00eancia e a Tecnologia\u2014Minist\u00e9rio da Ci\u00eancia, Tecnologia e Ensino Superior (FCT-MCTES, Portugal)","doi-asserted-by":"publisher","award":["2022.02763.PTDC"],"award-info":[{"award-number":["2022.02763.PTDC"]}],"id":[{"id":"10.13039\/501100001871","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100001871","name":"Funda\u00e7\u00e3o para a Ci\u00eancia e a Tecnologia\u2014Minist\u00e9rio da Ci\u00eancia, Tecnologia e Ensino Superior (FCT-MCTES, Portugal)","doi-asserted-by":"publisher","award":["2022.02763"],"award-info":[{"award-number":["2022.02763"]}],"id":[{"id":"10.13039\/501100001871","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100001871","name":"Funda\u00e7\u00e3o para a Ci\u00eancia e a Tecnologia\u2014Minist\u00e9rio da Ci\u00eancia, Tecnologia e Ensino Superior (FCT-MCTES, Portugal)","doi-asserted-by":"publisher","award":["IF\/00772\/2013"],"award-info":[{"award-number":["IF\/00772\/2013"]}],"id":[{"id":"10.13039\/501100001871","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100001871","name":"Funda\u00e7\u00e3o para a Ci\u00eancia e a Tecnologia\u2014Minist\u00e9rio da Ci\u00eancia, Tecnologia e Ensino Superior (FCT-MCTES, Portugal)","doi-asserted-by":"publisher","award":["CEECIND\/01670\/2017"],"award-info":[{"award-number":["CEECIND\/01670\/2017"]}],"id":[{"id":"10.13039\/501100001871","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100001871","name":"Funda\u00e7\u00e3o para a Ci\u00eancia e a Tecnologia\u2014Minist\u00e9rio da Ci\u00eancia, Tecnologia e Ensino Superior (FCT-MCTES, Portugal)","doi-asserted-by":"publisher","award":["PD\/BD\/113698\/2015"],"award-info":[{"award-number":["PD\/BD\/113698\/2015"]}],"id":[{"id":"10.13039\/501100001871","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100001871","name":"Funda\u00e7\u00e3o para a Ci\u00eancia e a Tecnologia\u2014Minist\u00e9rio da Ci\u00eancia, Tecnologia e Ensino Superior (FCT-MCTES, Portugal)","doi-asserted-by":"publisher","award":["2022.02763"],"award-info":[{"award-number":["2022.02763"]}],"id":[{"id":"10.13039\/501100001871","id-type":"DOI","asserted-by":"publisher"}]},{"name":"Exploratory Project","award":["202D800013"],"award-info":[{"award-number":["202D800013"]}]},{"name":"Exploratory Project","award":["PTDC\/SAU-ENB\/117013\/2010"],"award-info":[{"award-number":["PTDC\/SAU-ENB\/117013\/2010"]}]},{"name":"Exploratory Project","award":["2022.02763.PTDC"],"award-info":[{"award-number":["2022.02763.PTDC"]}]},{"name":"Exploratory Project","award":["2022.02763"],"award-info":[{"award-number":["2022.02763"]}]},{"name":"Exploratory Project","award":["IF\/00772\/2013"],"award-info":[{"award-number":["IF\/00772\/2013"]}]},{"name":"Exploratory Project","award":["CEECIND\/01670\/2017"],"award-info":[{"award-number":["CEECIND\/01670\/2017"]}]},{"name":"Exploratory Project","award":["PD\/BD\/113698\/2015"],"award-info":[{"award-number":["PD\/BD\/113698\/2015"]}]},{"name":"Exploratory Project","award":["2022.02763"],"award-info":[{"award-number":["2022.02763"]}]},{"DOI":"10.13039\/501100001871","name":"Calouste Gulbenkian Foundation (FCG, Portugal)","doi-asserted-by":"publisher","award":["202D800013"],"award-info":[{"award-number":["202D800013"]}],"id":[{"id":"10.13039\/501100001871","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100001871","name":"Calouste Gulbenkian Foundation (FCG, Portugal)","doi-asserted-by":"publisher","award":["PTDC\/SAU-ENB\/117013\/2010"],"award-info":[{"award-number":["PTDC\/SAU-ENB\/117013\/2010"]}],"id":[{"id":"10.13039\/501100001871","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100001871","name":"Calouste Gulbenkian Foundation (FCG, Portugal)","doi-asserted-by":"publisher","award":["2022.02763.PTDC"],"award-info":[{"award-number":["2022.02763.PTDC"]}],"id":[{"id":"10.13039\/501100001871","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100001871","name":"Calouste Gulbenkian Foundation (FCG, Portugal)","doi-asserted-by":"publisher","award":["2022.02763"],"award-info":[{"award-number":["2022.02763"]}],"id":[{"id":"10.13039\/501100001871","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100001871","name":"Calouste Gulbenkian Foundation (FCG, Portugal)","doi-asserted-by":"publisher","award":["IF\/00772\/2013"],"award-info":[{"award-number":["IF\/00772\/2013"]}],"id":[{"id":"10.13039\/501100001871","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100001871","name":"Calouste Gulbenkian Foundation (FCG, Portugal)","doi-asserted-by":"publisher","award":["CEECIND\/01670\/2017"],"award-info":[{"award-number":["CEECIND\/01670\/2017"]}],"id":[{"id":"10.13039\/501100001871","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100001871","name":"Calouste Gulbenkian Foundation (FCG, Portugal)","doi-asserted-by":"publisher","award":["PD\/BD\/113698\/2015"],"award-info":[{"award-number":["PD\/BD\/113698\/2015"]}],"id":[{"id":"10.13039\/501100001871","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100001871","name":"Calouste Gulbenkian Foundation (FCG, Portugal)","doi-asserted-by":"publisher","award":["2022.02763"],"award-info":[{"award-number":["2022.02763"]}],"id":[{"id":"10.13039\/501100001871","id-type":"DOI","asserted-by":"publisher"}]},{"name":"Investigador FCT","award":["202D800013"],"award-info":[{"award-number":["202D800013"]}]},{"name":"Investigador FCT","award":["PTDC\/SAU-ENB\/117013\/2010"],"award-info":[{"award-number":["PTDC\/SAU-ENB\/117013\/2010"]}]},{"name":"Investigador FCT","award":["2022.02763.PTDC"],"award-info":[{"award-number":["2022.02763.PTDC"]}]},{"name":"Investigador FCT","award":["2022.02763"],"award-info":[{"award-number":["2022.02763"]}]},{"name":"Investigador FCT","award":["IF\/00772\/2013"],"award-info":[{"award-number":["IF\/00772\/2013"]}]},{"name":"Investigador FCT","award":["CEECIND\/01670\/2017"],"award-info":[{"award-number":["CEECIND\/01670\/2017"]}]},{"name":"Investigador FCT","award":["PD\/BD\/113698\/2015"],"award-info":[{"award-number":["PD\/BD\/113698\/2015"]}]},{"name":"Investigador FCT","award":["2022.02763"],"award-info":[{"award-number":["2022.02763"]}]},{"name":"Stimulus of Scientific Employment","award":["202D800013"],"award-info":[{"award-number":["202D800013"]}]},{"name":"Stimulus of Scientific Employment","award":["PTDC\/SAU-ENB\/117013\/2010"],"award-info":[{"award-number":["PTDC\/SAU-ENB\/117013\/2010"]}]},{"name":"Stimulus of Scientific Employment","award":["2022.02763.PTDC"],"award-info":[{"award-number":["2022.02763.PTDC"]}]},{"name":"Stimulus of Scientific Employment","award":["2022.02763"],"award-info":[{"award-number":["2022.02763"]}]},{"name":"Stimulus of Scientific Employment","award":["IF\/00772\/2013"],"award-info":[{"award-number":["IF\/00772\/2013"]}]},{"name":"Stimulus of Scientific Employment","award":["CEECIND\/01670\/2017"],"award-info":[{"award-number":["CEECIND\/01670\/2017"]}]},{"name":"Stimulus of Scientific Employment","award":["PD\/BD\/113698\/2015"],"award-info":[{"award-number":["PD\/BD\/113698\/2015"]}]},{"name":"Stimulus of Scientific Employment","award":["2022.02763"],"award-info":[{"award-number":["2022.02763"]}]},{"DOI":"10.13039\/501100001871","name":"FCT-MCTES fellowship","doi-asserted-by":"publisher","award":["202D800013"],"award-info":[{"award-number":["202D800013"]}],"id":[{"id":"10.13039\/501100001871","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100001871","name":"FCT-MCTES fellowship","doi-asserted-by":"publisher","award":["PTDC\/SAU-ENB\/117013\/2010"],"award-info":[{"award-number":["PTDC\/SAU-ENB\/117013\/2010"]}],"id":[{"id":"10.13039\/501100001871","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100001871","name":"FCT-MCTES fellowship","doi-asserted-by":"publisher","award":["2022.02763.PTDC"],"award-info":[{"award-number":["2022.02763.PTDC"]}],"id":[{"id":"10.13039\/501100001871","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100001871","name":"FCT-MCTES fellowship","doi-asserted-by":"publisher","award":["2022.02763"],"award-info":[{"award-number":["2022.02763"]}],"id":[{"id":"10.13039\/501100001871","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100001871","name":"FCT-MCTES fellowship","doi-asserted-by":"publisher","award":["IF\/00772\/2013"],"award-info":[{"award-number":["IF\/00772\/2013"]}],"id":[{"id":"10.13039\/501100001871","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100001871","name":"FCT-MCTES fellowship","doi-asserted-by":"publisher","award":["CEECIND\/01670\/2017"],"award-info":[{"award-number":["CEECIND\/01670\/2017"]}],"id":[{"id":"10.13039\/501100001871","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100001871","name":"FCT-MCTES fellowship","doi-asserted-by":"publisher","award":["PD\/BD\/113698\/2015"],"award-info":[{"award-number":["PD\/BD\/113698\/2015"]}],"id":[{"id":"10.13039\/501100001871","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100001871","name":"FCT-MCTES fellowship","doi-asserted-by":"publisher","award":["2022.02763"],"award-info":[{"award-number":["2022.02763"]}],"id":[{"id":"10.13039\/501100001871","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100001871","name":"European Molecular Biology Organization","doi-asserted-by":"publisher","award":["202D800013"],"award-info":[{"award-number":["202D800013"]}],"id":[{"id":"10.13039\/501100001871","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100001871","name":"European Molecular Biology Organization","doi-asserted-by":"publisher","award":["PTDC\/SAU-ENB\/117013\/2010"],"award-info":[{"award-number":["PTDC\/SAU-ENB\/117013\/2010"]}],"id":[{"id":"10.13039\/501100001871","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100001871","name":"European Molecular Biology Organization","doi-asserted-by":"publisher","award":["2022.02763.PTDC"],"award-info":[{"award-number":["2022.02763.PTDC"]}],"id":[{"id":"10.13039\/501100001871","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100001871","name":"European Molecular Biology Organization","doi-asserted-by":"publisher","award":["2022.02763"],"award-info":[{"award-number":["2022.02763"]}],"id":[{"id":"10.13039\/501100001871","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100001871","name":"European Molecular Biology Organization","doi-asserted-by":"publisher","award":["IF\/00772\/2013"],"award-info":[{"award-number":["IF\/00772\/2013"]}],"id":[{"id":"10.13039\/501100001871","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100001871","name":"European Molecular Biology Organization","doi-asserted-by":"publisher","award":["CEECIND\/01670\/2017"],"award-info":[{"award-number":["CEECIND\/01670\/2017"]}],"id":[{"id":"10.13039\/501100001871","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100001871","name":"European Molecular Biology Organization","doi-asserted-by":"publisher","award":["PD\/BD\/113698\/2015"],"award-info":[{"award-number":["PD\/BD\/113698\/2015"]}],"id":[{"id":"10.13039\/501100001871","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100001871","name":"European Molecular Biology Organization","doi-asserted-by":"publisher","award":["2022.02763"],"award-info":[{"award-number":["2022.02763"]}],"id":[{"id":"10.13039\/501100001871","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":["IJMS"],"abstract":"<jats:p>Dengue virus (DENV) is a single-stranded (+)-sense RNA virus that infects humans and mosquitoes, posing a significant health risk in tropical and subtropical regions. Mature virions are composed of an icosahedral shell of envelope (E) and membrane (M) proteins circumscribing a lipid bilayer, which in turn contains a complex of the approximately 11 kb genomic RNA with capsid (C) proteins. Whereas the structure of the envelope is clearly defined, the structure of the packaged genome in complex with C proteins remains elusive. Here, we investigated the interactions of C proteins with viral RNA, in solution and inside mature virions, via footprinting and cross-linking experiments. We demonstrated that C protein interaction with DENV genomes saturates at an RNA:C protein ratio below 1:250. Moreover, we also showed that the length of the RNA genome interaction sites varies, in a multimodal distribution, consistent with the C protein binding to each RNA site mostly in singlets or pairs (and, in some instances, higher numbers). We showed that interaction sites are preferentially sites with low base pairing, as previously measured by 2\u2032-acetylation analyzed by primer extension (SHAPE) reactivity indicating structuredness. We found a clear association pattern emerged: RNA-C protein binding sites are strongly associated with long-range RNA\u2013RNA interaction sites, particularly inside virions. This, in turn, explains the need for C protein in viral genome packaging: the protein has a chief role in coordinating these key interactions, promoting proper packaging of viral RNA. Such sites are, thus, highly consequential for viral assembly, and, as such, may be targeted in future drug development strategies against these and related viruses.<\/jats:p>","DOI":"10.3390\/ijms24098158","type":"journal-article","created":{"date-parts":[[2023,5,3]],"date-time":"2023-05-03T01:36:38Z","timestamp":1683077798000},"page":"8158","update-policy":"https:\/\/doi.org\/10.3390\/mdpi_crossmark_policy","source":"Crossref","is-referenced-by-count":10,"title":["Dengue Virus Capsid Protein Facilitates Genome Compaction and Packaging"],"prefix":"10.3390","volume":"24","author":[{"given":"Priscilla L. S.","family":"Boon","sequence":"first","affiliation":[{"name":"Bioinformatics Institute (BII), Agency for Science, Technology and Research (A*STAR), Singapore 138671, Singapore"},{"name":"Department of Biological Sciences (DBS), National University of Singapore (NUS), 16 Science Drive 4, Singapore 117558, Singapore"}]},{"given":"Ana S.","family":"Martins","sequence":"additional","affiliation":[{"name":"Instituto de Medicina Molecular, Faculdade de Medicina, Universidade de Lisboa, Av. Prof. Egas Moniz, 1649-028 Lisbon, Portugal"}]},{"given":"Xin Ni","family":"Lim","sequence":"additional","affiliation":[{"name":"Genome Institute of Singapore (GIS), Agency for Science, Technology and Research (A*STAR), Singapore 138672, Singapore"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-8072-8557","authenticated-orcid":false,"given":"Francisco J.","family":"Enguita","sequence":"additional","affiliation":[{"name":"Instituto de Medicina Molecular, Faculdade de Medicina, Universidade de Lisboa, Av. Prof. Egas Moniz, 1649-028 Lisbon, Portugal"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-0580-0475","authenticated-orcid":false,"given":"Nuno C.","family":"Santos","sequence":"additional","affiliation":[{"name":"Instituto de Medicina Molecular, Faculdade de Medicina, Universidade de Lisboa, Av. Prof. Egas Moniz, 1649-028 Lisbon, Portugal"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-2900-098X","authenticated-orcid":false,"given":"Peter J.","family":"Bond","sequence":"additional","affiliation":[{"name":"Bioinformatics Institute (BII), Agency for Science, Technology and Research (A*STAR), Singapore 138671, Singapore"},{"name":"Department of Biological Sciences (DBS), National University of Singapore (NUS), 16 Science Drive 4, Singapore 117558, Singapore"}]},{"given":"Yue","family":"Wan","sequence":"additional","affiliation":[{"name":"Genome Institute of Singapore (GIS), Agency for Science, Technology and Research (A*STAR), Singapore 138672, Singapore"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-9284-8599","authenticated-orcid":false,"given":"Ivo C.","family":"Martins","sequence":"additional","affiliation":[{"name":"Instituto de Medicina Molecular, Faculdade de Medicina, Universidade de Lisboa, Av. Prof. Egas Moniz, 1649-028 Lisbon, Portugal"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-5093-5988","authenticated-orcid":false,"given":"Roland G.","family":"Huber","sequence":"additional","affiliation":[{"name":"Bioinformatics Institute (BII), Agency for Science, Technology and Research (A*STAR), Singapore 138671, Singapore"}]}],"member":"1968","published-online":{"date-parts":[[2023,5,2]]},"reference":[{"key":"ref_1","doi-asserted-by":"crossref","first-page":"854","DOI":"10.1038\/s41564-019-0376-y","article-title":"Past and future spread of the arbovirus vectors Aedes aegypti and Aedes albopictus","volume":"4","author":"Kraemer","year":"2019","journal-title":"Nat. Microbiol."},{"key":"ref_2","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1016\/B978-0-12-385034-8.00001-6","article-title":"Recent developments in understanding dengue virus replication","volume":"77","author":"Torres","year":"2010","journal-title":"Adv. Virus Res."},{"key":"ref_3","doi-asserted-by":"crossref","first-page":"215","DOI":"10.1042\/BJ20140456","article-title":"Flaviviral RNAs: Weapons and targets in the war between virus and host","volume":"462","author":"Bidet","year":"2014","journal-title":"Biochem. J."},{"key":"ref_4","doi-asserted-by":"crossref","first-page":"13","DOI":"10.1038\/nrmicro1067","article-title":"A structural perspective of the Flavivirus life cycle","volume":"3","author":"Mukhopadhyay","year":"2005","journal-title":"Nat. Rev. Microbiol."},{"key":"ref_5","doi-asserted-by":"crossref","unstructured":"Silva, N.M., Santos, N.C., and Martins, I.C. (2020). Dengue and Zika viruses: Epidemiological history, potential therapies, and promising vaccines. Trop. Med. Infect. Dis., 5.","DOI":"10.3390\/tropicalmed5040150"},{"key":"ref_6","doi-asserted-by":"crossref","unstructured":"De Falco, L., Silva, N.M., Santos, N.C., Huber, R.G., and Martins, I.C. (2021). The Pseudo-Circular Genomes of Flaviviruses: Structures, Mechanisms, and Functions of Circularization. Cells, 10.","DOI":"10.3390\/cells10030642"},{"key":"ref_7","doi-asserted-by":"crossref","first-page":"2773","DOI":"10.1007\/s00018-010-0357-z","article-title":"Dengue virus life cycle: Viral and host factors modulating infectivity","volume":"67","author":"Wilschut","year":"2010","journal-title":"Cell. Mol. Life Sci."},{"key":"ref_8","doi-asserted-by":"crossref","first-page":"425","DOI":"10.1038\/nature17994","article-title":"Structure of the thermally stable Zika virus","volume":"533","author":"Kostyuchenko","year":"2016","journal-title":"Nature"},{"key":"ref_9","doi-asserted-by":"crossref","first-page":"443","DOI":"10.1038\/497443a","article-title":"Dengue virus: Two hosts, two structures","volume":"497","author":"Rey","year":"2013","journal-title":"Nature"},{"key":"ref_10","doi-asserted-by":"crossref","first-page":"105","DOI":"10.1038\/nsmb.2463","article-title":"Cryo-EM structure of the mature dengue virus at 3.5-\u00c5 resolution","volume":"20","author":"Zhang","year":"2013","journal-title":"Nat. Struct. Mol. Biol."},{"key":"ref_11","doi-asserted-by":"crossref","first-page":"3414","DOI":"10.1073\/pnas.0305892101","article-title":"Solution structure of dengue virus capsid protein reveals another fold","volume":"101","author":"Ma","year":"2004","journal-title":"Proc. Natl. Acad. Sci. USA"},{"key":"ref_12","doi-asserted-by":"crossref","first-page":"948","DOI":"10.1016\/j.jmb.2018.02.006","article-title":"Crystal Structure of the Capsid Protein from Zika Virus","volume":"430","author":"Shang","year":"2018","journal-title":"J. Mol. Biol."},{"key":"ref_13","doi-asserted-by":"crossref","first-page":"1157","DOI":"10.1016\/j.str.2004.04.024","article-title":"West Nile Virus Core Protein: Tetramer structure and ribbon formation","volume":"12","author":"Dokland","year":"2004","journal-title":"Structure"},{"key":"ref_14","doi-asserted-by":"crossref","first-page":"405","DOI":"10.1042\/BJ20112219","article-title":"The disordered N-terminal region of dengue virus capsid protein contains a lipid-droplet-binding motif","volume":"444","author":"Martins","year":"2012","journal-title":"Biochem. J."},{"key":"ref_15","doi-asserted-by":"crossref","first-page":"517","DOI":"10.1021\/cb500640t","article-title":"Understanding dengue virus capsid protein disordered N-terminus and pep14-23-based inhibition","volume":"10","author":"Faustino","year":"2015","journal-title":"ACS Chem. Biol."},{"key":"ref_16","doi-asserted-by":"crossref","unstructured":"Faustino, A.F., Martins, A.S., Karguth, N., Artilheiro, V., Enguita, F.J., Ricardo, J.C., Santos, N.C., and Martins, I.C. (2019). Structural and functional properties of the capsid protein of dengue and related flavivirus. Int. J. Mol. Sci., 20.","DOI":"10.3390\/ijms20163870"},{"key":"ref_17","doi-asserted-by":"crossref","first-page":"717","DOI":"10.1016\/S0092-8674(02)00660-8","article-title":"Structure of Dengue Virus: Implications for Flavivirus Organization, Maturation, and Fusion","volume":"108","author":"Kuhn","year":"2002","journal-title":"Cell"},{"key":"ref_18","doi-asserted-by":"crossref","first-page":"2267","DOI":"10.1111\/febs.13274","article-title":"Rethinking the capsid proteins of enveloped viruses: Multifunctionality from genome packaging to genome transfection","volume":"282","author":"Freire","year":"2015","journal-title":"FEBS J."},{"key":"ref_19","doi-asserted-by":"crossref","first-page":"2604","DOI":"10.1093\/emboj\/cdg270","article-title":"Structures of immature flavivirus particles","volume":"22","author":"Zhang","year":"2003","journal-title":"EMBO J."},{"key":"ref_20","doi-asserted-by":"crossref","first-page":"146","DOI":"10.1016\/j.sbi.2019.12.019","article-title":"Multiscale modelling and simulation of viruses","volume":"61","author":"Marzinek","year":"2020","journal-title":"Curr. Opin. Struct. Biol."},{"key":"ref_21","doi-asserted-by":"crossref","first-page":"1610","DOI":"10.1038\/nprot.2006.249","article-title":"Selective 2\u2032-hydroxyl acylation analyzed by primer extension (SHAPE): Quantitative RNA structure analysis at single nucleotide resolution","volume":"1","author":"Wilkinson","year":"2006","journal-title":"Nat. Protoc."},{"key":"ref_22","doi-asserted-by":"crossref","first-page":"1408","DOI":"10.1038\/s41467-019-09391-8","article-title":"Structure mapping of dengue and Zika viruses reveals functional long-range interactions","volume":"10","author":"Huber","year":"2019","journal-title":"Nat. Commun."},{"key":"ref_23","doi-asserted-by":"crossref","first-page":"1643","DOI":"10.1038\/nprot.2015.103","article-title":"Selective 2\u2032-hydroxyl acylation analyzed by primer extension and mutational profiling (SHAPE-MaP) for direct, versatile and accurate RNA structure analysis","volume":"10","author":"Smola","year":"2015","journal-title":"Nat. Protoc."},{"key":"ref_24","doi-asserted-by":"crossref","first-page":"785","DOI":"10.1038\/s41592-018-0121-0","article-title":"COMRADES determines in vivo RNA structures and interactions","volume":"15","author":"Ziv","year":"2018","journal-title":"Nat. Methods"},{"key":"ref_25","doi-asserted-by":"crossref","first-page":"875","DOI":"10.1016\/j.chom.2018.10.011","article-title":"Integrative Analysis of Zika Virus Genome RNA Structure Reveals Critical Determinants of Viral Infectivity","volume":"24","author":"Li","year":"2018","journal-title":"Cell Host Microbe"},{"key":"ref_26","doi-asserted-by":"crossref","first-page":"1647","DOI":"10.1038\/s41598-018-37599-z","article-title":"Fast NMR method to probe solvent accessibility and disordered regions in proteins","volume":"9","author":"Faustino","year":"2019","journal-title":"Sci. Rep."},{"key":"ref_27","doi-asserted-by":"crossref","first-page":"491","DOI":"10.1038\/nrmicro2368","article-title":"Biology and pathogenesis of chikungunya virus","volume":"8","author":"Schwartz","year":"2010","journal-title":"Nat. Rev. Microbiol."},{"key":"ref_28","doi-asserted-by":"crossref","first-page":"2135","DOI":"10.1016\/j.molcel.2021.02.036","article-title":"The SARS-CoV-2 subgenome landscape and its novel regulatory features","volume":"81","author":"Wang","year":"2021","journal-title":"Mol. Cell"},{"key":"ref_29","doi-asserted-by":"crossref","first-page":"9789","DOI":"10.1093\/nar\/gkz686","article-title":"Circularization of flavivirus genomic RNA inhibits de novo translation initiation","volume":"47","author":"Sanford","year":"2019","journal-title":"Nucleic Acids Res."},{"key":"ref_30","doi-asserted-by":"crossref","first-page":"8968","DOI":"10.1093\/nar\/gkx584","article-title":"Genome-wide analysis of influenza viral RNA and nucleoprotein association","volume":"45","author":"Lee","year":"2017","journal-title":"Nucleic Acids Res."},{"key":"ref_31","doi-asserted-by":"crossref","first-page":"712","DOI":"10.1093\/nar\/gkm1051","article-title":"RNA chaperoning and intrinsic disorder in the core proteins of Flaviviridae","volume":"36","author":"Lavergne","year":"2008","journal-title":"Nucleic Acids Res."}],"container-title":["International Journal of Molecular Sciences"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/www.mdpi.com\/1422-0067\/24\/9\/8158\/pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2025,10,10]],"date-time":"2025-10-10T19:28:31Z","timestamp":1760124511000},"score":1,"resource":{"primary":{"URL":"https:\/\/www.mdpi.com\/1422-0067\/24\/9\/8158"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2023,5,2]]},"references-count":31,"journal-issue":{"issue":"9","published-online":{"date-parts":[[2023,5]]}},"alternative-id":["ijms24098158"],"URL":"https:\/\/doi.org\/10.3390\/ijms24098158","relation":{},"ISSN":["1422-0067"],"issn-type":[{"value":"1422-0067","type":"electronic"}],"subject":[],"published":{"date-parts":[[2023,5,2]]}}}