{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,7,7]],"date-time":"2026-07-07T23:08:44Z","timestamp":1783465724836,"version":"3.55.0"},"reference-count":59,"publisher":"Springer Science and Business Media LLC","issue":"1","license":[{"start":{"date-parts":[[2017,11,8]],"date-time":"2017-11-08T00:00:00Z","timestamp":1510099200000},"content-version":"tdm","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0"},{"start":{"date-parts":[[2017,11,8]],"date-time":"2017-11-08T00:00:00Z","timestamp":1510099200000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0"}],"content-domain":{"domain":["link.springer.com"],"crossmark-restriction":false},"short-container-title":["Sci Rep"],"abstract":"<jats:title>Abstract<\/jats:title><jats:p>Influenza A virus is a threat for humans due to seasonal epidemics and occasional pandemics. This virus can generate new strains that are dangerous through nucleotide\/amino acid changes or through segmental recombination of the viral RNA genome. It is important to gain wider knowledge about influenza virus RNA to create new strategies for drugs that will inhibit its spread. Here, we present the experimentally determined secondary structure of the influenza segment 5 (+)RNA. Two RNAs were studied: the full-length segment 5 (+)RNA and a shorter construct containing only the coding region. Chemical mapping data combined with thermodynamic energy minimization were used in secondary structure prediction. Sequence\/structure analysis showed that the determined secondary structure of segment 5 (+)RNA is mostly conserved between influenza virus type A strains. Microarray mapping and RNase H cleavage identified accessible sites for oligonucleotides in the revealed secondary structure of segment 5 (+)RNA. Antisense oligonucleotides were designed based on the secondary structure model and tested against influenza virus in cell culture. Inhibition of influenza virus proliferation was noticed, identifying good targets for antisense strategies. Effective target sites fall within two domains, which are conserved in sequence\/structure indicating their importance to the virus.<\/jats:p>","DOI":"10.1038\/s41598-017-15317-5","type":"journal-article","created":{"date-parts":[[2017,11,2]],"date-time":"2017-11-02T19:46:54Z","timestamp":1509652014000},"update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":18,"title":["Influenza virus segment 5 (+)RNA - secondary structure and new targets for antiviral strategies"],"prefix":"10.1038","volume":"7","author":[{"given":"Marta","family":"Soszynska-Jozwiak","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Paula","family":"Michalak","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Walter N.","family":"Moss","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Ryszard","family":"Kierzek","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Julita","family":"Kesy","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Elzbieta","family":"Kierzek","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"297","published-online":{"date-parts":[[2017,11,8]]},"reference":[{"key":"15317_CR1","doi-asserted-by":"publisher","first-page":"10602","DOI":"10.1073\/pnas.191268798","volume":"98","author":"SH Bae","year":"2001","unstructured":"Bae, S. H. et al. Structural features of an influenza virus promoter and their implications for viral RNA synthesis. Proc. Natl. Acad. Sci. USA \n                           98, 10602\u201310607 (2001).","journal-title":"Proc. Natl. Acad. Sci. USA"},{"key":"15317_CR2","doi-asserted-by":"publisher","first-page":"e0156906","DOI":"10.1371\/journal.pone.0156906","volume":"11","author":"T Jiang","year":"2016","unstructured":"Jiang, T., Nogales, A., Baker, S. F., Martinez-Sobrido, L. & Turner, D. H. Mutations designed by ensemble defect to misfold conserved RNA structures of influenza A segments 7 and 8 affect splicing and attenuate viral replication in cell culture. Plos One \n                           11, e0156906 (2016).","journal-title":"Plos One"},{"key":"15317_CR3","doi-asserted-by":"publisher","first-page":"475","DOI":"10.1089\/hum.2015.070","volume":"26","author":"KE Lundin","year":"2015","unstructured":"Lundin, K. E., Gissberg, O. & Smith, C. I. E. Oligonucleotide therapies: the past and the present. Hum. Gene Therapy \n                           26, 475\u2013485 (2015).","journal-title":"Hum. Gene Therapy"},{"key":"15317_CR4","doi-asserted-by":"publisher","first-page":"238","DOI":"10.1038\/nbt.3765","volume":"35","author":"A Khvorova","year":"2017","unstructured":"Khvorova, A. & Watts, J. K. The chemical evolution of oligonucleotide therapies of clinical utility. Nature Biotech. \n                           35, 238\u2013248 (2017).","journal-title":"Nature Biotech."},{"key":"15317_CR5","doi-asserted-by":"publisher","first-page":"249","DOI":"10.1038\/nbt.3784","volume":"35","author":"O Khorkova","year":"2017","unstructured":"Khorkova, O. & Wahlestedt, C. Oligonucleotide therapies for disorders of the nervous system. Nature Biotech. \n                           35, 249\u2013263 (2017).","journal-title":"Nature Biotech."},{"key":"15317_CR6","doi-asserted-by":"publisher","first-page":"e35989","DOI":"10.1371\/journal.pone.0035989","volume":"7","author":"SF Priore","year":"2012","unstructured":"Priore, S. F., Moss, W. N. & Turner, D. H. Influenza A virus coding regions exhibit host-specific global ordered RNA structure. Plos One \n                           7, e35989 (2012).","journal-title":"Plos One"},{"key":"15317_CR7","doi-asserted-by":"publisher","first-page":"991","DOI":"10.1261\/rna.2619511","volume":"17","author":"WN Moss","year":"2011","unstructured":"Moss, W. N., Priore, S. F. & Turner, D. H. Identification of potential conserved RNA secondary structure throughout influenza A coding regions. RNA-Publ. RNA Soc. \n                           17, 991\u20131011 (2011).","journal-title":"RNA-Publ. RNA Soc."},{"key":"15317_CR8","doi-asserted-by":"publisher","first-page":"e0141132","DOI":"10.1371\/journal.pone.0141132","volume":"10","author":"M Soszynska-Jozwiak","year":"2015","unstructured":"Soszynska-Jozwiak, M., Michalak, P., Moss, W. N., Kierzek, R. & Kierzek, E. A conserved secondary structural element in the coding region of the influenza A virus nucleoprotein (NP) mRNA is important for the regulation of viral proliferation. Plos One \n                           10, e0141132 (2015).","journal-title":"Plos One"},{"key":"15317_CR9","doi-asserted-by":"publisher","first-page":"e70615","DOI":"10.1371\/journal.pone.0070615","volume":"8","author":"SF Priore","year":"2013","unstructured":"Priore, S. F. et al. Secondary structure of a conserved domain in the intron of influenza A NS1 mRNA. Plos One \n                           8, e70615 (2013).","journal-title":"Plos One"},{"key":"15317_CR10","doi-asserted-by":"publisher","first-page":"3269","DOI":"10.1021\/acs.biochem.5b00012","volume":"54","author":"JL Chen","year":"2015","unstructured":"Chen, J. L., Kennedy, S. D. & Turner, D. H. Structural Features of a 3\u2032 Splice Site in Influenza A. Biochemistry \n                           54, 3269\u20133285 (2015).","journal-title":"Biochemistry"},{"key":"15317_CR11","doi-asserted-by":"publisher","first-page":"e0148281","DOI":"10.1371\/journal.pone.0148281","volume":"11","author":"E Lenartowicz","year":"2016","unstructured":"Lenartowicz, E. et al. Self-folding of naked segment 8 genomic RNA of influenza A virus. Plos One \n                           11, e0148281 (2016).","journal-title":"Plos One"},{"key":"15317_CR12","doi-asserted-by":"publisher","first-page":"4327","DOI":"10.1042\/BCJ20160651","volume":"473","author":"A Ruszkowska","year":"2016","unstructured":"Ruszkowska, A., Lenartowicz, E., Moss, W. N., Kierzek, R. & Kierzek, E. Secondary structure model of the naked segment 7 influenza A virus genomic RNA. Biochem. J. \n                           473, 4327\u20134348 (2016).","journal-title":"Biochem. J."},{"key":"15317_CR13","doi-asserted-by":"publisher","first-page":"277","DOI":"10.1089\/nat.2016.0619","volume":"26","author":"E Lenartowicz","year":"2016","unstructured":"Lenartowicz, E. et al. Antisense oligonucleotides targeting influenza A segment 8 genomic RNA inhibit viral replication. Nucl. Acid Therapeutics \n                           26, 277\u2013285 (2016).","journal-title":"Nucl. Acid Therapeutics"},{"key":"15317_CR14","doi-asserted-by":"publisher","first-page":"e38323","DOI":"10.1371\/journal.pone.0038323","volume":"7","author":"WN Moss","year":"2012","unstructured":"Moss, W. N. et al. The 3\u2032 splice site of influenza A segment 7 mRNA can exist in two conformations: a pseudoknot and a hairpin. Plos One \n                           7, e38323 (2012).","journal-title":"Plos One"},{"key":"15317_CR15","doi-asserted-by":"publisher","first-page":"5236","DOI":"10.1021\/bi500611j","volume":"53","author":"T Jiang","year":"2014","unstructured":"Jiang, T., Kennedy, S. D., Moss, W. N., Kierzek, E. & Turner, D. H. Secondary structure of a conserved domain in an intron of influenza A M1 mRNA. Biochemistry \n                           53, 5236\u20135248 (2014).","journal-title":"Biochemistry"},{"key":"15317_CR16","doi-asserted-by":"publisher","first-page":"D49","DOI":"10.1016\/j.vaccine.2008.07.039","volume":"26","author":"NM Bouvier","year":"2008","unstructured":"Bouvier, N. M. & Palese, P. The biology of influenza viruses. Vaccine \n                           26, D49\u2013D53 (2008).","journal-title":"Vaccine"},{"key":"15317_CR17","doi-asserted-by":"publisher","first-page":"2057","DOI":"10.1016\/j.intimp.2011.08.019","volume":"11","author":"T Zhang","year":"2011","unstructured":"Zhang, T. et al. Antisense oligonucleotides targeting the RNA binding region of the NP gene inhibit replication of highly pathogenic avian influenza virus H5N1. Internat. Immunopharm. \n                           11, 2057\u20132061 (2011).","journal-title":"Internat. Immunopharm."},{"key":"15317_CR18","doi-asserted-by":"publisher","first-page":"942","DOI":"10.4161\/rna.29730","volume":"11","author":"AP Gultyaev","year":"2014","unstructured":"Gultyaev, A. P. et al. RNA structural constraints in the evolution of the influenza A virus genome NP segment. RNA Biology \n                           11, 942\u2013952 (2014).","journal-title":"RNA Biology"},{"key":"15317_CR19","doi-asserted-by":"publisher","first-page":"533","DOI":"10.3109\/08830185.2010.507828","volume":"29","author":"AP Gultyaev","year":"2010","unstructured":"Gultyaev, A. P., Fouchier, R. A. M. & Olsthoorn, R. C. L. Influenza virus RNAstructure: unique and common features. Internat. Rev. Immun. \n                           29, 533\u2013556 (2010).","journal-title":"Internat. Rev. Immun."},{"key":"15317_CR20","doi-asserted-by":"publisher","first-page":"4197","DOI":"10.1093\/nar\/24.21.4197","volume":"24","author":"HK Cheong","year":"1996","unstructured":"Cheong, H. K., Cheong, C. & Choi, B. S. Secondary structure of the panhandle RNA of influenza virus A studied by NMR spectroscopy. Nucl. Acids Res. \n                           24, 4197\u20134201 (1996).","journal-title":"Nucl. Acids Res."},{"key":"15317_CR21","doi-asserted-by":"publisher","first-page":"13398","DOI":"10.1128\/JVI.06250-11","volume":"85","author":"RG Brinson","year":"2011","unstructured":"Brinson, R. G., Szakal, A. L. & Marino, J. P. Structural characterization of the viral and cRNA panhandle motifs from the infectious salmon anemia virus. J. Virol. \n                           85, 13398\u201313408 (2011).","journal-title":"J. Virol."},{"key":"15317_CR22","doi-asserted-by":"publisher","first-page":"9109","DOI":"10.1093\/nar\/15.22.9109","volume":"15","author":"C Ehresmann","year":"1987","unstructured":"Ehresmann, C. et al. Probing the structure of RNAs in solution. Nucl. Acids Res. \n                           15, 9109\u20139128 (1987).","journal-title":"Nucl. Acids Res."},{"key":"15317_CR23","doi-asserted-by":"crossref","unstructured":"Ziehler, W. A. & Engelke, D. R. Probing RNA structure with chemical reagents and enzymes. Curr. Protoc. Nucl. Acid Chem. 6 unit 6.1 (2001).","DOI":"10.1002\/0471142700.nc0601s00"},{"key":"15317_CR24","doi-asserted-by":"publisher","first-page":"4223","DOI":"10.1021\/ja043822v","volume":"127","author":"EJ Merino","year":"2005","unstructured":"Merino, E. J., Wilkinson, K. A., Coughlan, J. L. & Weeks, K. M. RNA structure analysis at single nucleotide resolution by selective 2\u2032-hydroxyl acylation and primer extension (SHAPE). J. Am. Chem. Soc. \n                           127, 4223\u20134231 (2005).","journal-title":"J. Am. Chem. Soc."},{"key":"15317_CR25","doi-asserted-by":"publisher","first-page":"11725","DOI":"10.1128\/JVI.01477-12","volume":"86","author":"NA Ilyushina","year":"2012","unstructured":"Ilyushina, N. A. et al. Comparative study of influenza virus replication in MDCK cells and in primary cells derived from adenoids and airway epithelium. J. Virol. \n                           86, 11725\u201311734 (2012).","journal-title":"J. Virol."},{"key":"15317_CR26","doi-asserted-by":"publisher","first-page":"34504","DOI":"10.1074\/jbc.M111.262048","volume":"286","author":"S Aggarwal","year":"2011","unstructured":"Aggarwal, S., Dewhurst, S., Takimoto, T. & Kim, B. Biochemical impact of the host adaptation-associated PB2 E627K mutation on the temperature-dependent RNA synthesis kinetics of influenza A virus polymerase complex. J. Biol. Chem. \n                           286, 34504\u201334513 (2011).","journal-title":"J. Biol. Chem."},{"key":"15317_CR27","doi-asserted-by":"publisher","first-page":"2824","DOI":"10.1093\/nar\/gkg387","volume":"31","author":"CJ Park","year":"2003","unstructured":"Park, C. J., Bae, S. H., Lee, M. K., Varani, G. & Choi, B. S. Solution structure of the influenza A virus cRNA promoter: implications for differential recognition of viral promoter structures by RNA-dependent RNA polymerase. Nucl. Acids Res. \n                           31, 2824\u20132832 (2003).","journal-title":"Nucl. Acids Res."},{"key":"15317_CR28","doi-asserted-by":"publisher","first-page":"1805","DOI":"10.1261\/rna.1643609","volume":"15","author":"ZJ Lu","year":"2009","unstructured":"Lu, Z. J., Gloor, J. W. & Mathews, D. H. Improved RNA secondary structure prediction by maximizing expected pair accuracy. RNA-Publ. RNA Soc. \n                           15, 1805\u20131813 (2009).","journal-title":"RNA-Publ. RNA Soc."},{"key":"15317_CR29","doi-asserted-by":"publisher","first-page":"596","DOI":"10.1128\/JVI.02005-07","volume":"82","author":"Y Bao","year":"2008","unstructured":"Bao, Y. et al. The influenza virus resource at the national center for biotechnology information. J. Virol. \n                           82, 596\u2013601 (2008).","journal-title":"J. Virol."},{"key":"15317_CR30","first-page":"273","volume":"1","author":"AP Gultyaev","year":"2014","unstructured":"Gultyaev, A. P., Olsthoorn, R. C. L., Spronken, M. I. J. & Fouchier, R. A. M. Detection of structural constraints and conformational transitions in the influenza virus RNA genome using structure predictions and mutual information calculations. Proc. IWBBIO 2014, International Work-Conference on Bioinformatics and Biomedicinal Engineering \n                           1, 273\u2013284 (2014).","journal-title":"Proc. IWBBIO 2014, International Work-Conference on Bioinformatics and Biomedicinal Engineering"},{"key":"15317_CR31","doi-asserted-by":"publisher","first-page":"428","DOI":"10.1016\/j.jmb.2009.04.048","volume":"390","author":"E Kierzek","year":"2009","unstructured":"Kierzek, E. et al. Secondary structures for 5\u2032 regions of R2 retrotransposon RNAs reveal a novel conserved pseudoknot and regions that evolve under different constraints. J. Mol. Biol. \n                           390, 428\u2013442 (2009).","journal-title":"J. Mol. Biol."},{"key":"15317_CR32","doi-asserted-by":"publisher","first-page":"1770","DOI":"10.1093\/nar\/gkm1085","volume":"36","author":"E Kierzek","year":"2008","unstructured":"Kierzek, E. et al. Isoenergetic penta- and hexanucleotide microarray probing and chemical mapping provide a secondary structure model for an RNA element orchestrating R2 retrotransposon protein function. Nucl. Acids Res. \n                           36, 1770\u20131782 (2008).","journal-title":"Nucl. Acids Res."},{"key":"15317_CR33","doi-asserted-by":"publisher","first-page":"11344","DOI":"10.1021\/bi901264v","volume":"48","author":"E Kierzek","year":"2009","unstructured":"Kierzek, E. Binding of short oligonucleotides to RNA: studies of the binding of common RNA structural motifs to isoenergetic microarrays. Biochemistry \n                           48, 11344\u201311356 (2009).","journal-title":"Biochemistry"},{"key":"15317_CR34","doi-asserted-by":"publisher","first-page":"4055","DOI":"10.1093\/nar\/gkm421","volume":"35","author":"A Pasternak","year":"2007","unstructured":"Pasternak, A., Kierzek, E., Pasternak, K., Turner, D. H. & Kierzek, R. A chemical synthesis of LNA-2,6-diaminopurine riboside, and the influence of 2\u2032-O-methyl-2,6-diaminopurine and LNA-2,6-diaminopurine ribosides on the thermodynamic properties of 2\u2032-O-methylRNA\/RNA heteroduplexes. Nucl. Acids Res. \n                           35, 4055\u20134063 (2007).","journal-title":"Nucl. Acids Res."},{"key":"15317_CR35","doi-asserted-by":"publisher","first-page":"1249","DOI":"10.1021\/bi701758z","volume":"47","author":"A Pasternak","year":"2008","unstructured":"Pasternak, A. et al. The thermodynamics of 3\u2032-terminal pyrene and guanosine for the design of isoenergetic 2\u2032-O-methyl-RNA-LNA chimeric oligonucleotide probes of RNA structure. Biochemistry \n                           47, 1249\u20131258 (2008).","journal-title":"Biochemistry"},{"key":"15317_CR36","doi-asserted-by":"publisher","first-page":"5082","DOI":"10.1093\/nar\/gki789","volume":"33","author":"E Kierzek","year":"2005","unstructured":"Kierzek, E. et al. The influence of locked nucleic acid residues on the thermodynamic properties of 2\u2032-O-methylRNA\/RNA heteroduplexes. Nucl. Acids Res. \n                           33, 5082\u20135093 (2005).","journal-title":"Nucl. Acids Res."},{"key":"15317_CR37","doi-asserted-by":"publisher","first-page":"207","DOI":"10.4161\/rna.8.2.14513","volume":"8","author":"P Resa-Infante","year":"2011","unstructured":"Resa-Infante, P., Jorba, N., Coloma, R. & Ort\u00edn, J. The influenza virus RNA synthesis machine. RNA Biology \n                           8, 207\u2013215 (2011).","journal-title":"RNA Biology"},{"key":"15317_CR38","doi-asserted-by":"publisher","first-page":"e00070","DOI":"10.1128\/mBio.00070-14","volume":"5","author":"J Dubois","year":"2014","unstructured":"Dubois, J., Terrier, O. & Rosa-Calatrava, M. Influenza viruses and mRNA splicing: doing more with less. mBio \n                           5, e00070\u201314 (2014).","journal-title":"mBio"},{"key":"15317_CR39","doi-asserted-by":"publisher","first-page":"238","DOI":"10.1073\/pnas.1315068110","volume":"110","author":"A York","year":"2013","unstructured":"York, A., Hengrung, N., Vreede, F. T., Huiskonen, J. T. & Fodor, E. Isolation and characterization of the positive-sense replicative intermediate of a negative-strand RNA virus. Proc. Natl. Acad. Sci. USA \n                           110, 238\u2013245 (2013).","journal-title":"Proc. Natl. Acad. Sci. USA"},{"key":"15317_CR40","doi-asserted-by":"publisher","first-page":"8968","DOI":"10.1093\/nar\/gkx584","volume":"45","author":"N Lee","year":"2017","unstructured":"Lee, N. et al. Genome-wide analysis of influenza viral RNA and nucleoprotein association. Nucl. Acids Res. \n                           45, 8968\u20138977 (2017).","journal-title":"Nucl. Acids Res."},{"key":"15317_CR41","doi-asserted-by":"publisher","first-page":"253","DOI":"10.1177\/095632029800900306","volume":"9","author":"H Bai","year":"1998","unstructured":"Bai, H., You, Y., Bo, X. & Wang, S. Antisense antivirals: future oligonucleotides-based therapeutics for viral infectious diseases. Antivir. Chem. Chemother. \n                           9, 253\u2013262 (1998).","journal-title":"Antivir. Chem. Chemother."},{"key":"15317_CR42","doi-asserted-by":"publisher","first-page":"14719","DOI":"10.1021\/bi9809425","volume":"37","author":"T Xia","year":"1998","unstructured":"Xia, T. et al. Thermodynamic parameters for an expanded nearest-neighbor model for formation of RNA duplexes with Watson-Crick base pairs. Biochemistry \n                           37, 14719\u201314735 (1998).","journal-title":"Biochemistry"},{"key":"15317_CR43","doi-asserted-by":"publisher","first-page":"4472","DOI":"10.1093\/nar\/gkg633","volume":"31","author":"E Kierzek","year":"2003","unstructured":"Kierzek, E. & Kierzek, R. The thermodynamic stability of RNA duplexes and hairpins containing N6-alkyladenosines and 2-methylthio-N6-alkyladenosines. Nucl. Acids Res. \n                           31, 4472\u20134480 (2003).","journal-title":"Nucl. Acids Res."},{"key":"15317_CR44","doi-asserted-by":"publisher","first-page":"1979","DOI":"10.1261\/rna.1166808","volume":"14","author":"SM Vasa","year":"2008","unstructured":"Vasa, S. M., Guex, N., Wilkinson, K. A., Weeks, K. M. & Giddings, M. G. ShapeFinder: A software system for high-throughput quantitative analysis of nucleic acid reactivity information resolved by capillary electrophoresis. RNA-Publ. RNA Soc. \n                           14, 1979\u20131990 (2008).","journal-title":"RNA-Publ. RNA Soc."},{"key":"15317_CR45","doi-asserted-by":"publisher","first-page":"129","DOI":"10.1186\/1471-2105-11-129","volume":"11","author":"JS Reuter","year":"2010","unstructured":"Reuter, J. S. & Mathews, D. H. RNAstructure: software for RNA secondary structure prediction and analysis. BMC Bioinform. \n                           11, 129 (2010).","journal-title":"BMC Bioinform."},{"key":"15317_CR46","doi-asserted-by":"publisher","first-page":"7287","DOI":"10.1073\/pnas.0401799101","volume":"101","author":"DH Mathews","year":"2004","unstructured":"Mathews, D. H. et al. Incorporating chemical modification constraints into a dynamic programming algorithm for prediction of RNA secondary structure. Proc. Natl. Acad. Sci. USA \n                           101, 7287\u20137292 (2004).","journal-title":"Proc. Natl. Acad. Sci. USA"},{"key":"15317_CR47","doi-asserted-by":"publisher","first-page":"D280","DOI":"10.1093\/nar\/gkp892","volume":"38","author":"DH Turner","year":"2010","unstructured":"Turner, D. H. & Mathews, D. H. NNDB: the nearest neighbor parameter database for predicting stability of nucleic acid secondary structure. Nucl. Acids Res. \n                           38, D280\u2013D282 (2010).","journal-title":"Nucl. Acids Res."},{"key":"15317_CR48","doi-asserted-by":"publisher","first-page":"133","DOI":"10.1093\/nar\/9.1.133","volume":"9","author":"M Zuker","year":"1981","unstructured":"Zuker, M. & Stiegler, P. Optimal computer folding of large RNA sequences using thermodynamics and auxiliary information. Nucl. Acids Res. \n                           9, 133\u2013148 (1981).","journal-title":"Nucl. Acids Res."},{"key":"15317_CR49","doi-asserted-by":"publisher","first-page":"97","DOI":"10.1073\/pnas.0806929106","volume":"106","author":"KE Deigan","year":"2009","unstructured":"Deigan, K. E., Mathews, D. H. & Weeks, K. M. Accurate SHAPE-directed RNA structure determination. Proc. Natl. Acad. Sci. USA \n                           106, 97\u2013102 (2009).","journal-title":"Proc. Natl. Acad. Sci. USA"},{"key":"15317_CR50","doi-asserted-by":"publisher","first-page":"6728","DOI":"10.1021\/bi501051k","volume":"53","author":"SJ Schroeder","year":"2014","unstructured":"Schroeder, S. J. Probing viral genomic structure: alternative viewpoints and alternative structures for satellite tobacco mosaic virus RNA. Biochemistry \n                           53, 6728\u20136737 (2014).","journal-title":"Biochemistry"},{"key":"15317_CR51","doi-asserted-by":"publisher","first-page":"167","DOI":"10.1016\/j.bpj.2011.05.053","volume":"101","author":"SJ Schroeder","year":"2011","unstructured":"Schroeder, S. J., Stone, J. W., Bleckley, S., Gibbons, T. & Mathews, D. M. Ensemble of secondary structures for encapsidated satellite tobacco mosaic virus RNA consistent with chemical probing and crystallography constraints. Biophys. J. \n                           101, 167\u2013175 (2011).","journal-title":"Biophys. J."},{"key":"15317_CR52","doi-asserted-by":"publisher","first-page":"772","DOI":"10.1093\/molbev\/mst010","volume":"30","author":"K Katoh","year":"2013","unstructured":"Katoh, K. & Standley, D. M. MAFFT multiple sequence alignment software version 7: improvements in performance and isability. Mol. Biol. Evol. \n                           30, 772\u2013780 (2013).","journal-title":"Mol. Biol. Evol."},{"key":"15317_CR53","first-page":"95","volume":"41","author":"TA Hall","year":"1999","unstructured":"Hall, T. A. BioEdit: a user-friendly biological sequence alignment editor and analysis program for Windows 95\/98\/NT. Nucl. Acids Symp. Series \n                           41, 95\u201398 (1999).","journal-title":"Nucl. Acids Symp. Series"},{"key":"15317_CR54","doi-asserted-by":"publisher","first-page":"e66","DOI":"10.1093\/nar\/28.12.e66","volume":"28","author":"V Afanassiev","year":"2000","unstructured":"Afanassiev, V., Hanemann, V. & Wolfl, S. Preparation of DNA and protein microarrays on glass slides coated with an agarose film. Nucl. Acids Res. \n                           28, e66 (2000).","journal-title":"Acids Res."},{"key":"15317_CR55","doi-asserted-by":"publisher","first-page":"8591","DOI":"10.1128\/JVI.01081-13","volume":"87","author":"SF Baker","year":"2013","unstructured":"Baker, S. F. et al. Protection against lethal influenza with a viral mimic. J. Virol. \n                           87, 8591\u20138605 (2013).","journal-title":"J. Virol."},{"key":"15317_CR56","doi-asserted-by":"publisher","first-page":"296","DOI":"10.1016\/j.virol.2005.06.023","volume":"340","author":"TJ Chapman","year":"2005","unstructured":"Chapman, T. J., Castrucci, M. R., Padrick, R. C., Bradley, L. M. & Topham, D. J. Antigen-specific and non-specific CD4+ T cell recruitment and proliferation during influenza infection. Virology \n                           340, 296\u2013306 (2005).","journal-title":"Virology"},{"key":"15317_CR57","doi-asserted-by":"publisher","first-page":"581","DOI":"10.1038\/nprot.2006.83","volume":"1","author":"P Chromczynski","year":"2006","unstructured":"Chromczynski, P. & Sacchi, N. The single-step method of RNA isolation by acid guanidinium thiocyanate-phenol-chloroform extraction: twenty-something years on. Nat. Protoc. \n                           1, 581\u2013585 (2006).","journal-title":"Nat. Protoc."},{"key":"15317_CR58","doi-asserted-by":"publisher","first-page":"2165","DOI":"10.1128\/AEM.01929-09","volume":"76","author":"CI Dovas","year":"2010","unstructured":"Dovas, C. I. et al. Detection and quantification of infectious avian influenza A (H5N1) virus in environmental water by using real-time reverse transcription-PCR. Appl. Environ. Microbiol. \n                           76, 2165\u20132174 (2010).","journal-title":"Appl. Environ. Microbiol."},{"key":"15317_CR59","doi-asserted-by":"publisher","first-page":"63","DOI":"10.1016\/j.jviromet.2010.04.017","volume":"168","author":"D Vester","year":"2010","unstructured":"Vester, D. et al. Real-time RT-qPCR assay for the analysis of human influenza A virus transcription and replication dynamics. J. Virol. Meth. \n                           168, 63\u201371 (2010).","journal-title":"J. Virol. Meth."}],"container-title":["Scientific Reports"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/www.nature.com\/articles\/s41598-017-15317-5.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/www.nature.com\/articles\/s41598-017-15317-5","content-type":"text\/html","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/www.nature.com\/articles\/s41598-017-15317-5.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2022,12,23]],"date-time":"2022-12-23T13:16:44Z","timestamp":1671801404000},"score":1,"resource":{"primary":{"URL":"https:\/\/www.nature.com\/articles\/s41598-017-15317-5"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2017,11,8]]},"references-count":59,"journal-issue":{"issue":"1","published-online":{"date-parts":[[2017,12]]}},"alternative-id":["15317"],"URL":"https:\/\/doi.org\/10.1038\/s41598-017-15317-5","relation":{},"ISSN":["2045-2322"],"issn-type":[{"value":"2045-2322","type":"electronic"}],"subject":[],"published":{"date-parts":[[2017,11,8]]},"assertion":[{"value":"30 August 2017","order":1,"name":"received","label":"Received","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"24 October 2017","order":2,"name":"accepted","label":"Accepted","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"8 November 2017","order":3,"name":"first_online","label":"First Online","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"The authors declare that they have no competing interests.","order":1,"name":"Ethics","group":{"name":"EthicsHeading","label":"Competing Interests"}}],"article-number":"15041"}}