RNA Secondary Structure Motifs of the Influenza A Virus as Targets for siRNA-Mediated RNA Interference
Tài liệu tham khảo
Shin, 2019, Novel antiviral drug discovery strategies to tackle drug-resistant mutants of influenza virus strains, Expert Opin. Drug Discov., 14, 153, 10.1080/17460441.2019.1560261
Hu, 2017, Influenza A virus nucleoprotein: a highly conserved multi-functional viral protein as a hot antiviral drug target, Curr. Top. Med. Chem., 17, 2271, 10.2174/1568026617666170224122508
Samji, 2009, Influenza A: understanding the viral life cycle, Yale J. Biol. Med., 82, 153
Bouvier, 2008, The biology of influenza viruses, Vaccine, 26, D49, 10.1016/j.vaccine.2008.07.039
Gultyaev, 2010, Influenza virus RNA structure: unique and common features, Int. Rev. Immunol., 29, 533, 10.3109/08830185.2010.507828
Moss, 2011, Identification of potential conserved RNA secondary structure throughout influenza A coding regions, RNA, 17, 991, 10.1261/rna.2619511
Priore, 2013, Secondary structure of a conserved domain in the intron of influenza A NS1 mRNA, PLoS ONE, 8, e70615, 10.1371/journal.pone.0070615
Jiang, 2014, Secondary structure of a conserved domain in an intron of influenza A M1 mRNA, Biochemistry, 53, 5236, 10.1021/bi500611j
Jiang, 2016, 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, 11, e0156906, 10.1371/journal.pone.0156906
Moss, 2012, The 3′ splice site of influenza A segment 7 mRNA can exist in two conformations: a pseudoknot and a hairpin, PLoS ONE, 7, e38323, 10.1371/journal.pone.0038323
Gultyaev, 2014, RNA structural constraints in the evolution of the influenza A virus genome NP segment, RNA Biol., 11, 942, 10.4161/rna.29730
Ruszkowska, 2016, Secondary structure model of the naked segment 7 influenza A virus genomic RNA, Biochem. J., 473, 4327, 10.1042/BCJ20160651
Lenartowicz, 2016, Self-folding of naked segment 8 genomic rna of influenza A virus, PLoS ONE, 11, e0148281, 10.1371/journal.pone.0148281
Soszynska-Jozwiak, 2017, Influenza virus segment 5 (+)RNA—secondary structure and new targets for antiviral strategies, Sci. Rep., 7, 15041, 10.1038/s41598-017-15317-5
Soszynska-Jozwiak, 2015, 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, 10, e0141132, 10.1371/journal.pone.0141132
Kobayashi, 2016, Computational and molecular analysis of conserved influenza A virus RNA secondary structures involved in infectious virion production, RNA Biol., 13, 883, 10.1080/15476286.2016.1208331
Williams, 2018, Nucleotide resolution mapping of influenza A virus nucleoprotein-RNA interactions reveals RNA features required for replication, Nat. Commun., 9, 465, 10.1038/s41467-018-02886-w
Fournier, 2012, A supramolecular assembly formed by influenza A virus genomic RNA segments, Nucleic Acids Res., 40, 2197, 10.1093/nar/gkr985
Fournier, 2012, Interaction network linking the human H3N2 influenza A virus genomic RNA segments, Vaccine, 30, 7359, 10.1016/j.vaccine.2012.09.079
Ferhadian, 2018, Structural and functional motifs in influenza virus RNAs, Front. Microbiol., 9, 559, 10.3389/fmicb.2018.00559
Simon, 2019, In vivo analysis of influenza A mRNA secondary structures identifies critical regulatory motifs, Nucleic Acids Res., 47, 7003, 10.1093/nar/gkz318
Michalak, 2019, Secondary structure of the segment 5 genomic RNA of influenza A virus and its application for designing antisense oligonucleotides, Sci. Rep., 9, 3801, 10.1038/s41598-019-40443-7
Kesy, 2019, A short chemically modified dsRNA-binding PNA (dbPNA) inhibits influenza viral replication by targeting viral RNA panhandle structure, Bioconjug. Chem., 30, 931, 10.1021/acs.bioconjchem.9b00039
Lenartowicz, 2016, Antisense oligonucleotides targeting influenza A segment 8 genomic RNA inhibit viral replication, Nucleic Acid Ther., 26, 277, 10.1089/nat.2016.0619
Price, 2015, Cas9-mediated targeting of viral RNA in eukaryotic cells, Proc. Natl. Acad. Sci. USA, 112, 6164, 10.1073/pnas.1422340112
Asha, 2018, Advancements in nucleic acid based therapeutics against respiratory viral infections, J. Clin. Med., 8, E6, 10.3390/jcm8010006
Elbashir, 2002, Analysis of gene function in somatic mammalian cells using small interfering RNAs, Methods, 26, 199, 10.1016/S1046-2023(02)00023-3
Westerhout, 2007, A systematic analysis of the effect of target RNA structure on RNA interference, Nucleic Acids Res., 35, 4322, 10.1093/nar/gkm437
Sagan, 2010, The efficacy of siRNAs against hepatitis C virus is strongly influenced by structure and target site accessibility, Chem. Biol., 17, 515, 10.1016/j.chembiol.2010.04.011
Elbashir, 2001, Duplexes of 21-nucleotide RNAs mediate RNA interference in cultured mammalian cells, Nature, 411, 494, 10.1038/35078107
Matsuoka, 2013, A comprehensive map of the influenza A virus replication cycle, BMC Syst. Biol., 7, 97, 10.1186/1752-0509-7-97
Te Velthuis, 2016, Influenza virus RNA polymerase: insights into the mechanisms of viral RNA synthesis, Nat. Rev. Microbiol., 14, 479, 10.1038/nrmicro.2016.87
Lai, 2018, mRNAs and lncRNAs intrinsically form secondary structures with short end-to-end distances, Nat. Commun., 9, 4328, 10.1038/s41467-018-06792-z
Mathews, 2002, Dynalign: an algorithm for finding the secondary structure common to two RNA sequences, J. Mol. Biol., 317, 191, 10.1006/jmbi.2001.5351
Fu, 2014, Dynalign II: common secondary structure prediction for RNA homologs with domain insertions, Nucleic Acids Res., 42, 13939, 10.1093/nar/gku1172
Harmanci, 2007, Efficient pairwise RNA structure prediction using probabilistic alignment constraints in Dynalign, BMC Bioinformatics, 8, 130, 10.1186/1471-2105-8-130
Ge, 2003, RNA interference of influenza virus production by directly targeting mRNA for degradation and indirectly inhibiting all viral RNA transcription, Proc. Natl. Acad. Sci. USA, 100, 2718, 10.1073/pnas.0437841100
Zhiqiang, 2010, Effective siRNAs inhibit the replication of novel influenza A (H1N1) virus, Antiviral Res., 85, 559, 10.1016/j.antiviral.2009.12.010
Chiu, 2003, siRNA function in RNAi: a chemical modification analysis, RNA, 9, 1034, 10.1261/rna.5103703
Muhonen, 2007, RNA interference tolerates 2′-fluoro modifications at the Argonaute2 cleavage site, Chem. Biodivers., 4, 858, 10.1002/cbdv.200790073
Braasch, 2003, RNA interference in mammalian cells by chemically-modified RNA, Biochemistry, 42, 7967, 10.1021/bi0343774
Choung, 2006, Chemical modification of siRNAs to improve serum stability without loss of efficacy, Biochem. Biophys. Res. Commun., 342, 919, 10.1016/j.bbrc.2006.02.049
Nowak, 2009, A new and efficient method for inhibition of RNA viruses by DNA interference, FEBS J., 276, 4372, 10.1111/j.1742-4658.2009.07145.x
Lamberton, 2003, Varying the nucleic acid composition of siRNA molecules dramatically varies the duration and degree of gene silencing, Mol. Biotechnol., 24, 111, 10.1385/MB:24:2:111
Hohjoh, 2002, RNA interference (RNAi) induction with various types of synthetic oligonucleotide duplexes in cultured human cells, FEBS Lett., 521, 195, 10.1016/S0014-5793(02)02860-0
Kraynack, 2006, Small interfering RNAs containing full 2′-O-methylribonucleotide-modified sense strands display Argonaute2/eIF2C2-dependent activity, RNA, 12, 163, 10.1261/rna.2150806
Amarzguioui, 2003, Tolerance for mutations and chemical modifications in a siRNA, Nucleic Acids Res., 31, 589, 10.1093/nar/gkg147
Czauderna, 2003, Structural variations and stabilising modifications of synthetic siRNAs in mammalian cells, Nucleic Acids Res., 31, 2705, 10.1093/nar/gkg393
Kierzek, 2006, Nearest neighbor parameters for Watson-Crick complementary heteroduplexes formed between 2′-O-methyl RNA and RNA oligonucleotides, Nucleic Acids Res., 34, 3609, 10.1093/nar/gkl232
Schroeder, 2018, Challenges and approaches to predicting RNA with multiple functional structures, RNA, 24, 1615, 10.1261/rna.067827.118
Zhang, 2010, [Screening efficient siRNAs in vitro as the candidate genes for chicken anti-avian influenza virus H5N1 breeding], Mol. Biol. (Mosk.), 44, 42, 10.1134/S0026893310010061
Huang, 2017, In vivo inhibition of influenza A virus replication by RNA interference targeting the PB2 subunit via intratracheal delivery, PLoS ONE, 12, e0174523, 10.1371/journal.pone.0174523
Tompkins, 2004, Protection against lethal influenza virus challenge by RNA interference in vivo, Proc. Natl. Acad. Sci. USA, 101, 8682, 10.1073/pnas.0402630101
Ge, 2004, Inhibition of influenza virus production in virus-infected mice by RNA interference, Proc. Natl. Acad. Sci. USA, 101, 8676, 10.1073/pnas.0402486101
Zhou, 2008, RNA interference of avian influenza virus H5N1 by inhibiting viral mRNA with siRNA expression plasmids, J. Biotechnol., 135, 140, 10.1016/j.jbiotec.2008.03.007
Zhou, 2007, Effective small interfering RNAs targeting matrix and nucleocapsid protein gene inhibit influenza A virus replication in cells and mice, Antiviral Res., 76, 186, 10.1016/j.antiviral.2007.07.002
Zhang, 2009, Inhibition of highly pathogenic avian influenza virus H5N1 replication by the small interfering RNA targeting polymerase A gene, Biochem. Biophys. Res. Commun., 390, 421, 10.1016/j.bbrc.2009.09.039
Li, 2011, Inhibition of influenza A virus replication by RNA interference targeted against the PB1 subunit of the RNA polymerase gene, Arch. Virol., 156, 1979, 10.1007/s00705-011-1087-8
Kim, 2019, Rekindling RNAi therapy: materials design requirements for in vivo siRNA delivery, Adv. Mater., 31, e1903637, 10.1002/adma.201903637
Smith, 2019, Therapeutic oligonucleotides: state of the art, Annu. Rev. Pharmacol. Toxicol., 59, 605, 10.1146/annurev-pharmtox-010818-021050
Prakash, 2005, Positional effect of chemical modifications on short interference RNA activity in mammalian cells, J. Med. Chem., 48, 4247, 10.1021/jm050044o
Kandeel, 2018, Molecular dynamics and binding selectivity of nucleotides and polynucleotide substrates with EIF2C2/Ago2 PAZ domain, Int. J. Biol. Macromol., 107, 2566, 10.1016/j.ijbiomac.2017.10.145
Kandeel, 2014, Bioenergetics and gene silencing approaches for unraveling nucleotide recognition by the human EIF2C2/Ago2 PAZ domain, PLoS ONE, 9, e94538, 10.1371/journal.pone.0094538
Geary, 2015, Pharmacokinetics, biodistribution and cell uptake of antisense oligonucleotides, Adv. Drug Deliv. Rev., 87, 46, 10.1016/j.addr.2015.01.008
Zheng, 2013, Single modification at position 14 of siRNA strand abolishes its gene-silencing activity by decreasing both RISC loading and target degradation, FASEB J., 27, 4017, 10.1096/fj.13-228668
Parrish, 2000, Functional anatomy of a dsRNA trigger: differential requirement for the two trigger strands in RNA interference, Mol. Cell, 6, 1077, 10.1016/S1097-2765(00)00106-4
Smalheiser, 2014, Mammalian Argonaute-DNA binding?, Biol. Direct, 10, 27, 10.1186/PREACCEPT-1466302485137399
Palauqui, 1999, Activation of systemic acquired silencing by localised introduction of DNA, Curr. Biol., 9, 59, 10.1016/S0960-9822(99)80016-5
Voinnet, 1998, Systemic spread of sequence-specific transgene RNA degradation in plants is initiated by localized introduction of ectopic promoterless DNA, Cell, 95, 177, 10.1016/S0092-8674(00)81749-3
Wu, 2014, 2′-OMe-phosphorodithioate-modified siRNAs show increased loading into the RISC complex and enhanced anti-tumour activity, Nat. Commun., 5, 3459, 10.1038/ncomms4459
Kierzek, 2003, The thermodynamic stability of RNA duplexes and hairpins containing N6-alkyladenosines and 2-methylthio-N6-alkyladenosines, Nucleic Acids Res., 31, 4472, 10.1093/nar/gkg633
Xia, 1998, Thermodynamic parameters for an expanded nearest-neighbor model for formation of RNA duplexes with Watson-Crick base pairs, Biochemistry, 37, 14719, 10.1021/bi9809425
Kierzek, 2003, The synthesis of oligoribonucleotides containing N6-alkyladenosines and 2-methylthio-N6-alkyladenosines via post-synthetic modification of precursor oligomers, Nucleic Acids Res., 31, 4461, 10.1093/nar/gkg632
Chomczynski, 2006, The single-step method of RNA isolation by acid guanidinium thiocyanate-phenol-chloroform extraction: twenty-something years on, Nat. Protoc., 1, 581, 10.1038/nprot.2006.83
Dovas, 2010, Detection and quantification of infectious avian influenza A (H5N1) virus in environmental water by using real-time reverse transcription-PCR, Appl. Environ. Microbiol., 76, 2165, 10.1128/AEM.01929-09
Vester, 2010, Real-time RT-qPCR assay for the analysis of human influenza A virus transcription and replication dynamics, J. Virol. Methods, 168, 63, 10.1016/j.jviromet.2010.04.017
McDowell, 1996, Investigation of the structural basis for thermodynamic stabilities of tandem GU mismatches: solution structure of (rGAGGUCUC)2 by two-dimensional NMR and simulated annealing, Biochemistry, 35, 14077, 10.1021/bi9615710