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Volumn 27, Issue 24, 2011, Pages 3364-3370

The design of optimal therapeutic small interfering RNA molecules targeting diverse strains of influenza a virus

Author keywords

[No Author keywords available]

Indexed keywords

SMALL INTERFERING RNA;

EID: 83355174912     PISSN: 13674803     EISSN: 14602059     Source Type: Journal    
DOI: 10.1093/bioinformatics/btr555     Document Type: Article
Times cited : (14)

References (48)
  • 1
    • 1642273831 scopus 로고    scopus 로고
    • An algorithm for selection of functional siRNA sequences
    • Amarzguioui, M. and Prydz, H. (2004) An algorithm for selection of functional siRNA sequences. Biochem. Biophys. Res. Commun., 316, 1050-1058.
    • (2004) Biochem. Biophys. Res. Commun. , vol.316 , pp. 1050-1058
    • Amarzguioui, M.1    Prydz, H.2
  • 2
    • 35448980010 scopus 로고    scopus 로고
    • Functional genomic and serological analysis of the protective immune response resulting from vaccination of macaques with an NS1-truncated influenza virus
    • Baskin, C.R. et al. (2007) Functional genomic and serological analysis of the protective immune response resulting from vaccination of macaques with an NS1-truncated influenza virus. J. Virol., 81, 11817-11827.
    • (2007) J. Virol. , vol.81 , pp. 11817-11827
    • Baskin, C.R.1
  • 3
    • 33646188259 scopus 로고    scopus 로고
    • 3' UTR seed matches, but not overall identity, are associated with RNAi off-targets
    • Birmingham, A. et al. (2006) 3' UTR seed matches, but not overall identity, are associated with RNAi off-targets. Nat. Methods, 3, 199-204.
    • (2006) Nat. Methods , vol.3 , pp. 199-204
    • Birmingham, A.1
  • 4
    • 38449100230 scopus 로고    scopus 로고
    • A protocol for designing siRNAs with high functionality and specificity
    • Birmingham, A. et al. (2007) A protocol for designing siRNAs with high functionality and specificity. Nat. Protoc., 2, 2068-2078.
    • (2007) Nat. Protoc. , vol.2 , pp. 2068-2078
    • Birmingham, A.1
  • 5
    • 38049161918 scopus 로고    scopus 로고
    • RNAi for treating hepatitis B viral infection
    • Chen, Y. et al.. (2008) RNAi for treating hepatitis B viral infection. Pharm. Res., 25, 72-86.
    • (2008) Pharm. Res. , vol.25 , pp. 72-86
    • Chen, Y.1
  • 6
    • 3242877996 scopus 로고    scopus 로고
    • Sfold web server for statistical folding and rational design of nucleic acids
    • Ding, Y. et al. (2004) Sfold web server for statistical folding and rational design of nucleic acids. Nucleic Acids Res., 32, W135-W141.
    • (2004) Nucleic Acids Res. , vol.32
    • Ding, Y.1
  • 7
    • 83355174356 scopus 로고    scopus 로고
    • Gene silencing in the therapy of influenza and other respiratory diseases: targeting to RNase P by use of External Guide Sequences (EGS)
    • Dreyfus, D.H. et al. (2007) Gene silencing in the therapy of influenza and other respiratory diseases: targeting to RNase P by use of External Guide Sequences (EGS). Biologics, 1, 425-432.
    • (2007) Biologics , vol.1 , pp. 425-432
    • Dreyfus, D.H.1
  • 8
    • 0035942736 scopus 로고    scopus 로고
    • Duplexes of 21-nucleotide RNAs mediate RNAinterference in cultured mammalian cells
    • Elbashir, S.M. et al. (2001) Duplexes of 21-nucleotide RNAs mediate RNAinterference in cultured mammalian cells. Nature, 411, 494-498.
    • (2001) Nature , vol.411 , pp. 494-498
    • Elbashir, S.M.1
  • 9
    • 79251550432 scopus 로고    scopus 로고
    • Identification of novel conserved functional motifs across most Influenza a viral strains
    • ElHefnawi, M. et al. (2011) Identification of novel conserved functional motifs across most Influenza a viral strains. Virol. J., 8, 44.
    • (2011) Virol. J. , vol.8 , pp. 44
    • ElHefnawi, M.1
  • 10
    • 0037418322 scopus 로고    scopus 로고
    • RNAinterference of influenza virus production by directly targeting mRNA for degradation and indirectly inhibiting all viral RNA transcription
    • Ge, Q. et al. (2003) RNAinterference of influenza virus production by directly targeting mRNA for degradation and indirectly inhibiting all viral RNA transcription. Proc. Natl Acad. Sci. USA, 100, 2718-2723.
    • (2003) Proc. Natl Acad. Sci. USA , vol.100 , pp. 2718-2723
    • Ge, Q.1
  • 11
    • 43249105382 scopus 로고    scopus 로고
    • Impact of target mRNA structure on siRNA silencing efficiency: a large-scale study
    • Gredell, J.A. et al. (2008) Impact of target mRNA structure on siRNA silencing efficiency: a large-scale study. Biotechnol. Bioeng., 100, 744-755.
    • (2008) Biotechnol. Bioeng. , vol.100 , pp. 744-755
    • Gredell, J.A.1
  • 12
    • 77953784997 scopus 로고    scopus 로고
    • Inefficient control of host gene expression by the 2009 pandemic H1N1 influenza A virus NS1 protein
    • Hale, B.G. et al. (2010) Inefficient control of host gene expression by the 2009 pandemic H1N1 influenza A virus NS1 protein. J. Virol., 84, 6909-6922.
    • (2010) J. Virol. , vol.84 , pp. 6909-6922
    • Hale, B.G.1
  • 13
    • 77952312477 scopus 로고    scopus 로고
    • Designing optimal siRNA based on target site accessibility
    • Hofacker, I.L. and Tafer, H. (2010) Designing optimal siRNA based on target site accessibility. Methods Mol. Biol., 623, 137-154.
    • (2010) Methods Mol. Biol. , vol.623 , pp. 137-154
    • Hofacker, I.L.1    Tafer, H.2
  • 14
    • 2342564353 scopus 로고    scopus 로고
    • A library of siRNA duplexes targeting the phosphoinositide 3-kinase pathway: determinants of gene silencing for use in cell-based screens
    • Hsieh, A.C. et al. (2004) A library of siRNA duplexes targeting the phosphoinositide 3-kinase pathway: determinants of gene silencing for use in cell-based screens. Nucleic Acids Res., 32, 893-901.
    • (2004) Nucleic Acids Res. , vol.32 , pp. 893-901
    • Hsieh, A.C.1
  • 16
    • 23444437819 scopus 로고    scopus 로고
    • Design of a genome-wide siRNA library using an artificial neural network
    • Huesken, D. et al. (2005) Design of a genome-wide siRNA library using an artificial neural network. Nat. Biotechnol., 23, 995-1001.
    • (2005) Nat. Biotechnol. , vol.23 , pp. 995-1001
    • Huesken, D.1
  • 17
    • 35548980865 scopus 로고    scopus 로고
    • Thermodynamic instability of siRNA duplex is a prerequisite for dependable prediction of siRNA activities
    • Ichihara, M. et al. (2007) Thermodynamic instability of siRNA duplex is a prerequisite for dependable prediction of siRNA activities. Nucleic Acids Res., 35, e123.
    • (2007) Nucleic Acids Res , vol.35
    • Ichihara, M.1
  • 18
    • 3543009635 scopus 로고    scopus 로고
    • RNA interference: a potent tool for gene-specific therapeutics
    • Ichim, T.E. et al. (2004) RNA interference: a potent tool for gene-specific therapeutics. Am. J. Transplant., 4, 1227-1236.
    • (2004) Am. J. Transplant. , vol.4 , pp. 1227-1236
    • Ichim, T.E.1
  • 19
    • 33745614074 scopus 로고    scopus 로고
    • Position-specific chemical modification of siRNAs reduces "off-target" transcript silencing
    • Jackson, A.L. et al. (2006a) Position-specific chemical modification of siRNAs reduces "off-target" transcript silencing. RNA, 12, 1197-1205.
    • (2006) RNA , vol.12 , pp. 1197-1205
    • Jackson, A.L.1
  • 20
    • 33745612464 scopus 로고    scopus 로고
    • Widespread siRNA"off-target" transcript silencing mediated by seed region sequence complementarity
    • Jackson, A.L. et al. (2006b)Widespread siRNA"off-target" transcript silencing mediated by seed region sequence complementarity. RNA, 12, 1179-1187.
    • (2006) RNA , vol.12 , pp. 1179-1187
    • Jackson, A.L.1
  • 21
    • 74049124186 scopus 로고    scopus 로고
    • Recognizing and avoiding siRNAoff-target effects for target identification and therapeutic application
    • Jackson, A.L. and Linsley, P.S. (2010) Recognizing and avoiding siRNAoff-target effects for target identification and therapeutic application. Nat. Rev. Drug Discov., 9, 57-67.
    • (2010) Nat. Rev. Drug Discov. , vol.9 , pp. 57-67
    • Jackson, A.L.1    Linsley, P.S.2
  • 22
    • 33847036990 scopus 로고    scopus 로고
    • Strategies for silencing human disease using RNA interference
    • Kim, D.H. and Rossi, J.J. (2007) Strategies for silencing human disease using RNA interference. Nat. Rev. Genet., 8, 173-184.
    • (2007) Nat. Rev. Genet. , vol.8 , pp. 173-184
    • Kim, D.H.1    Rossi, J.J.2
  • 23
    • 67649236703 scopus 로고    scopus 로고
    • Approximate Bayesian feature selection on a large metadataset offers novel insights on factors that effect siRNA potency
    • Klingelhoefer, J.W. et al. (2009)Approximate Bayesian feature selection on a large metadataset offers novel insights on factors that effect siRNA potency. Bioinformatics, 25, 1594-1601.
    • (2009) Bioinformatics , vol.25 , pp. 1594-1601
    • Klingelhoefer, J.W.1
  • 24
    • 39149106448 scopus 로고    scopus 로고
    • Efficient siRNA selection using hybridization thermodynamics
    • Lu, Z.J. and Mathews, D.H. (2008) Efficient siRNA selection using hybridization thermodynamics. Nucleic Acids Res., 36, 640-647.
    • (2008) Nucleic Acids Res. , vol.36 , pp. 640-647
    • Lu, Z.J.1    Mathews, D.H.2
  • 25
    • 34250309149 scopus 로고    scopus 로고
    • Comparison of approaches for rational siRNA design leading to a new efficient and transparent method
    • Matveeva, O. et al. (2007) Comparison of approaches for rational siRNA design leading to a new efficient and transparent method. Nucleic Acids Res., 35, e63.
    • (2007) Nucleic Acids Res , vol.35
    • Matveeva, O.1
  • 26
    • 41149161324 scopus 로고    scopus 로고
    • Apotential treatment for pandemic influenza using siRNAs targeting conserved regions of influenza A
    • McSwiggen, J.A. and Seth, S.; (2008)Apotential treatment for pandemic influenza using siRNAs targeting conserved regions of influenza A. Expert Opin. Biol. Ther., 8, 299-313.
    • (2008) Expert Opin. Biol. Ther. , vol.8 , pp. 299-313
    • McSwiggen, J.A.1    Seth, S.2
  • 27
    • 1242318826 scopus 로고    scopus 로고
    • Sequence-specific inhibition of microRNA- and siRNA-induced RNA silencing
    • Meister, G. et al. (2004) Sequence-specific inhibition of microRNA- and siRNA-induced RNA silencing. RNA, 10, 544-550.
    • (2004) RNA , vol.10 , pp. 544-550
    • Meister, G.1
  • 28
    • 33646877072 scopus 로고    scopus 로고
    • Thermodynamics of RNA-RNA binding
    • Muckstein, U. et al. (2006) Thermodynamics of RNA-RNA binding. Bioinformatics, 22, 1177-1182.
    • (2006) Bioinformatics , vol.22 , pp. 1177-1182
    • Muckstein, U.1
  • 29
    • 38349166714 scopus 로고    scopus 로고
    • Optimal design and validation of antiviral siRNA for targeting HIV-1
    • Naito, Y. et al. (2007) Optimal design and validation of antiviral siRNA for targeting HIV-1. Retrovirology, 4, 80.
    • (2007) Retrovirology , vol.4 , pp. 80
    • Naito, Y.1
  • 30
    • 33747869038 scopus 로고    scopus 로고
    • siVirus: web-based antiviral siRNA design software for highly divergent viral sequences
    • Naito, Y. et al. (2006) siVirus: web-based antiviral siRNA design software for highly divergent viral sequences. Nucleic Acids Res., 34, W448-W450.
    • (2006) Nucleic Acids Res , vol.34
    • Naito, Y.1
  • 31
    • 3242889236 scopus 로고    scopus 로고
    • siDirect: highly effective, target-specific siRNA design software for mammalian RNA interference
    • Naito, Y. et al. (2004) siDirect: highly effective, target-specific siRNA design software for mammalian RNA interference. Nucleic Acids Res., 32, W124-W129.
    • (2004) Nucleic Acids Res , vol.32
    • Naito, Y.1
  • 32
    • 72549097028 scopus 로고    scopus 로고
    • siDirect 2.0: updated software for designing functional siRNA with reduced seed-dependent off-target effect
    • Naito, Y. et al. (2009) siDirect 2.0: updated software for designing functional siRNA with reduced seed-dependent off-target effect. BMC Bioinformatics, 10, 392.
    • (2009) BMC Bioinformatics , vol.10 , pp. 392
    • Naito, Y.1
  • 33
    • 33846614547 scopus 로고    scopus 로고
    • In silico selection of active siRNA
    • Patzel, V. (2007) In silico selection of active siRNA. Drug Discov. Today, 12, 139-148.
    • (2007) Drug Discov. Today , vol.12 , pp. 139-148
    • Patzel, V.1
  • 34
    • 27944473306 scopus 로고    scopus 로고
    • Design of siRNAs producing unstructured guide-RNAs results in improved RNA interference efficiency
    • Patzel, V. et al. (2005) Design of siRNAs producing unstructured guide-RNAs results in improved RNA interference efficiency. Nat. Biotechnol., 23, 1440-1444.
    • (2005) Nat. Biotechnol. , vol.23 , pp. 1440-1444
    • Patzel, V.1
  • 35
    • 1542336952 scopus 로고    scopus 로고
    • Rational siRNAdesign forRNAinterference
    • Reynolds, A. et al. (2004) Rational siRNAdesign forRNAinterference. Nat. Biotechnol., 22, 326-330.
    • (2004) Nat. Biotechnol. , vol.22 , pp. 326-330
    • Reynolds, A.1
  • 36
    • 33645822531 scopus 로고    scopus 로고
    • siRecords: an extensive database of mammalian siRNAs with efficacy ratings
    • Ren, Y. et al. (2006) siRecords: an extensive database of mammalian siRNAs with efficacy ratings. Bioinformatics, 22, 1027-1028.
    • (2006) Bioinformatics , vol.22 , pp. 1027-1028
    • Ren, Y.1
  • 37
    • 33748701701 scopus 로고    scopus 로고
    • Computational models with thermodynamic and composition features improve siRNA design
    • Shabalina, S.A. et al. (2006) Computational models with thermodynamic and composition features improve siRNA design. BMC Bioinformatics, 7, 65.
    • (2006) BMC Bioinformatics , vol.7 , pp. 65
    • Shabalina, S.A.1
  • 38
    • 62049083943 scopus 로고    scopus 로고
    • Structural and functional bases for broad-spectrum neutralization of avian and human influenza A viruses
    • Sui, J. et al. (2009) Structural and functional bases for broad-spectrum neutralization of avian and human influenza A viruses. Nat. Struct. Mol. Biol., 16, 265-273.
    • (2009) Nat. Struct. Mol. Biol. , vol.16 , pp. 265-273
    • Sui, J.1
  • 39
    • 53149132028 scopus 로고    scopus 로고
    • Closed chromatin architecture is induced by an RNA duplex targeting the HIV-1 promoter region
    • Suzuki, K. et al. (2008) Closed chromatin architecture is induced by an RNA duplex targeting the HIV-1 promoter region. J. Biol. Chem., 283, 23353-23363.
    • (2008) J. Biol. Chem. , vol.283 , pp. 23353-23363
    • Suzuki, K.1
  • 40
    • 43449124403 scopus 로고    scopus 로고
    • The impact of target site accessibility on the design of effective siRNAs
    • Tafer, H. et al. (2008) The impact of target site accessibility on the design of effective siRNAs. Nat. Biotechnol., 26, 578-583.
    • (2008) Nat. Biotechnol. , vol.26 , pp. 578-583
    • Tafer, H.1
  • 41
    • 83355170006 scopus 로고    scopus 로고
    • High content screening: a powerful approach to systems cell biology and drug discovery
    • Gregory Moore, K. et al. (eds) Humana Press, United States, NY
    • Taylor1, D.L. et al. (2008) High content screening: a powerful approach to systems cell biology and drug discovery. In Gregory Moore, K. et al. (eds) Methods in Molecular Biology Part III. Humana Press, United States, NY, pp. 245-251.
    • (2008) Methods in Molecular Biology Part III , pp. 245-251
    • Taylor1, D.L.1
  • 42
    • 77957925036 scopus 로고    scopus 로고
    • A status report on RNAi therapeutics
    • Vaishnaw, A.K. et al. (2011) A status report on RNAi therapeutics. Silence, 1, 14.
    • (2011) Silence , vol.1 , pp. 14
    • Vaishnaw, A.K.1
  • 43
    • 11844283922 scopus 로고    scopus 로고
    • Gene knockdown with intrathecal siRNA of NMDA receptor NR2B subunit reduces formalin-induced nociception in the rat
    • Tan, P.H. et al. (2005) Gene knockdown with intrathecal siRNA of NMDA receptor NR2B subunit reduces formalin-induced nociception in the rat. Gene Ther., 12, 59.
    • (2005) Gene Ther , vol.12 , pp. 59
    • Tan, P.H.1
  • 44
    • 1642346273 scopus 로고    scopus 로고
    • Guidelines for the selection of highly effective siRNA sequences for mammalian and chick RNA interference
    • Ui-Tei, K. et al. (2004) Guidelines for the selection of highly effective siRNA sequences for mammalian and chick RNA interference. Nucleic Acids Res., 32, 936-948.
    • (2004) Nucleic Acids Res. , vol.32 , pp. 936-948
    • Ui-Tei, K.1
  • 45
    • 33845663097 scopus 로고    scopus 로고
    • An accurate and interpretable model for siRNAefficacy prediction
    • Vert, J.P. et al. (2006)An accurate and interpretable model for siRNAefficacy prediction. BMC Bioinformatics, 7, 520.
    • (2006) BMC Bioinformatics , vol.7 , pp. 520
    • Vert, J.P.1
  • 46
    • 13444282536 scopus 로고    scopus 로고
    • Filtering of ineffective siRNAs and improved siRNA design tool
    • Yiu, S.M. et al. (2005) Filtering of ineffective siRNAs and improved siRNA design tool. Bioinformatics, 21, 144-151.
    • (2005) Bioinformatics , vol.21 , pp. 144-151
    • Yiu, S.M.1
  • 47
    • 34548637012 scopus 로고    scopus 로고
    • Effective small interfering RNAs targeting matrix and nucleocapsid protein gene inhibit influenza A virus replication in cells and mice
    • Zhou, H. et al. (2007) Effective small interfering RNAs targeting matrix and nucleocapsid protein gene inhibit influenza A virus replication in cells and mice. Antiviral Res., 76, 186-193.
    • (2007) Antiviral Res. , vol.76 , pp. 186-193
    • Zhou, H.1
  • 48
    • 43849112336 scopus 로고    scopus 로고
    • RNA interference of avian influenza virus H5N1 by inhibiting viral mRNA with siRNA expression plasmids
    • Zhou, K. et al. (2008) RNA interference of avian influenza virus H5N1 by inhibiting viral mRNA with siRNA expression plasmids. J. Biotechnol., 135, 140-144.
    • (2008) J. Biotechnol. , vol.135 , pp. 140-144
    • Zhou, K.1


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