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Volumn 281, Issue 1, 2014, Pages 320-330

Improved asymmetry prediction for short interfering RNAs

Author keywords

asymmetry; dsRNA dependent protein kinase R; enhanced green fluorescent protein; short interfering RNA

Indexed keywords

MESSENGER RNA; PROTEIN KINASE R; SMALL INTERFERING RNA;

EID: 84891778982     PISSN: 1742464X     EISSN: 17424658     Source Type: Journal    
DOI: 10.1111/febs.12599     Document Type: Article
Times cited : (9)

References (53)
  • 1
    • 0032545933 scopus 로고    scopus 로고
    • Potent and specific genetic interference by double-stranded RNA in Caenorhabditis elegans
    • Fire A, Xu S, Montgomery M, Kostas S, Driver S, &, Mello C, (1998) Potent and specific genetic interference by double-stranded RNA in Caenorhabditis elegans. Nature 391, 806-811.
    • (1998) Nature , vol.391 , pp. 806-811
    • Fire, A.1    Xu, S.2    Montgomery, M.3    Kostas, S.4    Driver, S.5    Mello, C.6
  • 2
    • 27744590896 scopus 로고    scopus 로고
    • Passenger-strand cleavage facilitates assembly of siRNA into Ago2-containing RNAi enzyme complexes
    • Matranga C, Tomari Y, Shin C, Bartel DP, &, Zamore PD, (2005) Passenger-strand cleavage facilitates assembly of siRNA into Ago2-containing RNAi enzyme complexes. Cell 123, 607-620.
    • (2005) Cell , vol.123 , pp. 607-620
    • Matranga, C.1    Tomari, Y.2    Shin, C.3    Bartel, D.P.4    Zamore, P.D.5
  • 3
    • 0035942736 scopus 로고    scopus 로고
    • Duplexes of 21-nucleotide RNAs mediate RNA interference in cultured mammalian cells
    • Elbashir SM, Harborth J, Lendeckel W, Yalcin A, Weber K, &, Tuschl T, (2001) Duplexes of 21-nucleotide RNAs mediate RNA interference in cultured mammalian cells. Nature 411, 494-498.
    • (2001) Nature , vol.411 , pp. 494-498
    • Elbashir, S.M.1    Harborth, J.2    Lendeckel, W.3    Yalcin, A.4    Weber, K.5    Tuschl, T.6
  • 5
    • 79957928508 scopus 로고    scopus 로고
    • Is RNAi dead?
    • Krieg AM, (2011) Is RNAi dead? Mol Ther 19, 1001-1002.
    • (2011) Mol Ther , vol.19 , pp. 1001-1002
    • Krieg, A.M.1
  • 6
    • 84870506768 scopus 로고    scopus 로고
    • Use of siRNA in therapeutic arena on the upswing
    • Gitig D, (2012) Use of siRNA in therapeutic arena on the upswing. Genet Eng Biotech News, 12, 24-26.
    • (2012) Genet Eng Biotech News , vol.12 , pp. 24-26
    • Gitig, D.1
  • 7
    • 79954580272 scopus 로고    scopus 로고
    • Current prospects for RNA interference-based therapies
    • Davidson BL, &, McCray PB, (2011) Current prospects for RNA interference-based therapies. Nat Rev Genet 12, 329-340.
    • (2011) Nat Rev Genet , vol.12 , pp. 329-340
    • Davidson, B.L.1    McCray, P.B.2
  • 8
    • 84875908270 scopus 로고    scopus 로고
    • Design of siRNA therapeutics from the molecular scale
    • Angart P, Vocelle D, Chan C, &, Walton SP, (2013) Design of siRNA therapeutics from the molecular scale. Pharmaceuticals 6, 440-468.
    • (2013) Pharmaceuticals , vol.6 , pp. 440-468
    • Angart, P.1    Vocelle, D.2    Chan, C.3    Walton, S.P.4
  • 9
    • 77956905696 scopus 로고    scopus 로고
    • Confocal microscopy for the analysis of siRNA delivery by polymeric nanoparticles
    • Portis AM, Carballo G, Baker GL, Chan C, &, Walton SP, (2010) Confocal microscopy for the analysis of siRNA delivery by polymeric nanoparticles. Microsc Res Tech 73, 878-885.
    • (2010) Microsc Res Tech , vol.73 , pp. 878-885
    • Portis, A.M.1    Carballo, G.2    Baker, G.L.3    Chan, C.4    Walton, S.P.5
  • 10
    • 67249105434 scopus 로고    scopus 로고
    • A novel mechanism is involved in cationic lipid-mediated functional siRNA delivery
    • Lu JJ, Langer R, &, Chen JZ, (2009) A novel mechanism is involved in cationic lipid-mediated functional siRNA delivery. Mol Pharmaceut 6, 763-771.
    • (2009) Mol Pharmaceut , vol.6 , pp. 763-771
    • Lu, J.J.1    Langer, R.2    Chen, J.Z.3
  • 12
    • 34447102459 scopus 로고    scopus 로고
    • Molecular basis for target RNA recognition and cleavage by human RISC
    • Ameres SL, Martinez J, &, Schroeder R, (2007) Molecular basis for target RNA recognition and cleavage by human RISC. Cell 130, 101-112.
    • (2007) Cell , vol.130 , pp. 101-112
    • Ameres, S.L.1    Martinez, J.2    Schroeder, R.3
  • 13
    • 20444455464 scopus 로고    scopus 로고
    • Target accessibility dictates the potency of human RISC
    • Brown KM, Chu C-Y, &, Rana TM, (2005) Target accessibility dictates the potency of human RISC. Nat Struct Mol Biol 12, 469-470.
    • (2005) Nat Struct Mol Biol , vol.12 , pp. 469-470
    • Brown, K.M.1    Chu, C.-Y.2    Rana, T.M.3
  • 14
    • 43249105382 scopus 로고    scopus 로고
    • Impact of target mRNA structure on siRNA silencing efficiency: A large-scale study
    • Gredell JA, Berger AK, &, Walton SP, (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    Berger, A.K.2    Walton, S.P.3
  • 15
    • 79959488106 scopus 로고    scopus 로고
    • A detailed investigation of accessibilities around target sites of siRNAs and miRNAs
    • Kiryu H, Terai G, Imamura O, Yoneyama H, Suzuki K, &, Asai K, (2011) A detailed investigation of accessibilities around target sites of siRNAs and miRNAs. Bioinformatics 27, 1788-1797.
    • (2011) Bioinformatics , vol.27 , pp. 1788-1797
    • Kiryu, H.1    Terai, G.2    Imamura, O.3    Yoneyama, H.4    Suzuki, K.5    Asai, K.6
  • 17
    • 29144431656 scopus 로고    scopus 로고
    • A human, ATP-independent, RISC assembly machine fueled by pre-miRNA
    • Maniataki E, &, Mourelatos Z, (2005) A human, ATP-independent, RISC assembly machine fueled by pre-miRNA. Genes Dev 19, 2979-2990.
    • (2005) Genes Dev , vol.19 , pp. 2979-2990
    • Maniataki, E.1    Mourelatos, Z.2
  • 19
    • 70350442453 scopus 로고    scopus 로고
    • Effect of siRNA terminal mismatches on TRBP and Dicer binding and silencing efficacy
    • Kini HK, &, Walton SP, (2009) Effect of siRNA terminal mismatches on TRBP and Dicer binding and silencing efficacy. FEBS J 276, 6576-6585.
    • (2009) FEBS J , vol.276 , pp. 6576-6585
    • Kini, H.K.1    Walton, S.P.2
  • 22
    • 27144550559 scopus 로고    scopus 로고
    • TRBP, a regulator of cellular PKR and HIV-1 virus expression, interacts with Dicer and functions in RNA silencing
    • Haase AD, Jaskiewicz L, Zhang H, Laine S, Sack R, Gatignol A, &, Filipowicz W, (2005) TRBP, a regulator of cellular PKR and HIV-1 virus expression, interacts with Dicer and functions in RNA silencing. EMBO Rep 6, 961-967.
    • (2005) EMBO Rep , vol.6 , pp. 961-967
    • Haase, A.D.1    Jaskiewicz, L.2    Zhang, H.3    Laine, S.4    Sack, R.5    Gatignol, A.6    Filipowicz, W.7
  • 23
    • 59049105558 scopus 로고    scopus 로고
    • Human Dicer binds short single-strand and double-strand RNA with high affinity and interacts with different regions of the nucleic acids
    • Lima WF, Murray H, Nichols JG, Wu H, Sun H, Prakash TP, Berdeja AR, Gaus HJ, &, Crooke ST, (2009) Human Dicer binds short single-strand and double-strand RNA with high affinity and interacts with different regions of the nucleic acids. J Biol Chem 284, 2535-2548.
    • (2009) J Biol Chem , vol.284 , pp. 2535-2548
    • Lima, W.F.1    Murray, H.2    Nichols, J.G.3    Wu, H.4    Sun, H.5    Prakash, T.P.6    Berdeja, A.R.7    Gaus, H.J.8    Crooke, S.T.9
  • 24
    • 34547115237 scopus 로고    scopus 로고
    • Human TRBP and PACT directly interact with each other and associate with dicer to facilitate the production of small interfering RNA
    • Kok KH, Ng MHJ, Ching YP, &, Jin DY, (2007) Human TRBP and PACT directly interact with each other and associate with dicer to facilitate the production of small interfering RNA. J Biol Chem 282, 17649-17657.
    • (2007) J Biol Chem , vol.282 , pp. 17649-17657
    • Kok, K.H.1    Ng, M.H.J.2    Ching, Y.P.3    Jin, D.Y.4
  • 28
    • 33645763485 scopus 로고    scopus 로고
    • Cleavage of the siRNA passenger strand during RISC assembly in human cells
    • Leuschner PJF, Ameres SL, Kueng S, &, Martinez J, (2006) Cleavage of the siRNA passenger strand during RISC assembly in human cells. EMBO Rep 7, 314-320.
    • (2006) EMBO Rep , vol.7 , pp. 314-320
    • Leuschner, P.J.F.1    Ameres, S.L.2    Kueng, S.3    Martinez, J.4
  • 29
    • 10744225153 scopus 로고    scopus 로고
    • Asymmetry in the assembly of the RNAi enzyme complex
    • Schwarz D, Hutvagner G, Du T, Xu Z, Aronin N, &, Zamore P, (2003) Asymmetry in the assembly of the RNAi enzyme complex. Cell 115, 199-208.
    • (2003) Cell , vol.115 , pp. 199-208
    • Schwarz, D.1    Hutvagner, G.2    Du, T.3    Xu, Z.4    Aronin, N.5    Zamore, P.6
  • 30
    • 77953479619 scopus 로고    scopus 로고
    • Structural basis for 5′-nucleotide base-specific recognition of guide RNA by human AGO2
    • Frank F, Sonenberg N, &, Nagar B, (2010) Structural basis for 5′-nucleotide base-specific recognition of guide RNA by human AGO2. Nature 465, 818-822.
    • (2010) Nature , vol.465 , pp. 818-822
    • Frank, F.1    Sonenberg, N.2    Nagar, B.3
  • 31
    • 79959872313 scopus 로고    scopus 로고
    • SiRNA repositioning for guide strand selection by human dicer complexes
    • Noland CL, Ma E, &, Doudna JA, (2011) siRNA repositioning for guide strand selection by human dicer complexes. Mol Cell 43, 110-121.
    • (2011) Mol Cell , vol.43 , pp. 110-121
    • Noland, C.L.1    Ma, E.2    Doudna, J.A.3
  • 32
    • 84055222215 scopus 로고    scopus 로고
    • Dicer is dispensable for asymmetric RISC loading in mammals
    • Betancur JG, &, Tomari Y, (2012) Dicer is dispensable for asymmetric RISC loading in mammals. RNA 18, 24-30.
    • (2012) RNA , vol.18 , pp. 24-30
    • Betancur, J.G.1    Tomari, Y.2
  • 34
    • 1642273831 scopus 로고    scopus 로고
    • An algorithm for selection of functional siRNA sequences
    • Amarzguioui M, &, 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
  • 36
    • 39149106448 scopus 로고    scopus 로고
    • Efficient siRNA selection using hybridization thermodynamics
    • Lu ZJ, &, Mathews DH, (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
  • 38
    • 78449296513 scopus 로고    scopus 로고
    • Designing highly active siRNAs for therapeutic applications
    • Walton SP, Wu M, Gredell JA, &, Chan C, (2010) Designing highly active siRNAs for therapeutic applications. FEBS J 277, 4806-4813.
    • (2010) FEBS J , vol.277 , pp. 4806-4813
    • Walton, S.P.1    Wu, M.2    Gredell, J.A.3    Chan, C.4
  • 39
    • 64149098793 scopus 로고    scopus 로고
    • Repression of PKR mediates palmitate-induced apoptosis in HepG2 cells through regulation of Bcl-2
    • Yang X, &, Chan C, (2009) Repression of PKR mediates palmitate-induced apoptosis in HepG2 cells through regulation of Bcl-2. Cell Res 19, 469-486.
    • (2009) Cell Res , vol.19 , pp. 469-486
    • Yang, X.1    Chan, C.2
  • 40
    • 45849141942 scopus 로고    scopus 로고
    • Interactions between the double-stranded RNA-binding proteins TRBP and PACT define the Medipal domain that mediates protein-protein interactions
    • Laraki G, Clerzius G, Daher A, Melendez-Pena C, Daniels S, &, Gatignol A, (2008) Interactions between the double-stranded RNA-binding proteins TRBP and PACT define the Medipal domain that mediates protein-protein interactions. RNA Biol 5, 92-103.
    • (2008) RNA Biol , vol.5 , pp. 92-103
    • Laraki, G.1    Clerzius, G.2    Daher, A.3    Melendez-Pena, C.4    Daniels, S.5    Gatignol, A.6
  • 42
    • 80055056681 scopus 로고    scopus 로고
    • MysiRNA-Designer: A workflow for efficient siRNA design
    • Mysara M, Garibaldi JM, &, El Hefnawi M, (2011) MysiRNA-Designer: a workflow for efficient siRNA design. PLoS ONE 6, e25642.
    • (2011) PLoS ONE , vol.6
    • Mysara, M.1    Garibaldi, J.M.2    El Hefnawi, M.3
  • 44
    • 33748701701 scopus 로고    scopus 로고
    • Computational models with thermodynamic and composition features improve siRNA design
    • Shabalina SA, Spiridonov AN, &, Ogurtsov AY, (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    Spiridonov, A.N.2    Ogurtsov, A.Y.3
  • 45
    • 3242890471 scopus 로고    scopus 로고
    • SiRNA selection server: An automated siRNA oligonucleotide prediction server
    • Yuan B, Latek R, Hossbach M, Tuschl T, &, Lewitter F, (2004) siRNA selection server: an automated siRNA oligonucleotide prediction server. Nucleic Acids Res 32, W130-W134.
    • (2004) Nucleic Acids Res , vol.32
    • Yuan, B.1    Latek, R.2    Hossbach, M.3    Tuschl, T.4    Lewitter, F.5
  • 46
    • 70349203686 scopus 로고    scopus 로고
    • Selecting effective siRNA target sequences by using Bayes' theorem
    • Takasaki S, (2009) Selecting effective siRNA target sequences by using Bayes' theorem. Comput Biol Chem 33, 368-372.
    • (2009) Comput Biol Chem , vol.33 , pp. 368-372
    • Takasaki, S.1
  • 47
    • 33846906687 scopus 로고    scopus 로고
    • More complete gene silencing by fewer siRNAs: Transparent optimized design and biophysical signature
    • Ladunga I, (2006) More complete gene silencing by fewer siRNAs: transparent optimized design and biophysical signature. Nucleic Acids Res 35, 433-440.
    • (2006) Nucleic Acids Res , vol.35 , pp. 433-440
    • Ladunga, I.1
  • 49
    • 0142165224 scopus 로고    scopus 로고
    • Functional siRNAs and miRNAs exhibit strand bias
    • Khvorova A, Reynolds A, &, Jayasena SD, (2003) Functional siRNAs and miRNAs exhibit strand bias. Cell 115, 209-216.
    • (2003) Cell , vol.115 , pp. 209-216
    • Khvorova, A.1    Reynolds, A.2    Jayasena, S.D.3
  • 52
    • 84856542174 scopus 로고    scopus 로고
    • A 5′-uridine amplifies miRNA/miRNA* asymmetry in Drosophila by promoting RNA-induced silencing complex formation
    • Seitz H, Tushir J, &, Zamore P, (2011) A 5′-uridine amplifies miRNA/miRNA* asymmetry in Drosophila by promoting RNA-induced silencing complex formation. Silence 2011, 2:4.
    • (2011) Silence , vol.2011 , pp. 24
    • Seitz, H.1    Tushir, J.2    Zamore, P.3
  • 53
    • 0032552882 scopus 로고    scopus 로고
    • Thermodynamic parameters for an expanded nearest-neighbor model for formation of RNA duplexes with Watson-Crick base pairs
    • Xia T, SantaLucia J Jr, Burkard ME, Kierzek R, Schroeder SJ, Jiao X, Cox C, &, Turner DH, (1998) Thermodynamic parameters for an expanded nearest-neighbor model for formation of RNA duplexes with Watson-Crick base pairs. Biochemistry 37, 14719-14735.
    • (1998) Biochemistry , vol.37 , pp. 14719-14735
    • Xia, T.1    Santalucia Jr., J.2    Burkard, M.E.3    Kierzek, R.4    Schroeder, S.J.5    Jiao, X.6    Cox, C.7    Turner, D.H.8


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.