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Volumn 35, Issue 18, 2007, Pages

Thermodynamic instability of siRNA duplex is a prerequisite for dependable prediction of siRNA activities

Author keywords

[No Author keywords available]

Indexed keywords

SMALL INTERFERING RNA;

EID: 35548980865     PISSN: 03051048     EISSN: 13624962     Source Type: Journal    
DOI: 10.1093/nar/gkm699     Document Type: Article
Times cited : (109)

References (38)
  • 1
    • 0036788304 scopus 로고    scopus 로고
    • Gene silencing in mammals by small interfering RNAs
    • McManus,M.T. and Sharp,P.A. (2002) Gene silencing in mammals by small interfering RNAs. Nat. Rev. Genet., 3, 737-747.
    • (2002) Nat. Rev. Genet , vol.3 , pp. 737-747
    • McManus, M.T.1    Sharp, P.A.2
  • 2
    • 0037062951 scopus 로고    scopus 로고
    • RNA interference
    • Hannon,G.J. (2002) RNA interference. Nature, 418, 244-251.
    • (2002) Nature , vol.418 , pp. 244-251
    • Hannon, G.J.1
  • 3
    • 3242677639 scopus 로고    scopus 로고
    • siRNAs: Applications in functional genomics and potential as therapeutics
    • Dorsett,Y. and Tuschl,T. (2004) siRNAs: Applications in functional genomics and potential as therapeutics. Nat. Rev. Drug Discov., 3, 318-329.
    • (2004) Nat. Rev. Drug Discov , vol.3 , pp. 318-329
    • Dorsett, Y.1    Tuschl, T.2
  • 4
    • 0037686295 scopus 로고    scopus 로고
    • Killing the messenger: Short RNAs that silence gene expression
    • Dykxhoorn,D.M., Novina,C.D. and Sharp,P.A. (2003) Killing the messenger: short RNAs that silence gene expression. Nat. Rev. Mol. Cell Biol. 4, 457-467.
    • (2003) Nat. Rev. Mol. Cell Biol , vol.4 , pp. 457-467
    • Dykxhoorn, D.M.1    Novina, C.D.2    Sharp, P.A.3
  • 5
    • 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
  • 6
    • 0142165224 scopus 로고    scopus 로고
    • Functional siRNAs and miRNAs exhibit strand bias
    • Khvorova,A., Reynolds,A. and Jayasena,S.D. (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
  • 10
    • 3542992506 scopus 로고    scopus 로고
    • An effective method for selecting siRNA target sequences in mammalian cells
    • Takasaki,S., Kotani,S. and Konagaya,A. (2004) An effective method for selecting siRNA target sequences in mammalian cells. Cell Cycle, 3, 790-795.
    • (2004) Cell Cycle , vol.3 , pp. 790-795
    • Takasaki, S.1    Kotani, S.2    Konagaya, A.3
  • 11
    • 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
  • 12
    • 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., Bo,R., Manola,J., Vazquez,F., Bare,O., Khvorova,A., Scaringe,S. and Sellers,W.R. (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    Bo, R.2    Manola, J.3    Vazquez, F.4    Bare, O.5    Khvorova, A.6    Scaringe, S.7    Sellers, W.R.8
  • 13
    • 0037089135 scopus 로고    scopus 로고
    • Positional effects of short interfering RNAs targeting the human coagulation trigger tissue factor
    • Holen,T., Amarzguioui,M., Wiiger,M.T., Babaie,E. and Prydz,H. (2002) Positional effects of short interfering RNAs targeting the human coagulation trigger tissue factor. Nucleic Acids Res., 30, 1757-1766.
    • (2002) Nucleic Acids Res , vol.30 , pp. 1757-1766
    • Holen, T.1    Amarzguioui, M.2    Wiiger, M.T.3    Babaie, E.4    Prydz, H.5
  • 14
    • 1942488998 scopus 로고    scopus 로고
    • The gene-silencing efficiency of siRNA is strongly dependent on the local structure of mRNA at the targeted region
    • Luo,K.Q. and Chang,D.C. (2004) The gene-silencing efficiency of siRNA is strongly dependent on the local structure of mRNA at the targeted region. Biochem. Biophys. Res. Commun., 318, 303-310.
    • (2004) Biochem. Biophys. Res. Commun , vol.318 , pp. 303-310
    • Luo, K.Q.1    Chang, D.C.2
  • 15
    • 26444437334 scopus 로고    scopus 로고
    • siRNA target site secondary structure predictions using local stable substructures
    • Heale,B.S., Soifer,H.S., Bowers,C. and Rossi,J.J. (2005) siRNA target site secondary structure predictions using local stable substructures. Nucleic Acids Res., 33, e30.
    • (2005) Nucleic Acids Res , vol.33
    • Heale, B.S.1    Soifer, H.S.2    Bowers, C.3    Rossi, J.J.4
  • 16
    • 17444412299 scopus 로고    scopus 로고
    • Local RNA target structure influences siRNA efficacy: Systematic analysis of intentionally designed binding regions
    • Schubert,S., Grunweller,A., Erdmann,V.A. and Kurreck,J. (2005) Local RNA target structure influences siRNA efficacy: Systematic analysis of intentionally designed binding regions. J. Mol. Biol., 348, 883-893.
    • (2005) J. Mol. Biol , vol.348 , pp. 883-893
    • Schubert, S.1    Grunweller, A.2    Erdmann, V.A.3    Kurreck, J.4
  • 17
    • 3543036224 scopus 로고    scopus 로고
    • Predicting the efficacy of short oligonucleotides in antisense and RNAi experiments with boosted genetic programming
    • Saetrom,P. (2004) Predicting the efficacy of short oligonucleotides in antisense and RNAi experiments with boosted genetic programming. Bioinformatics, 20, 3055-3063.
    • (2004) Bioinformatics , vol.20 , pp. 3055-3063
    • Saetrom, P.1
  • 18
    • 2542607603 scopus 로고    scopus 로고
    • Efficient RNA interference depends on global context of the target sequence: Quantitative analysis of silencing efficiency using Eulerian graph representation of siRNA
    • Pancoska,P., Moravek,Z. and Moll,U.M. (2004) Efficient RNA interference depends on global context of the target sequence: Quantitative analysis of silencing efficiency using Eulerian graph representation of siRNA. Nucleic Acids Res., 32, 1469-1479.
    • (2004) Nucleic Acids Res , vol.32 , pp. 1469-1479
    • Pancoska, P.1    Moravek, Z.2    Moll, U.M.3
  • 19
    • 1942499451 scopus 로고    scopus 로고
    • Improving the efficiency of RNA interference in mammals
    • Mittal,V. (2004) Improving the efficiency of RNA interference in mammals. Nat. Rev. Genet., 5, 355-365.
    • (2004) Nat. Rev. Genet , vol.5 , pp. 355-365
    • Mittal, V.1
  • 20
    • 25644448153 scopus 로고    scopus 로고
    • Mammalian RNAi: A practical guide
    • Sandy,P., Ventura,A. and Jacks,T. (2005) Mammalian RNAi: A practical guide. Biotechniques, 39, 215-224.
    • (2005) Biotechniques , vol.39 , pp. 215-224
    • Sandy, P.1    Ventura, A.2    Jacks, T.3
  • 21
    • 4344619826 scopus 로고    scopus 로고
    • Picking a winner: New mechanistic insights into the design of effective siRNAs
    • Gong,D. and Ferrell,J.E.Jr. (2004) Picking a winner: New mechanistic insights into the design of effective siRNAs. Trends Biotechnol., 22, 451-454.
    • (2004) Trends Biotechnol , vol.22 , pp. 451-454
    • Gong, D.1    Ferrell Jr., J.E.2
  • 22
    • 33645822531 scopus 로고    scopus 로고
    • siRecords: An extensive database of mammalian siRNAs with efficacy ratings
    • Ren,Y., Gong,W., Xu,Q., Zheng,X., Lin,D., Wang,Y. and Li,T. (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    Gong, W.2    Xu, Q.3    Zheng, X.4    Lin, D.5    Wang, Y.6    Li, T.7
  • 24
    • 33748701701 scopus 로고    scopus 로고
    • Computational models with thermodynamic and composition features improve siRNA design
    • Shabalina,S.A., Spiridonov,A.N. and Ogurtsov,A.Y. (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
  • 25
    • 33746772726 scopus 로고    scopus 로고
    • Demonstration of two novel methods for predicting functional siRNA efficiency
    • Jia,P., Shi,T., Cai,Y. and Li,Y. (2006) Demonstration of two novel methods for predicting functional siRNA efficiency. BMC Bioinformatics, 7, 271.
    • (2006) BMC Bioinformatics , vol.7 , pp. 271
    • Jia, P.1    Shi, T.2    Cai, Y.3    Li, Y.4
  • 26
    • 33845631509 scopus 로고    scopus 로고
    • Integrated siRNA design based on surveying of features associated with high RNAi effectiveness
    • Gong,W., Ren,Y., Xu,Q., Wang,Y., Lin,D., Zhou,H. and Li,T. (2006) Integrated siRNA design based on surveying of features associated with high RNAi effectiveness. BMC Bioinformatics, 7, 516.
    • (2006) BMC Bioinformatics , vol.7 , pp. 516
    • Gong, W.1    Ren, Y.2    Xu, Q.3    Wang, Y.4    Lin, D.5    Zhou, H.6    Li, T.7
  • 28
    • 33846906687 scopus 로고    scopus 로고
    • More complete gene silencing by fewer siRNAs: Transparent optimized design and biophysical signature
    • Ladunga,I. (2007) More complete gene silencing by fewer siRNAs: transparent optimized design and biophysical signature. Nucleic Acids Res., 35, 433-440.
    • (2007) Nucleic Acids Res , vol.35 , pp. 433-440
    • Ladunga, I.1
  • 31
    • 24344500241 scopus 로고    scopus 로고
    • Sequence, chemical, and structural variation of small interfering RNAs and short hairpin RNAs and the effect on mammalian gene silencing
    • Harborth,J., Elbashir,S.M., Vandenburgh,K., Manninga,H., Scaringe,S.A., Weber,K. and Tuschl,T. (2003) Sequence, chemical, and structural variation of small interfering RNAs and short hairpin RNAs and the effect on mammalian gene silencing. Antisense Nucleic Acid Drug Dev. 13, 83-105.
    • (2003) Antisense Nucleic Acid Drug Dev , vol.13 , pp. 83-105
    • Harborth, J.1    Elbashir, S.M.2    Vandenburgh, K.3    Manninga, H.4    Scaringe, S.A.5    Weber, K.6    Tuschl, T.7
  • 32
    • 0037470145 scopus 로고    scopus 로고
    • Efficient reduction of target RNAs by small interfering RNA and RNase H-dependent antisense agents. A comparative analysis
    • Vickers,T.A., Koo,S., Bennett,C.F., Crooke,S.T., Dean,N.M. and Baker,B.F. (2003) Efficient reduction of target RNAs by small interfering RNA and RNase H-dependent antisense agents. A comparative analysis. J. Biol. Chem., 278, 7108-7118.
    • (2003) J. Biol. Chem , vol.278 , pp. 7108-7118
    • Vickers, T.A.1    Koo, S.2    Bennett, C.F.3    Crooke, S.T.4    Dean, N.M.5    Baker, B.F.6
  • 33
    • 34047177954 scopus 로고    scopus 로고
    • Specific residues at every third position of siRNA shape its efficient RNAi activity
    • Katoh,T. and Suzuki,T. (2007) Specific residues at every third position of siRNA shape its efficient RNAi activity. Nucleic Acids Res., 35, e27.
    • (2007) Nucleic Acids Res , vol.35
    • Katoh, T.1    Suzuki, T.2
  • 34
    • 19444386649 scopus 로고    scopus 로고
    • Prediction of siRNA functionality using generalized string kernel and support vector machine
    • Teramoto,R., Aoki,M., Kimura,T. and Kanaoka,M. (2005) Prediction of siRNA functionality using generalized string kernel and support vector machine. FEBS Lett., 579, 2878-2882.
    • (2005) FEBS Lett , vol.579 , pp. 2878-2882
    • Teramoto, R.1    Aoki, M.2    Kimura, T.3    Kanaoka, M.4
  • 36
    • 33745200043 scopus 로고    scopus 로고
    • A novel siRNA validation system for functional screening and identification of effective RNAi probes in mammalian cells
    • Hung,C.F., Lu,K.C., Cheng,T.L., Wu,R.H., Huang,L.Y., Teng,C.F. and Chang,W.T. (2006) A novel siRNA validation system for functional screening and identification of effective RNAi probes in mammalian cells. Biochem. Biophys. Res. Commun., 346, 707-720.
    • (2006) Biochem. Biophys. Res. Commun , vol.346 , pp. 707-720
    • Hung, C.F.1    Lu, K.C.2    Cheng, T.L.3    Wu, R.H.4    Huang, L.Y.5    Teng, C.F.6    Chang, W.T.7
  • 38
    • 0042121256 scopus 로고    scopus 로고
    • Mfold web server for nucleic acid folding and hybridization prediction
    • Zuker,M. (2003) Mfold web server for nucleic acid folding and hybridization prediction. Nucleic Acids Res., 31, 3406-3415.
    • (2003) Nucleic Acids Res , vol.31 , pp. 3406-3415
    • Zuker, M.1


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.