메뉴 건너뛰기




Volumn 41, Issue 3, 2013, Pages 1383-1394

Improved nucleic acid descriptors for siRNA efficacy prediction

Author keywords

[No Author keywords available]

Indexed keywords

SMALL INTERFERING RNA;

EID: 84873667029     PISSN: 03051048     EISSN: 13624962     Source Type: Journal    
DOI: 10.1093/nar/gks1191     Document Type: Article
Times cited : (21)

References (54)
  • 1
    • 19344375743 scopus 로고    scopus 로고
    • RNAi therapeutics: How likely, how soon?
    • Robinson,R. (2004) RNAi therapeutics: How likely, how soon? PLoS Biol., 2, 18-20.
    • (2004) PLoS Biol , vol.2 , pp. 18-20
    • Robinson, R.1
  • 3
    • 4644223259 scopus 로고    scopus 로고
    • Mechanisms of gene silencing by double-stranded RNA
    • Meister,G. and Tuschl,T. (2004) Mechanisms of gene silencing by double-stranded RNA. Nature, 431, 343-349.
    • (2004) Nature , vol.431 , pp. 343-349
    • Meister, G.1    Tuschl, T.2
  • 4
    • 4644350944 scopus 로고    scopus 로고
    • Unlocking the potential of the human genome with RNA interference
    • Hannon,G.J. and Rossi,J.J. (2004) Unlocking the potential of the human genome with RNA interference. Nature, 431, 371-378.
    • (2004) Nature , vol.431 , pp. 371-378
    • Hannon, G.J.1    Rossi, J.J.2
  • 7
    • 34249810892 scopus 로고    scopus 로고
    • Argonaute proteins: Mediators of RNA silencing
    • Peters,L. and Meister,G. (2007) Argonaute proteins: Mediators of RNA silencing. Mol. Cell, 26, 611-623.
    • (2007) Mol. Cell , vol.26 , pp. 611-623
    • Peters, L.1    Meister, G.2
  • 9
    • 0033572660 scopus 로고    scopus 로고
    • Targeted mRNA degradation by double-stranded RNA in vitro
    • Tuschl,T., Zamore,P., Lehmann,R., Bartel,D. and Sharp,P. (1999) Targeted mRNA degradation by double-stranded RNA in vitro. Genes Dev., 13, 3191-3197.
    • (1999) Genes Dev , vol.13 , pp. 3191-3197
    • Tuschl, T.1    Zamore, P.2    Lehmann, R.3    Bartel, D.4    Sharp, P.5
  • 10
    • 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
  • 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
  • 16
    • 33748701701 scopus 로고    scopus 로고
    • Computational models with thermodynamic and composition features improve siRNA design
    • Shabalina,S., Spiridonov,A. and Ogurtsov,A. (2006) Computational models with thermodynamic and composition features improve siRNA design. BMC Bioinformatics, 7, 65.
    • (2006) BMC Bioinformatics , vol.7 , pp. 65
    • Shabalina, S.1    Spiridonov, A.2    Ogurtsov, A.3
  • 19
    • 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
  • 20
    • 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
  • 21
    • 56249145105 scopus 로고    scopus 로고
    • Structure of the guide-strand-containing argonaute silencing complex
    • Wang,Y., Sheng,G., Juranek,S., Tuschl,T. and Patel,D.J. (2008) Structure of the guide-strand-containing argonaute silencing complex. Nature, 456, 209-213.
    • (2008) Nature , vol.456 , pp. 209-213
    • Wang, Y.1    Sheng, G.2    Juranek, S.3    Tuschl, T.4    Patel, D.J.5
  • 23
    • 77957350921 scopus 로고    scopus 로고
    • Toward a consensus view of duplex RNA flexibility
    • Faustino,I., Perez,A. and Orozco,M. (2010) Toward a consensus view of duplex RNA flexibility. Biophys. J., 99, 1876-1885.
    • (2010) Biophys. J. , vol.99 , pp. 1876-1885
    • Faustino, I.1    Perez, A.2    Orozco, M.3
  • 25
    • 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
  • 26
    • 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
  • 29
    • 0032552882 scopus 로고    scopus 로고
    • Thermodynamic parameters for an expanded nearest-neighbor model for ormation of RNA duplexes with Watson-Crick base Pairs
    • Xia,T., SantaLucia,J., Burkard,M.E., Kierzek,R., Schroeder,S.J., Jiao,X., Cox,C. and Turner,D.H. (1998) Thermodynamic parameters for an expanded nearest-neighbor model for ormation of RNA duplexes with Watson-Crick base Pairs. Biochemistry, 37, 14719-14735.
    • (1998) Biochemistry , vol.37 , pp. 14719-14735
    • Xia, T.1    Santalucia, J.2    Burkard, M.E.3    Kierzek, R.4    Schroeder, S.J.5    Jiao, X.6    Cox, C.7    Turner, D.H.8
  • 31
    • 34250318638 scopus 로고    scopus 로고
    • Refinement of the AMBER force field for nucleic acids: Improving the description of alpha/ gamma conformers
    • Perez,A., Marchan,I., Svozil,D., Sponer,J., Cheatham,T.E. III, Laughton,C.A. and Orozco,M. (2007) Refinement of the AMBER force field for nucleic acids: Improving the description of alpha/ gamma conformers. Biophys. J., 92, 3817-3829.
    • (2007) Biophys. J. , vol.92 , pp. 3817-3829
    • Perez, A.1    Marchan, I.2    Svozil, D.3    Sponer, J.4    Cheathamiii, T.E.5    Laughton, C.A.6    Orozco, M.7
  • 33
    • 36749098380 scopus 로고    scopus 로고
    • Dynamics of B-DNA on the microsecond time scale
    • Perez,A., Luque,F.J. and Orozco,M. (2007) Dynamics of B-DNA on the microsecond time scale. J. Am. Chem. Soc., 129, 14739-14745.
    • (2007) J. Am. Chem. Soc , vol.129 , pp. 14739-14745
    • Perez, A.1    Luque, F.J.2    Orozco, M.3
  • 36
    • 0034682870 scopus 로고    scopus 로고
    • A-tract bending: Insights into experimental structures by computational models
    • Strahs,D. and Schlick,T. (2000) A-tract bending: Insights into experimental structures by computational models. J. Mol. Biol., 301, 643-663.
    • (2000) J. Mol. Biol , vol.301 , pp. 643-663
    • Strahs, D.1    Schlick, T.2
  • 37
    • 0042161890 scopus 로고    scopus 로고
    • The activity of siRNA in mammalian cells is related to structural target accessibility: A comparison with antisense oligonucleotides
    • Kretschmer-Kazemi Far,R. and Sczakiel,G. (2003) The activity of siRNA in mammalian cells is related to structural target accessibility: A comparison with antisense oligonucleotides. Nucleic Acids Res., 31, 4417-4424.
    • (2003) Nucleic Acids Res , vol.31 , pp. 4417-4424
    • Kretschmer-Kazemi Far, R.1    Sczakiel, G.2
  • 38
    • 27944473306 scopus 로고    scopus 로고
    • Design of siRNAs producing unstructured guide-RNAs results in improved RNA interference efficiency
    • Patzel,V., Rutz,S., Dietrich,I., Koberle,C., Scheffold,A. and Kaufmann,S.H.E. (2005) Design of siRNAs producing unstructured guide-RNAs results in improved RNA interference efficiency. Nat. Biotech., 23, 1440-1444.
    • (2005) Nat. Biotech , vol.23 , pp. 1440-1444
    • Patzel, V.1    Rutz, S.2    Dietrich, I.3    Koberle, C.4    Scheffold, A.5    Kaufmann, S.H.E.6
  • 39
    • 33746907851 scopus 로고    scopus 로고
    • SiRNA efficiency: Structure or sequence-that is the question
    • doi: 10.1155/JBB/ 2006/83757
    • Kurreck,J. (2006) siRNA efficiency: Structure or sequence - that is the question. J. Biomed. Biotechnol., 2006, 1-7; doi: 10.1155/JBB/ 2006/83757.
    • (2006) J. Biomed. Biotechnol , vol.2006 , pp. 1-7
    • Kurreck, J.1
  • 40
    • 26444437334 scopus 로고    scopus 로고
    • SiRNA target site secondary structure predictions using local stable substructures
    • Heale,B.S.E., 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.E.1    Soifer, H.S.2    Bowers, C.3    Rossi, J.J.4
  • 41
    • 43249105382 scopus 로고    scopus 로고
    • Impact of target mRNA structure on siRNA silencing efficiency: A large-scale study
    • Gredell,J.A., Berger,A.K. and Walton,S.P. (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
  • 44
    • 33846829987 scopus 로고    scopus 로고
    • The pls package: Principal component and partial least squares regression in R
    • Mevik,B.-H. and Wehrens,R. (2007) The pls package: principal component and partial least squares regression in R. J. Stat. Softw., 18.
    • (2007) J. Stat. Softw , vol.18
    • Mevik, B.-H.1    Wehrens, R.2
  • 46
    • 84873664393 scopus 로고    scopus 로고
    • Information science and statistics
    • Jordan,M., Nowak,R. and Scho lkopf,B. (eds Springer, Germany
    • Vapnik,V. (2000) Information science and statistics. In: Jordan,M., Nowak,R. and Scholkopf,B. (eds), The Nature of Statistical Learning Theory, Vol. 19. Springer, Germany, p. 48.
    • (2000) Nature of Statistical Learning Theory , vol.19 , pp. 48
    • Vapnik, V.1
  • 48
    • 0035478854 scopus 로고    scopus 로고
    • Random forests
    • Breiman,L. (2001) Random forests. Mach. Learn., 45, 5-32.
    • (2001) Mach. Learn , vol.45 , pp. 5-32
    • Breiman, L.1
  • 49
    • 0027310371 scopus 로고
    • Generating optimal linear PLS estimations (GOLPE): An advanced chemometric tool for handling 3D-QSAR problems
    • Baroni,M., Costantino,G., Cruciani,G., Riganelli,D., Valigi,R. and Clementi,S. (1993) Generating optimal linear PLS estimations (GOLPE): An advanced chemometric tool for handling 3D-QSAR problems. Quant. Struct. Act. Relat., 12, 9-20.
    • (1993) Quant. Struct. Act. Relat , vol.12 , pp. 9-20
    • Baroni, M.1    Costantino, G.2    Cruciani, G.3    Riganelli, D.4    Valigi, R.5    Clementi, S.6
  • 51
    • 78449310037 scopus 로고    scopus 로고
    • MRNA turnover rate limits siRNA and microRNA efficacy
    • Larsson,E., Sander,C. and Marks,D. (2010) mRNA turnover rate limits siRNA and microRNA efficacy. Mol. Syst. Biol., 6, 433.
    • (2010) Mol. Syst. Biol , vol.6 , pp. 433
    • Larsson, E.1    Sander, C.2    Marks, D.3
  • 53
    • 0023517027 scopus 로고
    • Rapid cytoplasmic turnover of c-myc mRNA: Requirement of the 30 untranslated sequences
    • Jones,T.R. and Cole,M.D. (1987) Rapid cytoplasmic turnover of c-myc mRNA: requirement of the 30 untranslated sequences. Mol. Cell. Biol., 7, 4513-4521.
    • (1987) Mol. Cell. Biol , vol.7 , pp. 4513-4521
    • Jones, T.R.1    Cole, M.D.2


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.