메뉴 건너뛰기




Volumn 6, Issue 10, 2011, Pages

Mysirna-Designer: A workflow for efficient siRNA design

Author keywords

[No Author keywords available]

Indexed keywords

MESSENGER RNA; SMALL INTERFERING RNA;

EID: 80055056681     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0025642     Document Type: Article
Times cited : (34)

References (41)
  • 3
    • 1642273831 scopus 로고    scopus 로고
    • An algorithm for selection of functional siRNA sequences
    • doi:10.1016/j.bbrc.2004.02.157
    • Amarzguioui M, Prydz H, (2004) An algorithm for selection of functional siRNA sequences. Biochemical and biophysical research communications 316: 1050-8 doi:10.1016/j.bbrc.2004.02.157.
    • (2004) Biochemical and Biophysical Research Communications , vol.316 , pp. 1050-1058
    • Amarzguioui, M.1    Prydz, H.2
  • 4
    • 3542992506 scopus 로고    scopus 로고
    • An effective method for selecting siRNA target sequences in mammalian cells
    • Takasaki S, Kotani S, Konagaya A, (2004) An effective method for selecting siRNA target sequences in mammalian cells. Cell cycle (Georgetown, Tex.) 3: 790-5.
    • (2004) Cell Cycle (Georgetown, Tex.) , vol.3 , pp. 790-795
    • Takasaki, S.1    Kotani, S.2    Konagaya, A.3
  • 5
    • 34047177954 scopus 로고    scopus 로고
    • Specific residues at every third position of siRNA shape its efficient RNAi activity
    • doi: 10.1093/nar/gkl1120
    • Katoh T, Suzuki T, (2007) Specific residues at every third position of siRNA shape its efficient RNAi activity. Nucleic acids research 35: e27 doi:10.1093/nar/gkl1120.
    • (2007) Nucleic Acids Research , vol.35
    • Katoh, T.1    Suzuki, T.2
  • 7
    • 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
    • doi:10.1093/nar/gkh238
    • Hsieh AC, Bo R, Manola J, Vazquez F, Bare O, 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 research 32: 893-901 doi:10.1093/nar/gkh238.
    • (2004) Nucleic Acids Research , vol.32 , pp. 893-901
    • Hsieh, A.C.1    Bo, R.2    Manola, J.3    Vazquez, F.4    Bare, O.5
  • 8
    • 35548980865 scopus 로고    scopus 로고
    • Thermodynamic instability of siRNA duplex is a prerequisite for dependable prediction of siRNA activities
    • doi:10.1093/nar/gkm699
    • Ichihara M, Murakumo Y, Masuda A, Matsuura T, Asai N, et al. (2007) Thermodynamic instability of siRNA duplex is a prerequisite for dependable prediction of siRNA activities. Nucleic Acids Research pp. 1-10 doi:10.1093/nar/gkm699.
    • (2007) Nucleic Acids Research , pp. 1-10
    • Ichihara, M.1    Murakumo, Y.2    Masuda, A.3    Matsuura, T.4    Asai, N.5
  • 9
    • 23444437819 scopus 로고    scopus 로고
    • Design of a genome-wide siRNA library using an artificial neural network
    • doi:10.1038/nbt1118
    • Huesken D, Lange J, Mickanin C, Weiler J, Asselbergs F, et al. (2006) Design of a genome-wide siRNA library using an artificial neural network. Nature Biotechnology 23: 995-1002 doi:10.1038/nbt1118.
    • (2006) Nature Biotechnology , vol.23 , pp. 995-1002
    • Huesken, D.1    Lange, J.2    Mickanin, C.3    Weiler, J.4    Asselbergs, F.5
  • 10
    • 33748701701 scopus 로고    scopus 로고
    • Computational models with thermodynamic and composition features improve siRNA design
    • doi:10.1186/1471-2105-7-65
    • Shabalina SA, Spiridonov AN, Ogurtsov AY, (2006) Computational models with thermodynamic and composition features improve siRNA design. BMC bioinformatics 7: 65 doi:10.1186/1471-2105-7-65.
    • (2006) BMC Bioinformatics , vol.7 , pp. 65
    • Shabalina, S.A.1    Spiridonov, A.N.2    Ogurtsov, A.Y.3
  • 11
    • 33845663097 scopus 로고    scopus 로고
    • An accurate and interpretable model for siRNA efficacy prediction
    • doi:10.1186/1471-2105-7-520
    • Vert J-P, Foveau N, Lajaunie C, Vandenbrouck Y, (2006) An accurate and interpretable model for siRNA efficacy prediction. BMC bioinformatics 7: 520 doi:10.1186/1471-2105-7-520.
    • (2006) BMC Bioinformatics , vol.7 , pp. 520
    • Vert, J.-P.1    Foveau, N.2    Lajaunie, C.3    Vandenbrouck, Y.4
  • 12
    • 34250309149 scopus 로고    scopus 로고
    • Comparison of approaches for rational siRNA design leading to a new efficient and transparent method
    • doi:10.1093/nar/gkm088
    • Matveeva O, Nechipurenko Y, Rossi L, Moore B, Ogurtsov AY, et al. (2007) Comparison of approaches for rational siRNA design leading to a new efficient and transparent method. Access 35: 1-10 doi:10.1093/nar/gkm088.
    • (2007) Access , vol.35 , pp. 1-10
    • Matveeva, O.1    Nechipurenko, Y.2    Rossi, L.3    Moore, B.4    Ogurtsov, A.Y.5
  • 13
    • 0037440005 scopus 로고    scopus 로고
    • Tolerance for mutations and chemical modifications in a siRNA
    • doi:10.1093/nar/gkg147
    • Amarzguioui M, (2003) Tolerance for mutations and chemical modifications in a siRNA. Nucleic Acids Research 31: 589-595 doi:10.1093/nar/gkg147.
    • (2003) Nucleic Acids Research , vol.31 , pp. 589-595
    • Amarzguioui, M.1
  • 14
    • 0036351317 scopus 로고    scopus 로고
    • Analysis of gene function in somatic mammalian cells using small interfering RNAs
    • doi:10.1016/S1046-2023(02)00023-3
    • Elbashir SM, Harborth J, Weber K, Tuschl T, (2002) Analysis of gene function in somatic mammalian cells using small interfering RNAs. Methods (San Diego, Calif.) 26: 199-213 doi:10.1016/S1046-2023(02)00023-3.
    • (2002) Methods (San Diego, Calif.) , vol.26 , pp. 199-213
    • Elbashir, S.M.1    Harborth, J.2    Weber, K.3    Tuschl, T.4
  • 15
    • 0038606999 scopus 로고    scopus 로고
    • Structural variations and stabilising modifications of synthetic siRNAs in mammalian cells
    • Czauderna F, Fechtner M, Dames S, Aygün H, Klippel A, et al. (2003) Structural variations and stabilising modifications of synthetic siRNAs in mammalian cells. Nucleic acids research 31: 2705-16.
    • (2003) Nucleic Acids Research , vol.31 , pp. 2705-2716
    • Czauderna, F.1    Fechtner, M.2    Dames, S.3    Aygün, H.4    Klippel, A.5
  • 16
    • 10744225153 scopus 로고    scopus 로고
    • Asymmetry in the Assembly of the RNAi Enzyme Complex
    • doi:10.1016/S0092-8674(03)00759-1
    • Schwarz DS, Hutvágner G, Du T, Xu Z, Aronin N, et al. (2003) Asymmetry in the Assembly of the RNAi Enzyme Complex. Cell 115: 199-208 doi:10.1016/S0092-8674(03)00759-1.
    • (2003) Cell , vol.115 , pp. 199-208
    • Schwarz, D.S.1    Hutvágner, G.2    Du, T.3    Xu, Z.4    Aronin, N.5
  • 17
    • 3242677639 scopus 로고    scopus 로고
    • siRNAs: applications in functional genomics and potential as therapeutics. Nature reviews
    • doi:10.1038/nrd1345
    • Dorsett Y, Tuschl T, (2004) siRNAs: applications in functional genomics and potential as therapeutics. Nature reviews. Drug discovery 3: 318-29 doi:10.1038/nrd1345.
    • (2004) Drug Discovery , vol.3 , pp. 318-329
    • Dorsett, Y.1    Tuschl, T.2
  • 18
    • 27944473306 scopus 로고    scopus 로고
    • Design of siRNAs producing unstructured guide-RNAs results in improved RNA interference efficiency
    • doi:10.1038/nbt1151
    • Patzel V, Rutz S, Dietrich I, Köberle C, Scheffold A, et al. (2005) Design of siRNAs producing unstructured guide-RNAs results in improved RNA interference efficiency. Nature biotechnology 23: 1440-4 doi:10.1038/nbt1151.
    • (2005) Nature Biotechnology , vol.23 , pp. 1440-1444
    • Patzel, V.1    Rutz, S.2    Dietrich, I.3    Köberle, C.4    Scheffold, A.5
  • 20
    • 43249105382 scopus 로고    scopus 로고
    • Impact of Target mRNA Structure on siRNA Silencing Efficiency: A Large-Scale Study
    • doi:10.1002/bit.21798
    • Gredell JA, Berger AK, Walton SP, (2008) Impact of Target mRNA Structure on siRNA Silencing Efficiency: A Large-Scale Study. Biotechnology 100: 744-755 doi:10.1002/bit.21798.
    • (2008) Biotechnology , vol.100 , pp. 744-755
    • Gredell, J.A.1    Berger, A.K.2    Walton, S.P.3
  • 21
    • 33846906687 scopus 로고    scopus 로고
    • More complete gene silencing by fewer siRNAs: transparent optimized design and biophysical signature
    • doi:10.1093/nar/gkl1065
    • Ladunga I, (2007) More complete gene silencing by fewer siRNAs: transparent optimized design and biophysical signature. Nucleic acids research 35: 433-40 doi:10.1093/nar/gkl1065.
    • (2007) Nucleic Acids Research , vol.35 , pp. 433-440
    • Ladunga, I.1
  • 22
    • 3242877996 scopus 로고    scopus 로고
    • Sfold web server for statistical folding and rational design of nucleic acids
    • doi:10.1093/nar/gkh449
    • Ding Y, Chan CY, Lawrence CE, (2004) Sfold web server for statistical folding and rational design of nucleic acids. Nucleic acids research 32: W135-41 doi:10.1093/nar/gkh449.
    • (2004) Nucleic Acids Research , vol.32 , pp. 135-141
    • Ding, Y.1    Chan, C.Y.2    Lawrence, C.E.3
  • 24
    • 48449098277 scopus 로고    scopus 로고
    • OligoWalk: an online siRNA design tool utilizing hybridization thermodynamics
    • doi:10.1093/nar/gkn250
    • Lu ZJ, Mathews DH, (2008) OligoWalk: an online siRNA design tool utilizing hybridization thermodynamics. Nucleic acids research 36: W104-8 doi:10.1093/nar/gkn250.
    • (2008) Nucleic Acids Research , vol.36 , pp. 104-108
    • Lu, Z.J.1    Mathews, D.H.2
  • 25
    • 39149106448 scopus 로고    scopus 로고
    • Efficient siRNA selection using hybridization thermodynamics
    • doi:10.1093/nar/gkm920
    • Lu ZJ, Mathews DH, (2008) Efficient siRNA selection using hybridization thermodynamics. Nucleic acids research 36: 640-7 doi:10.1093/nar/gkm920.
    • (2008) Nucleic Acids Research , vol.36 , pp. 640-647
    • Lu, Z.J.1    Mathews, D.H.2
  • 26
    • 43449124403 scopus 로고    scopus 로고
    • The impact of target site accessibility on the design of effective siRNAs
    • doi:10.1038/nbt1404
    • Tafer H, Ameres SL, Obernosterer G, Gebeshuber CA, Schroeder R, et al. (2008) The impact of target site accessibility on the design of effective siRNAs. Nature biotechnology 26: 578-83 doi:10.1038/nbt1404.
    • (2008) Nature Biotechnology , vol.26 , pp. 578-583
    • Tafer, H.1    Ameres, S.L.2    Obernosterer, G.3    Gebeshuber, C.A.4    Schroeder, R.5
  • 27
    • 38449100230 scopus 로고    scopus 로고
    • A protocol for designing siRNAs with high functionality and specificity
    • doi:10.1038/nprot.2007.278
    • Birmingham A, Anderson E, Sullivan K, Reynolds A, Boese Q, et al. (2007) A protocol for designing siRNAs with high functionality and specificity. Nature protocols 2: 2068-78 doi:10.1038/nprot.2007.278.
    • (2007) Nature Protocols , vol.2 , pp. 2068-2078
    • Birmingham, A.1    Anderson, E.2    Sullivan, K.3    Reynolds, A.4    Boese, Q.5
  • 32
    • 33646188259 scopus 로고    scopus 로고
    • 3′ UTR seed matches, but not overall identity, are associated with RNAi off-targets
    • doi:10.1038/nmeth854
    • Birmingham A, Anderson EM, Reynolds A, Ilsley-Tyree D, Leake D, et al. (2006) 3′ UTR seed matches, but not overall identity, are associated with RNAi off-targets. Nature methods 3: 199-204 doi:10.1038/nmeth854.
    • (2006) Nature Methods , vol.3 , pp. 199-204
    • Birmingham, A.1    Anderson, E.M.2    Reynolds, A.3    Ilsley-Tyree, D.4    Leake, D.5
  • 33
    • 74049124186 scopus 로고    scopus 로고
    • Recognizing and avoiding siRNA off-target effects for target identification and therapeutic application. Nature reviews
    • doi:10.1038/nrd3010
    • Jackson AL, Linsley PS, (2010) Recognizing and avoiding siRNA off-target effects for target identification and therapeutic application. Nature reviews. Drug discovery 9: 57-67 doi:10.1038/nrd3010.
    • (2010) Drug Discovery , vol.9 , pp. 57-67
    • Jackson, A.L.1    Linsley, P.S.2
  • 34
    • 42449152837 scopus 로고    scopus 로고
    • Experimental validation of the importance of seed complement frequency to siRNA specificity
    • doi:10.1261/rna.704708
    • Anderson EM, Birmingham A, Baskerville S, Reynolds A, Maksimova E, et al. (2008) Experimental validation of the importance of seed complement frequency to siRNA specificity. RNA (New York, N.Y.) 14: 853-61 doi:10.1261/rna.704708.
    • (2008) RNA (New York, N.Y.) , vol.14 , pp. 853-861
    • Anderson, E.M.1    Birmingham, A.2    Baskerville, S.3    Reynolds, A.4    Maksimova, E.5
  • 35
    • 33846614547 scopus 로고    scopus 로고
    • In silico selection of active siRNA
    • doi:10.1016/j.drudis.2006.11.015
    • Patzel V, (2007) In silico selection of active siRNA. Drug Discovery Today 12: 139-48 doi:10.1016/j.drudis.2006.11.015.
    • (2007) Drug Discovery Today , vol.12 , pp. 139-148
    • Patzel, V.1
  • 36
    • 77952312477 scopus 로고    scopus 로고
    • Designing optimal siRNA based on target site accessibility
    • doi:10.1007/978-1-60761-588-0_9
    • Hofacker IL, Tafer H, (2010) Designing optimal siRNA based on target site accessibility. Methods in molecular biology (Clifton, N.J.) 623: 137-54 doi:10.1007/978-1-60761-588-0_9.
    • (2010) Methods in Molecular Biology (Clifton, N.J.) , vol.623 , pp. 137-154
    • Hofacker, I.L.1    Tafer, H.2
  • 37
    • 34447102459 scopus 로고    scopus 로고
    • Molecular basis for target RNA recognition and cleavage by human RISC
    • doi:10.1016/j.cell.2007.04.037
    • Ameres SL, Martinez J, Schroeder R, (2007) Molecular basis for target RNA recognition and cleavage by human RISC. Cell 130: 101-12 doi:10.1016/j.cell.2007.04.037.
    • (2007) Cell , vol.130 , pp. 101-112
    • Ameres, S.L.1    Martinez, J.2    Schroeder, R.3
  • 38
    • 0043123153 scopus 로고    scopus 로고
    • Vienna RNA secondary structure server
    • doi:10.1093/nar/gkg599
    • Hofacker IL, (2003) Vienna RNA secondary structure server. Nucleic Acids Research 31: 3429-3431 doi:10.1093/nar/gkg599.
    • (2003) Nucleic Acids Research , vol.31 , pp. 3429-3431
    • Hofacker, I.L.1
  • 39
    • 79952697845 scopus 로고    scopus 로고
    • Functional identification of optimized RNAi triggers using a massively parallel sensor assay
    • doi:10.1016/j.molcel.2011.02.008
    • Fellmann C, Zuber J, McJunkin K, Chang K, Malone CD, et al. (2011) Functional identification of optimized RNAi triggers using a massively parallel sensor assay. Molecular cell 41: 733-46 doi:10.1016/j.molcel.2011.02.008.
    • (2011) Molecular Cell , vol.41 , pp. 733-746
    • Fellmann, C.1    Zuber, J.2    McJunkin, K.3    Chang, K.4    Malone, C.D.5
  • 40
    • 84861532262 scopus 로고    scopus 로고
    • MysiRNA: Improving siRNA Efficacy Prediction Using a Machine- Learning Model Combining Multi-tools and Whole Stacking Energy (ΔG)
    • Mysara M, Elhefnawi M, Garibaldi JM, (2011) MysiRNA: Improving siRNA Efficacy Prediction Using a Machine- Learning Model Combining Multi-tools and Whole Stacking Energy (ΔG). Journal of Biomedical Informatics pp. 1-23.
    • (2011) Journal of Biomedical Informatics , pp. 1-23
    • Mysara, M.1    Elhefnawi, M.2    Garibaldi, J.M.3
  • 41
    • 84872419274 scopus 로고    scopus 로고
    • In-Silico Approaches for RNAi Post-transcriptional Gene regulation: Optimizing siRNA design and selection
    • In: Mahdavi MA, editors, InTech, In Press
    • ElHefnawi M, Mysara M, (2011) In-Silico Approaches for RNAi Post-transcriptional Gene regulation: Optimizing siRNA design and selection. In: Mahdavi MA, editors. Bioinformatics/Book 2 InTech In Press.
    • (2011) Bioinformatics/Book 2
    • ElHefnawi, M.1    Mysara, M.2


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.