-
1
-
-
0035803583
-
Functional anatomy of siRNAs for mediating efficient RNAi in Drosophila melanogaster embryo lysate
-
Elbashir,S.M., Martinez,J., Patkaniowska,A., Lendeckel,W. and Tuschl,T. (2001) Functional anatomy of siRNAs for mediating efficient RNAi in Drosophila melanogaster embryo lysate. EMBO J., 20, 6877-6888.
-
(2001)
EMBO J.
, vol.20
, pp. 6877-6888
-
-
Elbashir, S.M.1
Martinez, J.2
Patkaniowska, A.3
Lendeckel, W.4
Tuschl, T.5
-
2
-
-
0036351317
-
Analysis of gene function in somatic mammalian cells using small interfering RNAs
-
Elbashir,S.M., Harborth,J., Weber,K. and Tuschl,T. (2002) Analysis of gene function in somatic mammalian cells using small interfering RNAs. Methods, 26, 199-213.
-
(2002)
Methods
, vol.26
, pp. 199-213
-
-
Elbashir, S.M.1
Harborth, J.2
Weber, K.3
Tuschl, T.4
-
3
-
-
2542461104
-
Nucleic acid 3′-end recognition by the Argonaute 2 PAZ domain
-
Lingel,A., Simon,B., Izaurralde,E. and Sattler,M. (2004) Nucleic acid 3′-end recognition by the Argonaute 2 PAZ domain. Nature Struct. Mol. Biol., 11, 576-577.
-
(2004)
Nature Struct. Mol. Biol.
, vol.11
, pp. 576-577
-
-
Lingel, A.1
Simon, B.2
Izaurralde, E.3
Sattler, M.4
-
4
-
-
0345490960
-
The crystal structure of the Argonaute 2 PAZ domain reveals an RNA binding motif in RNAi effector complexes
-
Song,J.J., Liu,J., Tolia,N.H., Schneiderman,J., Smith,S.K., Martienssen,R.A., Hannon,G.J. and Joshua-Tor,L. (2003) The crystal structure of the Argonaute 2 PAZ domain reveals an RNA binding motif in RNAi effector complexes. Nature Struct. Biol., 10, 1026-1032.
-
(2003)
Nature Struct. Biol.
, vol.10
, pp. 1026-1032
-
-
Song, J.J.1
Liu, J.2
Tolia, N.H.3
Schneiderman, J.4
Smith, S.K.5
Martienssen, R.A.6
Hannon, G.J.7
Joshua-Tor, L.8
-
5
-
-
0345359925
-
Structure and nucleic-acid binding of the Drosophila Argonaute 2 PAZ domain
-
Lingel,A., Simon,B., Izaurralde,E. and Sattler,M. (2003) Structure and nucleic-acid binding of the Drosophila Argonaute 2 PAZ domain. Nature, 426, 465-469.
-
(2003)
Nature
, vol.426
, pp. 465-469
-
-
Lingel, A.1
Simon, B.2
Izaurralde, E.3
Sattler, M.4
-
6
-
-
0642345790
-
Structure and conserved RNA binding of the PAZ domain
-
Yan,K.S., Yan,S., Farooq,A., Han,A., Zeng,L. and Zhou,M.M. (2003) Structure and conserved RNA binding of the PAZ domain. Nature, 426, 468-474.
-
(2003)
Nature
, vol.426
, pp. 468-474
-
-
Yan, K.S.1
Yan, S.2
Farooq, A.3
Han, A.4
Zeng, L.5
Zhou, M.M.6
-
7
-
-
2442679207
-
Structural basis for overhang-specific small interfering RNA recognition by the PAZ domain
-
Ma,J.B., Ye,K. and Patel,D.J. (2004) Structural basis for overhang-specific small interfering RNA recognition by the PAZ domain. Nature, 429, 318-322.
-
(2004)
Nature
, vol.429
, pp. 318-322
-
-
Ma, J.B.1
Ye, K.2
Patel, D.J.3
-
8
-
-
1642487115
-
Characterization of the interactions between mammalian PAZ PIWI domain proteins and Dicer
-
Tahbaz,N., Kolb,F.A., Zhang,H., Jaronczyk,K., Filipowicz,W. and Hobman,T.C. (2004) Characterization of the interactions between mammalian PAZ PIWI domain proteins and Dicer. EMBO Rep., 5, 189-194.
-
(2004)
EMBO Rep.
, vol.5
, pp. 189-194
-
-
Tahbaz, N.1
Kolb, F.A.2
Zhang, H.3
Jaronczyk, K.4
Filipowicz, W.5
Hobman, T.C.6
-
9
-
-
24344500241
-
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
-
10
-
-
3042602447
-
Kinetic analysis of the RNAi enzyme complex
-
Haley,B. and Zamore,P.D. (2004) Kinetic analysis of the RNAi enzyme complex. Nature Struct. Mol. Biol., 11, 599-606.
-
(2004)
Nature Struct. Mol. Biol.
, vol.11
, pp. 599-606
-
-
Haley, B.1
Zamore, P.D.2
-
11
-
-
0037440005
-
Tolerance for mutations and chemical modifications in a siRNA
-
Amarzguioui,M., Holen,T., Babaie,E. and Prydz,H. (2003) Tolerance for mutations and chemical modifications in a siRNA. Nucleic Acids Res. 31, 589-595.
-
(2003)
Nucleic Acids Res.
, vol.31
, pp. 589-595
-
-
Amarzguioui, M.1
Holen, T.2
Babaie, E.3
Prydz, H.4
-
12
-
-
0041331496
-
siRNA function in RNAi: A chemical modification analysis
-
Chiu,Y.L. and Rana,T.M. (2003) siRNA function in RNAi: A chemical modification analysis. RNA, 9, 1034-1048.
-
(2003)
RNA
, vol.9
, pp. 1034-1048
-
-
Chiu, Y.L.1
Rana, T.M.2
-
13
-
-
2442495329
-
RISC is a 5′ phosphomonoester-producing RNA endonuclease
-
Martinez,J. and Tuschl,T. (2004) RISC is a 5′ phosphomonoester-producing RNA endonuclease. Genes Dev., 18, 975-980.
-
(2004)
Genes Dev.
, vol.18
, pp. 975-980
-
-
Martinez, J.1
Tuschl, T.2
-
14
-
-
4444302947
-
Crystal structure of Argonaute and its implications for RISC slicer activity
-
Song,J.J., Smith,S.K., Hannon,G.J. and Joshua-Tor,L. (2004) Crystal structure of Argonaute and its implications for RISC slicer activity. Science, 305, 1434-1437.
-
(2004)
Science
, vol.305
, pp. 1434-1437
-
-
Song, J.J.1
Smith, S.K.2
Hannon, G.J.3
Joshua-Tor, L.4
-
15
-
-
4444368187
-
Argonaute2 is the catalytic engine of mammalian RNAi
-
Liu,J., Carmell,M.A., Rivas,F.V., Marsden,C.G., Thomson,J.M., Song,J.J., Hammond,S.M., Joshua-Tor,L. and Hannon,G.J. (2004) Argonaute2 is the catalytic engine of mammalian RNAi. Science, 305, 1437-1441.
-
(2004)
Science
, vol.305
, pp. 1437-1441
-
-
Liu, J.1
Carmell, M.A.2
Rivas, F.V.3
Marsden, C.G.4
Thomson, J.M.5
Song, J.J.6
Hammond, S.M.7
Joshua-Tor, L.8
Hannon, G.J.9
-
16
-
-
0034653783
-
Effects of RNA secondary structure on cellular antisense activity
-
Vickers,T.A., Wyatt,J.R. and Freier,S.M. (2000) Effects of RNA secondary structure on cellular antisense activity. Nucleic Acids Res., 28, 1340-1347.
-
(2000)
Nucleic Acids Res.
, vol.28
, pp. 1340-1347
-
-
Vickers, T.A.1
Wyatt, J.R.2
Freier, S.M.3
-
17
-
-
0038521255
-
The efficacy of small interfering RNAs targeted to the type 1 insulin-like growth factor receptor (IGF1R) is influenced by secondary structure in the IGF1R transcript
-
Bohula,E.A., Salisbury,A.J., Sohail,M., Playford,M.P., Riedemamr,J., Southern,E.M. and Macaulay,V.M. (2003) The efficacy of small interfering RNAs targeted to the type 1 insulin-like growth factor receptor (IGF1R) is influenced by secondary structure in the IGF1R transcript. J. Biol. Chem., 278, 15991-15997.
-
(2003)
J. Biol. Chem.
, vol.278
, pp. 15991-15997
-
-
Bohula, E.A.1
Salisbury, A.J.2
Sohail, M.3
Playford, M.P.4
Riedemamr, J.5
Southern, E.M.6
Macaulay, V.M.7
-
18
-
-
0042121256
-
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
-
19
-
-
0033591465
-
Expanded sequence dependence of thermodynamic parameters improves prediction of RNA secondary structure
-
Mathews,D.H., Sabina,J., Zuker,M. and Turner,D.H. (1999) Expanded sequence dependence of thermodynamic parameters improves prediction of RNA secondary structure. J. Mol. Biol., 288, 911-940.
-
(1999)
J. Mol. Biol.
, vol.288
, pp. 911-940
-
-
Mathews, D.H.1
Sabina, J.2
Zuker, M.3
Turner, D.H.4
-
20
-
-
3242877996
-
Sfold web server for statistical folding and rational design of nucleic acids
-
Ding,Y., Chan,C.Y. and Lawrence,C.E. (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
Chan, C.Y.2
Lawrence, C.E.3
-
21
-
-
1942488998
-
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
-
22
-
-
1542336952
-
Rational siRNA design for RNA interference
-
Reynolds,A., Leake,D., Boese,Q., Scaringe,S., Marshall,W.S. and Khvorova,A. (2004) Rational siRNA design for RNA interference. Nat. Biotechnol., 22, 326-330.
-
(2004)
Nat. Biotechnol.
, vol.22
, pp. 326-330
-
-
Reynolds, A.1
Leake, D.2
Boese, Q.3
Scaringe, S.4
Marshall, W.S.5
Khvorova, A.6
-
23
-
-
0142165224
-
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
-
24
-
-
10744225153
-
Asymmetry in the assembly of the RNAi enzyme complex
-
Schwarz,D.S., Hutvagner,G., Du,T., Xu,Z., Aronin,N. and Zamore,P.D. (2003) Asymmetry in the assembly of the RNAi enzyme complex. Cell, 115, 199-208.
-
(2003)
Cell
, vol.115
, pp. 199-208
-
-
Schwarz, D.S.1
Hutvagner, G.2
Du, T.3
Xu, Z.4
Aronin, N.5
Zamore, P.D.6
-
25
-
-
1642346273
-
Guidelines for the selection of highly effective siRNA sequences for mammalian and chick RNA interference
-
Ui-Tei,K., Naito,Y., Takahashi,F., Haraguchi,T., Ohki-Hamazaki,H., Juni,A., Ueda,R. and Saigo,K. (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
Naito, Y.2
Takahashi, F.3
Haraguchi, T.4
Ohki-Hamazaki, H.5
Juni, A.6
Ueda, R.7
Saigo, K.8
-
26
-
-
1642273831
-
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
-
27
-
-
1542306855
-
Interferon induction by siRNAs and ssRNAs synthesized by phage polymerase
-
Kim,D.H., Longo,M., Han,Y., Lundberg,P., Cantin,E. and Rossi,J.J. (2004) Interferon induction by siRNAs and ssRNAs synthesized by phage polymerase. Nat. Biotechnol., 22, 321-325.
-
(2004)
Nat. Biotechnol.
, vol.22
, pp. 321-325
-
-
Kim, D.H.1
Longo, M.2
Han, Y.3
Lundberg, P.4
Cantin, E.5
Rossi, J.J.6
-
28
-
-
24144492099
-
Coupling of RNAi-mediated target downregulation with gene replacement
-
Kim,D.H. and Rossi,J.J. (2003) Coupling of RNAi-mediated target downregulation with gene replacement. Antisense Nucleic Acid Drug Dev., 13, 151-155.
-
(2003)
Antisense Nucleic Acid Drug Dev.
, vol.13
, pp. 151-155
-
-
Kim, D.H.1
Rossi, J.J.2
-
29
-
-
0021823907
-
A kinetic approach to the prediction of RNA secondary structures
-
Mironov,A.A., Dyakonova,L.P. and Kister,A.E. (1985) A kinetic approach to the prediction of RNA secondary structures. J. Biomol. Struct. Dyn., 2, 953-962.
-
(1985)
J. Biomol. Struct. Dyn.
, vol.2
, pp. 953-962
-
-
Mironov, A.A.1
Dyakonova, L.P.2
Kister, A.E.3
-
30
-
-
0026725254
-
Base-pair probability profiles of RNA secondary structures
-
Schmitz,M. and Steger,G. (1992) Base-pair probability profiles of RNA secondary structures. Comput. Appl. Biosci., 8, 389-399.
-
(1992)
Comput. Appl. Biosci.
, vol.8
, pp. 389-399
-
-
Schmitz, M.1
Steger, G.2
-
31
-
-
0033450944
-
A Boltzmann filter improves the prediction of RNA folding pathways in a massively parallel genetic algorithm
-
Wu,J.C. and Shapiro,B.A. (1999) A Boltzmann filter improves the prediction of RNA folding pathways in a massively parallel genetic algorithm. J. Biomol. Struct. Dyn., 17, 581-595.
-
(1999)
J. Biomol. Struct. Dyn.
, vol.17
, pp. 581-595
-
-
Wu, J.C.1
Shapiro, B.A.2
-
32
-
-
0025264854
-
The equilibrium partition function and base pair binding probabilities for RNA secondary structure
-
McCaskill,J.S. (1990) The equilibrium partition function and base pair binding probabilities for RNA secondary structure. Biopolymers, 29 ((6-7)), 1105-1119.
-
(1990)
Biopolymers
, vol.29
, Issue.6-7
, pp. 1105-1119
-
-
McCaskill, J.S.1
-
33
-
-
0037470145
-
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
-
34
-
-
0032729689
-
Predicting oligonucleotide affinity to nucleic acid targets
-
Mathews,D.H., Burkard,M.E., Freier,S.M., Wyatt,J.R. and Turner,D.H. (1999) Predicting oligonucleotide affinity to nucleic acid targets. RNA, 5, 1458-1469.
-
(1999)
RNA
, vol.5
, pp. 1458-1469
-
-
Mathews, D.H.1
Burkard, M.E.2
Freier, S.M.3
Wyatt, J.R.4
Turner, D.H.5
-
35
-
-
0026528771
-
Structural features in TAR RNA of human and simian immunodeficiency viruses: A phylogenetic analysis
-
Berkhout,B.(1992) Structural features in TAR RNA of human and simian immunodeficiency viruses: A phylogenetic analysis. Nucleic Acids Res. 20, 27-31.
-
(1992)
Nucleic Acids Res.
, vol.20
, pp. 27-31
-
-
Berkhout, B.1
-
36
-
-
0023614254
-
Regulation of mRNA accumulation by a human immunodeficiency virus trans-activator protein
-
Muesing,M.A., Smith,D.H. and Capon,D.J. (1987) Regulation of mRNA accumulation by a human immunodeficiency virus trans-activator protein. Cell, 48, 691-701.
-
(1987)
Cell
, vol.48
, pp. 691-701
-
-
Muesing, M.A.1
Smith, D.H.2
Capon, D.J.3
-
37
-
-
2942752043
-
Construction and transfection of PCR products expressing siRNAs or shRNAs in mammalian cells
-
Castanotto,D. and Rossi,J.J. (2004) Construction and transfection of PCR products expressing siRNAs or shRNAs in mammalian cells. Methods Mol. Biol., 252, 509-514.
-
(2004)
Methods Mol. Biol.
, vol.252
, pp. 509-514
-
-
Castanotto, D.1
Rossi, J.J.2
-
38
-
-
0030633027
-
Enhancement of ribozyme function by RNA binding proteins
-
Lee,N.S., Bertrand,E. and Rossi,J.J. (1997) Enhancement of ribozyme function by RNA binding proteins. Methods Mol. Biol., 74, 275-279.
-
(1997)
Methods Mol. Biol.
, vol.74
, pp. 275-279
-
-
Lee, N.S.1
Bertrand, E.2
Rossi, J.J.3
-
39
-
-
0028216716
-
An RNA chaperone activity of non-specific RNA binding proteins in hammerhead ribozyme catalysis
-
Herschlag,D., Khosla,M., Tsuchihashi,Z. and Karpel,R.L. (1994) An RNA chaperone activity of non-specific RNA binding proteins in hammerhead ribozyme catalysis. EMBO J., 13, 2913-2924.
-
(1994)
EMBO J.
, vol.13
, pp. 2913-2924
-
-
Herschlag, D.1
Khosla, M.2
Tsuchihashi, Z.3
Karpel, R.L.4
-
40
-
-
0028355964
-
Facilitation of hammerhead ribozyme catalysis by the nucleocapsid protein of HIV-1 and the heterogeneous nuclear ribonucleoprotein A1
-
Bertrand,E.L. and Rossi,J.J. (1994) Facilitation of hammerhead ribozyme catalysis by the nucleocapsid protein of HIV-1 and the heterogeneous nuclear ribonucleoprotein A1. EMBO J., 13, 2904-2912.
-
(1994)
EMBO J.
, vol.13
, pp. 2904-2912
-
-
Bertrand, E.L.1
Rossi, J.J.2
-
41
-
-
0037164732
-
RNA interference: The fragile X syndrome connection
-
Carthew,R.W. (2002) RNA interference: The fragile X syndrome connection. Curr. Biol., 12, R852-R854.
-
(2002)
Curr. Biol.
, vol.12
-
-
Carthew, R.W.1
-
42
-
-
0034672093
-
The spliceosome deposits multiple proteins 20-24 nucleotides upstream of mRNA exon-exon junctions
-
Le Hir,H., Izaurralde,E., Maquat,L.E. and Moore,M.J. (2000) The spliceosome deposits multiple proteins 20-24 nucleotides upstream of mRNA exon-exon junctions. EMBO J., 19, 6860-6869.
-
(2000)
EMBO J.
, vol.19
, pp. 6860-6869
-
-
Le Hir, H.1
Izaurralde, E.2
Maquat, L.E.3
Moore, M.J.4
-
43
-
-
17644443879
-
In vivo recruitment of exon junction complex proteins to transcription sites in mammalian cell nuclei
-
Custodio,N., Carvalho,C., Condado,I., Antoniou,M., Blencowe,B.J. and Carmo-Fonseca,M. (2004) In vivo recruitment of exon junction complex proteins to transcription sites in mammalian cell nuclei. RNA 10, 622-633.
-
(2004)
RNA
, vol.10
, pp. 622-633
-
-
Custodio, N.1
Carvalho, C.2
Condado, I.3
Antoniou, M.4
Blencowe, B.J.5
Carmo-Fonseca, M.6
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