-
1
-
-
1642273831
-
An algorithm for selection of functional siRNA sequences
-
doi: 10.1016/j.bbrc.2004.02.157
-
Amarzguioui, M., and Prydz, H. (2004). An algorithm for selection of functional siRNA sequences. Biochem. Biophys. Res. Commun. 316, 1050-1058. doi: 10.1016/j.bbrc.2004.02.157
-
(2004)
Biochem. Biophys. Res. Commun.
, vol.316
, pp. 1050-1058
-
-
Amarzguioui, M.1
Prydz, H.2
-
2
-
-
33646188259
-
3' UTR seed matches, but not overall identity, are associated with RNAi off-targets
-
doi: 10.1038/nmeth854
-
Birmingham, A., Anderson, E. M., Reynolds, A., Ilsley-Tyree, D., Leake, D., Fedorov, Y., et al. (2006). 3' UTR seed matches, but not overall identity, are associated with RNAi off-targets. Nat. Methods 3, 199-204. doi: 10.1038/nmeth854
-
(2006)
Nat. Methods
, vol.3
, pp. 199-204
-
-
Birmingham, A.1
Anderson, E.M.2
Reynolds, A.3
Ilsley-Tyree, D.4
Leake, D.5
Fedorov, Y.6
-
3
-
-
58749104364
-
The promises and pitfalls of RNA-interference-based therapeutics
-
doi: 10.1038/nature07758
-
Castanotto, D., and Rossi, J. J. (2009). The promises and pitfalls of RNA-interference-based therapeutics. Nature 457, 426-433. doi: 10.1038/nature07758
-
(2009)
Nature
, vol.457
, pp. 426-433
-
-
Castanotto, D.1
Rossi, J.J.2
-
4
-
-
79954580272
-
Current prospects for RNA interference-based therapies
-
doi: 10.1038/nrg2968
-
Davidson, B. L., and McCray, P. B. Jr. (2011). Current prospects for RNA interference-based therapies. Nat. Rev. Genetics 12, 329-340. doi: 10.1038/nrg2968
-
(2011)
Nat. Rev. Genetics
, vol.12
, pp. 329-340
-
-
Davidson, B.L.1
McCray, P.B.Jr.2
-
5
-
-
0035942736
-
Duplexes of 21-nucleotide RNAs mediate RNA interference in cultured mammalian cells
-
doi: 10.1038/35078107
-
Elbashir, S. M., Harborth, J., Lendeckel, W., Yalcin, A., Weber, K., and Tuschl, T. (2001). Duplexes of 21-nucleotide RNAs mediate RNA interference in cultured mammalian cells. Nature 411, 494-498. doi: 10.1038/35078107
-
(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
-
6
-
-
77953479619
-
Structural basis for 5'-nucleotide base-specific recognition of guide RNA by human AGO2
-
doi: 10.1038/nature09039
-
Frank, F., Sonenberg, N., and Nagar, B. (2010). Structural basis for 5'-nucleotide base-specific recognition of guide RNA by human AGO2. Nature 465, 818-822. doi: 10.1038/nature09039
-
(2010)
Nature
, vol.465
, pp. 818-822
-
-
Frank, F.1
Sonenberg, N.2
Nagar, B.3
-
7
-
-
34250805982
-
MicroRNA targeting specificity in mammals: determinants beyond seed pairing
-
doi: 10.1016/j.molcel.2007.06.017
-
Grimson, A., Farh, K. K., Johnston, W. K., Garrett-Engele, P., Lim, L. P., and Bartel, D. P. (2007). MicroRNA targeting specificity in mammals: determinants beyond seed pairing. Mol. Cell 27, 91-105. doi: 10.1016/j.molcel.2007.06.017
-
(2007)
Mol. Cell
, vol.27
, pp. 91-105
-
-
Grimson, A.1
Farh, K.K.2
Johnston, W.K.3
Garrett-Engele, P.4
Lim, L.P.5
Bartel, D.P.6
-
8
-
-
0035839109
-
Argonaute 2 link between genetic and biochemical analyses of RNAi
-
doi: 10.1126/science.1064023
-
Hammond, S. M., Boettcher, S., Caudy, A. A., Kobayashi, R., and Hannon, G. J. (2001). Argonaute 2 link between genetic and biochemical analyses of RNAi. Science 293, 1146-1150. doi: 10.1126/science.1064023
-
(2001)
Science
, vol.293
, pp. 1146-1150
-
-
Hammond, S.M.1
Boettcher, S.2
Caudy, A.A.3
Kobayashi, R.4
Hannon, G.J.5
-
9
-
-
24344500241
-
Sequence, chemical and structural variation of small interfering RNAs and short hairpin RNAs and the effect on mammalian gene silencing
-
doi: 10.1089/108729003321629638
-
Harborth, J., Elbashir, S. M., Vandenburgh, K., Manninga, H., Scaringe, S. A., Weber, K., et al. (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. doi: 10.1089/108729003321629638
-
(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
-
10
-
-
84871913482
-
Stability of miRNA 5' terminal and seed regions is correlated with experimentally observed miRNA-mediated silencing efficacy
-
doi: 10.1038/srep00996
-
Hibio, N., Hino, K., Shimizu, E., Nagata, Y., and Ui-Tei, K. (2012). Stability of miRNA 5' terminal and seed regions is correlated with experimentally observed miRNA-mediated silencing efficacy. Sci. Rep. 2, 996. doi: 10.1038/srep00996
-
(2012)
Sci. Rep.
, vol.2
, pp. 996
-
-
Hibio, N.1
Hino, K.2
Shimizu, E.3
Nagata, Y.4
Ui-Tei, K.5
-
11
-
-
0037089135
-
Positional effects of short interfering RNAs targeting the human coagulation trigger tissue factor
-
doi: 10.1093/nar/30.8.1757
-
Holen, T., Amrzguioui, 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. doi: 10.1093/nar/30.8.1757
-
(2002)
Nucleic Acids Res.
, vol.30
, pp. 1757-1766
-
-
Holen, T.1
Amrzguioui, M.2
Wiiger, M.T.3
Babaie, E.4
Prydz, H.5
-
12
-
-
37549014207
-
Argonaute proteins: key players in RNA silencing
-
doi: 10.1038/nrm2321
-
Hutvagner, G., and Simard, M. J. (2008). Argonaute proteins: key players in RNA silencing. Nat. Rev. Mol. Cell Biol. 9, 22-32. doi: 10.1038/nrm2321
-
(2008)
Nat. Rev. Mol. Cell Biol.
, vol.9
, pp. 22-32
-
-
Hutvagner, G.1
Simard, M.J.2
-
13
-
-
0037685280
-
Expression profiling reveals off-target gene regulation by RNAi
-
doi: 10.1038/nbt831
-
Jackson, A. L., Bartz, S. R., Schelter, J., Kobayashi, S. V., Burchard, J., Mao, M., et al. (2003). Expression profiling reveals off-target gene regulation by RNAi. Nat. Biotech. 21, 635-637. doi: 10.1038/nbt831
-
(2003)
Nat. Biotech.
, vol.21
, pp. 635-637
-
-
Jackson, A.L.1
Bartz, S.R.2
Schelter, J.3
Kobayashi, S.V.4
Burchard, J.5
Mao, M.6
-
14
-
-
33745612464
-
Widespread siRNA "off-target" transcript silencing mediated by seed region sequence complementarity
-
doi: 10.1261/rna.25706
-
Jackson, A. L., Burchard, J., Schelter, J., Chau, B. N., Cleary, M., Lim, L., et al. (2006). Widespread siRNA "off-target" transcript silencing mediated by seed region sequence complementarity. RNA 12, 1179-1187. doi: 10.1261/rna.25706
-
(2006)
RNA
, vol.12
, pp. 1179-1187
-
-
Jackson, A.L.1
Burchard, J.2
Schelter, J.3
Chau, B.N.4
Cleary, M.5
Lim, L.6
-
15
-
-
58749113430
-
A three-dimensional view of the molecular machinery of RNA interference
-
doi: 10.1038/nature07755
-
Jinek, M., and Doudna, J. A. (2009). A three-dimensional view of the molecular machinery of RNA interference. Nature 457, 405-412. doi: 10.1038/nature07755
-
(2009)
Nature
, vol.457
, pp. 405-412
-
-
Jinek, M.1
Doudna, J.A.2
-
16
-
-
69949127421
-
Structural determinants of miRNAs for RISC loading and slicer-independent unwinding
-
doi: 10.1038/nsmb.1630
-
Kawamata, T., Seitz, H., and Tomari, Y. (2009). Structural determinants of miRNAs for RISC loading and slicer-independent unwinding. Nature Struct. Mol. Biol. 16, 953-960. doi: 10.1038/nsmb.1630
-
(2009)
Nature Struct. Mol. Biol.
, vol.16
, pp. 953-960
-
-
Kawamata, T.1
Seitz, H.2
Tomari, Y.3
-
17
-
-
79751485564
-
The many faces of RNAi
-
doi: 10.1016/j.devcel.2011.01.012
-
Ketting, R. F. (2011). The many faces of RNAi. Dev. Cell 15, 148-161. doi: 10.1016/j.devcel.2011.01.012
-
(2011)
Dev. Cell
, vol.15
, pp. 148-161
-
-
Ketting, R.F.1
-
18
-
-
0142165224
-
Functional siRNAs and miRNAs exhibit strand bias
-
doi: 10.1016/S0092-8674(03)00801-8
-
Khvorova, A., Reynolds, A., and Jayasena, S. D. (2003). Functional siRNAs and miRNAs exhibit strand bias. Cell 115, 209-216. doi: 10.1016/S0092-8674(03)00801-8
-
(2003)
Cell
, vol.115
, pp. 209-216
-
-
Khvorova, A.1
Reynolds, A.2
Jayasena, S.D.3
-
19
-
-
33645763485
-
Cleavage of the siRNA passenger strand during RISC assembly in human cells
-
doi: 10.1038/sj.embor.7400637
-
Leuschner, P. J., Ameres, S. L., Kueng, S., and Martinez, J. (2006). Cleavage of the siRNA passenger strand during RISC assembly in human cells. EMBO Rep. 7, 314-320. doi: 10.1038/sj.embor.7400637
-
(2006)
EMBO Rep.
, vol.7
, pp. 314-320
-
-
Leuschner, P.J.1
Ameres, S.L.2
Kueng, S.3
Martinez, J.4
-
20
-
-
11844278458
-
Conserved seed pairing, often flanked by adenosines, indicates that thousands of human genes are microRNA targets
-
doi: 10.1016/j.cell.2004.12.035
-
Lewis, B. P., Burge, C. B., and Bartel, D. P. (2005). Conserved seed pairing, often flanked by adenosines, indicates that thousands of human genes are microRNA targets. Cell 120, 15-20. doi: 10.1016/j.cell.2004.12.035
-
(2005)
Cell
, vol.120
, pp. 15-20
-
-
Lewis, B.P.1
Burge, C.B.2
Bartel, D.P.3
-
21
-
-
13944282215
-
Microarray analysis shows that some microRNAs downregulate large numbers of target mRNAs
-
doi: 10.1038/nature03315
-
Lim, L. P., Lau, N. C., Garrett-Engele, P., Grimson, A., Schelter, J. M., Castle, J., et al. (2005). Microarray analysis shows that some microRNAs downregulate large numbers of target mRNAs. Nature 433, 769-773. doi: 10.1038/nature03315
-
(2005)
Nature
, vol.433
, pp. 769-773
-
-
Lim, L.P.1
Lau, N.C.2
Garrett-Engele, P.3
Grimson, A.4
Schelter, J.M.5
Castle, J.6
-
22
-
-
23344438420
-
siRNA-mediated off-target gene silencing triggered by a 7-nt complementation
-
doi: 10.1093/nar/gki762
-
Lin, X., Ruan, X., Anderson, M. G., McDowell, J. A., Kroeger, P. E., Resik, S. W., et al. (2005). siRNA-mediated off-target gene silencing triggered by a 7-nt complementation. Nucleic Acids Res. 33, 4527-4535. doi: 10.1093/nar/gki762
-
(2005)
Nucleic Acids Res.
, vol.33
, pp. 4527-4535
-
-
Lin, X.1
Ruan, X.2
Anderson, M.G.3
McDowell, J.A.4
Kroeger, P.E.5
Resik, S.W.6
-
23
-
-
15844371219
-
Structural basis for 5'-end-specific recognition of guide RNA by the A
-
doi: 10.1038/nature03514
-
Ma, J.-B., Yuan, Y. R., Meister, G., Pei, Y., Tuschl, T., and Patel, D. J. (2005). Structural basis for 5'-end-specific recognition of guide RNA by the A. fulgidus piwi protein. Nature 434, 666-670. doi: 10.1038/nature03514
-
(2005)
fulgidus piwi protein. Nature
, vol.434
, pp. 666-670
-
-
Ma, J.-B.1
Yuan, Y.R.2
Meister, G.3
Pei, Y.4
Tuschl, T.5
Patel, D.J.6
-
24
-
-
0037031576
-
Single-stranded antisense siRNAs guide target RNA cleavage in RNAi
-
doi: 10.1016/S0092-8674(02)00908-X
-
Martinez, J., Patkaniowska, A., Urlaub, H., Lührmann, R., and Tuschl, T. (2002). Single-stranded antisense siRNAs guide target RNA cleavage in RNAi. Cell 110, 563-574. doi: 10.1016/S0092-8674(02)00908-X
-
(2002)
Cell
, vol.110
, pp. 563-574
-
-
Martinez, J.1
Patkaniowska, A.2
Urlaub, H.3
Lührmann, R.4
Tuschl, T.5
-
25
-
-
27744590896
-
Passenger-strand cleavage facilitates assembly of siRNA into Ago2-containing RNAi enzyme complexes
-
doi: 10.1016/j.cell.2005.08.044
-
Matranga, C., Tomoari, Y., Shin, C., Bartel, D. P., and Zamore, P. S. (2005). Passenger-strand cleavage facilitates assembly of siRNA into Ago2-containing RNAi enzyme complexes. Cell 123, 607-620. doi: 10.1016/j.cell.2005.08.044
-
(2005)
Cell
, vol.123
, pp. 607-620
-
-
Matranga, C.1
Tomoari, Y.2
Shin, C.3
Bartel, D.P.4
Zamore, P.S.5
-
26
-
-
28444437427
-
Slicer function of Drosophila Argonautes and its involvement in RISC formation
-
doi: 10.1101/gad.1370605
-
Miyoshi, K., Tsukumo, H., Nagami, T., Siomi, H., and Siomi, M. C. (2005). Slicer function of Drosophila Argonautes and its involvement in RISC formation. Genes Dev. 19, 2837-2848. doi: 10.1101/gad.1370605
-
(2005)
Genes Dev.
, vol.19
, pp. 2837-2848
-
-
Miyoshi, K.1
Tsukumo, H.2
Nagami, T.3
Siomi, H.4
Siomi, M.C.5
-
27
-
-
84875890034
-
siRNA design software for a target gene-specific RNA interference
-
doi: 10.3389/fgene.2012.00102
-
Naito, Y., and Ui-Tei, K. (2012). siRNA design software for a target gene-specific RNA interference. Front. Genet. 3, 102. doi: 10.3389/fgene.2012.00102
-
(2012)
Front. Genet.
, vol.3
, pp. 102
-
-
Naito, Y.1
Ui-Tei, K.2
-
28
-
-
72549097028
-
siDirect 2.0: updated software for designing functional siRNA with reduced seed-dependent off-target effect.
-
doi: 10.1186/1471-2105-10-392
-
Naito, Y., Yoshimura, J., Morishita, S., and Ui-Tei, K. (2009). siDirect 2.0: updated software for designing functional siRNA with reduced seed-dependent off-target effect. BMC Bioinformatics 10, 392. doi: 10.1186/1471-2105-10-392
-
(2009)
BMC Bioinformatics
, vol.10
, pp. 392
-
-
Naito, Y.1
Yoshimura, J.2
Morishita, S.3
Ui-Tei, K.4
-
29
-
-
15844402005
-
Structural insights into mRNA recognition from a PIWI domain-siRNA guide complex
-
doi: 10.1038/nature03462
-
Parker, J. S., Roe, S. M., and Barford, D. (2005). Structural insights into mRNA recognition from a PIWI domain-siRNA guide complex. Nature 434, 663-666. doi: 10.1038/nature03462
-
(2005)
Nature
, vol.434
, pp. 663-666
-
-
Parker, J.S.1
Roe, S.M.2
Barford, D.3
-
30
-
-
27744506761
-
Argonaute2 cleaves the anti-guide strand of siRNA during RISC activation
-
doi: 10.1016/j.cell.2005.10.020
-
Rand, T. A., Petersen, S., Du, F., and Wang, X. (2005). Argonaute2 cleaves the anti-guide strand of siRNA during RISC activation. Cell 123, 621-629. doi: 10.1016/j.cell.2005.10.020
-
(2005)
Cell
, vol.123
, pp. 621-629
-
-
Rand, T.A.1
Petersen, S.2
Du, F.3
Wang, X.4
-
31
-
-
1542336952
-
Rational siRNA design for RNA interference
-
doi: 10.1038/nbt936
-
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. doi: 10.1038/nbt936
-
(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
-
32
-
-
10744225153
-
Asymmetry in the assembly of the RNAi enzyme complex
-
doi: 10.1016/S0092-8674(03)00759-1
-
Schwarz, D. S., Hutvágner, 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. 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
Zamore, P.D.6
-
33
-
-
84862317270
-
RNA interference trigger variants: getting the most out of RNA interference-based therapeutics
-
doi: 10.1089/nat.2012.0361
-
Snead, N. M., and Rossi, J. J. (2012). RNA interference trigger variants: getting the most out of RNA interference-based therapeutics. Nucleic Acid Ther. 22, 139-146. doi: 10.1089/nat.2012.0361
-
(2012)
Nucleic Acid Ther.
, vol.22
, pp. 139-146
-
-
Snead, N.M.1
Rossi, J.J.2
-
34
-
-
58749086586
-
Thermodynamic stability and Watson-Crick base pairing in the seed duplex are major determinants of the efficiency of the siRNA-based off-target effect
-
doi: 10.1093/nar/gkn902
-
Ui-Tei, K., Naito, Y., Nishi, K., Juni, A., and Saigo, K. (2008). Thermodynamic stability and Watson-Crick base pairing in the seed duplex are major determinants of the efficiency of the siRNA-based off-target effect. Nucleic Acids Res. 36, 7100-7109. doi: 10.1093/nar/gkn902
-
(2008)
Nucleic Acids Res.
, vol.36
, pp. 7100-7109
-
-
Ui-Tei, K.1
Naito, Y.2
Nishi, K.3
Juni, A.4
Saigo, K.5
-
35
-
-
1642346273
-
Guidelines for the selection of highly effective siRNA sequences for mammalian and chick RNA interference
-
doi: 10.1093/nar/gkh247
-
Ui-Tei, K., Naito, Y., Takahashi, F., Haraguchi, T., Ohki-Hamazaki, H., Juni, A., et al. (2004). Guidelines for the selection of highly effective siRNA sequences for mammalian and chick RNA interference. Nucleic Acids Res. 32, 936-948. doi: 10.1093/nar/gkh247
-
(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
-
36
-
-
84871419294
-
Thermodynamic control of small RNA-mediated gene silencing
-
doi: 10.3389/fgene.2012.00101
-
Ui-Tei, K., Nishi, K., Takahashi, T., and Nagasawa, T. (2012). Thermodynamic control of small RNA-mediated gene silencing. Front. Genet. 3, 101. doi: 10.3389/fgene.2012.00101
-
(2012)
Front. Genet.
, vol.3
, pp. 101
-
-
Ui-Tei, K.1
Nishi, K.2
Takahashi, T.3
Nagasawa, T.4
-
37
-
-
77449128456
-
ATP-dependent human RISC assembly pathways
-
doi: 10.1038/nsmb.1733
-
Yoda, M., Kawamata, T., Paroo, Z., Ye, X., Iwasaki, S., Liu, Q., et al. (2010). ATP-dependent human RISC assembly pathways. Nature Struct. Mol. Biol. 17, 117-123. doi: 10.1038/nsmb.1733
-
(2010)
Nature Struct. Mol. Biol.
, vol.17
, pp. 117-123
-
-
Yoda, M.1
Kawamata, T.2
Paroo, Z.3
Ye, X.4
Iwasaki, S.5
Liu, Q.6
-
38
-
-
23144438396
-
Crystal structure of A. aeolicus argonaute, a site-specific DNA-guided endoribonuclease, provides insights into RISC-mediated mRNA cleavage
-
doi: 10.1016/j.molcel.2005.07.011
-
Yuan, Y.-R., Pei, Y., Ma, J. B., Kuryavyi, V., Zhadina, M., Meister, G., et al. (2005). Crystal structure of A. aeolicus argonaute, a site-specific DNA-guided endoribonuclease, provides insights into RISC-mediated mRNA cleavage. Mol. Cell 19, 405-419. doi: 10.1016/j.molcel.2005.07.011
-
(2005)
Mol. Cell
, vol.19
, pp. 405-419
-
-
Yuan, Y.-R.1
Pei, Y.2
Ma, J.B.3
Kuryavyi, V.4
Zhadina, M.5
Meister, G.6
|