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Volumn 36, Issue 7, 2008, Pages 2136-2151

Functional dissection of siRNA sequence by systematic DNA substitution: Modified siRNA with a DNA seed arm is a powerful tool for mammalian gene silencing with significantly reduced off-target effect

Author keywords

[No Author keywords available]

Indexed keywords

ARGONAUTE 2 PROTEIN; DNA; GENE PRODUCT; SMALL INTERFERING RNA; TRANS ACTIVATING RESPONSE RNA BINDING PROTEIN 2; UNCLASSIFIED DRUG; DEOXYRIBONUCLEOTIDE; MESSENGER RNA; OCTAMER TRANSCRIPTION FACTOR 4; RIBONUCLEOTIDE; RNA BINDING PROTEIN;

EID: 42449091989     PISSN: 03051048     EISSN: 13624962     Source Type: Journal    
DOI: 10.1093/nar/gkn042     Document Type: Article
Times cited : (149)

References (57)
  • 1
    • 0035942736 scopus 로고    scopus 로고
    • Duplexes of 21-nucleotide RNAs mediate RNA interference in cultured mammalian cells
    • 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.
    • (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
  • 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
  • 4
    • 14644393684 scopus 로고    scopus 로고
    • Perspective: Machines for RNAi
    • Tomari,Y. and Zamore,P.D. (2006) Perspective: Machines for RNAi. Genes Dev., 19, 517-529.
    • (2006) Genes Dev , vol.19 , pp. 517-529
    • Tomari, Y.1    Zamore, P.D.2
  • 5
    • 15844402005 scopus 로고    scopus 로고
    • Structural insights into mRNA recognition from a PIWI-domain-siRNA-guide complex
    • 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.
    • (2005) Nature , vol.434 , pp. 663-666
    • Parker, J.S.1    Roe, S.M.2    Barford, D.3
  • 7
    • 23144438396 scopus 로고    scopus 로고
    • Crystal structure of A. aeolicus Argonaute, a site-specific DNA-guided endoribonuclease, provides insights into RISC-mediated mRNA cleavage
    • Yuan,Y.-R., Pei,Y., Ma,J-B., Kuryavyi,V., Zhadina,M., Meister,G., Chen,H.-Y., Dauter,Z., Tuschl,T. and Patel,D.J. (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.
    • (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    Chen, H.-Y.7    Dauter, Z.8    Tuschl, T.9    Patel, D.J.10
  • 8
    • 2442679207 scopus 로고    scopus 로고
    • Structural basis of overhang-specific small interfering RNA recognition by the PAZ domain
    • Ma,J.-B., Ye,K. and Patel,D.J. (2004) Structural basis of 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
  • 9
    • 27744569845 scopus 로고    scopus 로고
    • RNAi: RISC gets loaded
    • Preall,J.B. and Sontheimer,E.J. (2005) RNAi: RISC gets loaded. Cell 123, 543-545.
    • (2005) Cell , vol.123 , pp. 543-545
    • Preall, J.B.1    Sontheimer, E.J.2
  • 11
    • 4444302947 scopus 로고    scopus 로고
    • Crystal structure of Argonaute and its implications for RISC slicer activity
    • Song,J.J., Smith,S.K., Hannon,G.J. and Joshua-Tor,J. (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, J.4
  • 15
    • 33745612464 scopus 로고    scopus 로고
    • Widespread siRNA "off-target" transcript silencing mediated by seed region sequence complementarity
    • Jackson,A.L., Burchard,J., Schelter,J., Chau,B.M., Cleary,M., Lim,L. and Linsley,P.S. (2006) Widespread siRNA "off-target" transcript silencing mediated by seed region sequence complementarity. RNA, 12, 1179-1187.
    • (2006) RNA , vol.12 , pp. 1179-1187
    • Jackson, A.L.1    Burchard, J.2    Schelter, J.3    Chau, B.M.4    Cleary, M.5    Lim, L.6    Linsley, P.S.7
  • 16
    • 0035803583 scopus 로고    scopus 로고
    • Functional anatomy of siRNAs for mediating efficient RNAi in Drosophila melanogaster embryo lysate
    • Elbashir,S., 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.1    Martinez, J.2    Patkaniowska, A.3    Lendeckel, W.4    Tuschl, T.5
  • 17
    • 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
  • 18
    • 0037134623 scopus 로고    scopus 로고
    • RNA interference (RNA(i)) induction with various types of synthetic oligonucleotide duplexes in cultured human cells
    • Hohjoh,H. (2002) RNA interference (RNA(i)) induction with various types of synthetic oligonucleotide duplexes in cultured human cells. FEBS Lett., 19, 195-199.
    • (2002) FEBS Lett , vol.19 , pp. 195-199
    • Hohjoh, H.1
  • 19
    • 0041331496 scopus 로고    scopus 로고
    • siRNA function in RNAi: A chemical modi.cation analysis
    • Chiu,Y.-L. and Rana,T.M. (2003) siRNA function in RNAi: A chemical modi.cation analysis. RNA, 9, 1034-1048.
    • (2003) RNA , vol.9 , pp. 1034-1048
    • Chiu, Y.-L.1    Rana, T.M.2
  • 21
    • 4744373229 scopus 로고    scopus 로고
    • Noise amidst the silence: Off-target effects of siRNA?
    • Jackson,A.L. and Linsley,P.S. (2004) Noise amidst the silence: off-target effects of siRNA? Trends Genet., 20, 521-524.
    • (2004) Trends Genet , vol.20 , pp. 521-524
    • Jackson, A.L.1    Linsley, P.S.2
  • 25
    • 36549012190 scopus 로고    scopus 로고
    • Guidelines for the selection of effective short-interfering RNA sequences for functional genomics
    • Ui-Tei,K., Naito,Y. and Saigo,K. (2006) Guidelines for the selection of effective short-interfering RNA sequences for functional genomics. Methods Mol. Biol., 361, 201-216.
    • (2006) Methods Mol. Biol , vol.361 , pp. 201-216
    • Ui-Tei, K.1    Naito, Y.2    Saigo, K.3
  • 26
    • 15944415071 scopus 로고    scopus 로고
    • Comparison of different melting temperature calculation methods for short DNA sequences
    • Panjkovich,A. and Melo,F. (2005) Comparison of different melting temperature calculation methods for short DNA sequences. Bioinformatics, 21, 711-722.
    • (2005) Bioinformatics , vol.21 , pp. 711-722
    • Panjkovich, A.1    Melo, F.2
  • 29
    • 0036947892 scopus 로고    scopus 로고
    • Robust estimators for expression analysis
    • Hubbell,E., Liu,W.M. and Mei,R. (2002) Robust estimators for expression analysis. Bioinformatics, 18, 1585-1592.
    • (2002) Bioinformatics , vol.18 , pp. 1585-1592
    • Hubbell, E.1    Liu, W.M.2    Mei, R.3
  • 32
    • 35548996307 scopus 로고    scopus 로고
    • Determinants of targeting by endogenous and exogenous microRNAs and siRNA
    • Nielsen,C.B., Shomron,N., Sndberg,R., Hornstein,E., Kitzman,J. and Burge,C. (2007) Determinants of targeting by endogenous and exogenous microRNAs and siRNA. RNA, 13, 1-17.
    • (2007) RNA , vol.13 , pp. 1-17
    • Nielsen, C.B.1    Shomron, N.2    Sndberg, R.3    Hornstein, E.4    Kitzman, J.5    Burge, C.6
  • 33
    • 0035798415 scopus 로고    scopus 로고
    • ATP requirements and small interfering RNA structure in the RNA interference pathway
    • Nykänen,A., Haley,B. and Zamore,P.D. (2001) ATP requirements and small interfering RNA structure in the RNA interference pathway. Cell 107, 309-321.
    • (2001) Cell , vol.107 , pp. 309-321
    • Nykänen, A.1    Haley, B.2    Zamore, P.D.3
  • 34
    • 0034028901 scopus 로고    scopus 로고
    • Quantitative expression of Oct-3/4 defines differentiation, dedifferentiation or self-renewal of ES cells
    • Niwa,H., Miyazaki,J. and Smith,A.G. (2000) Quantitative expression of Oct-3/4 defines differentiation, dedifferentiation or self-renewal of ES cells. Nature, 24, 372-376.
    • (2000) Nature , vol.24 , pp. 372-376
    • Niwa, H.1    Miyazaki, J.2    Smith, A.G.3
  • 35
    • 0032754201 scopus 로고    scopus 로고
    • Psx homeobox gene is X-linked and specifically expressed in trophoblast cells of mouse placenta
    • Chun,J.-Y., Han,Y.-J. and Ahn,K.-Y. (1999) Psx homeobox gene is X-linked and specifically expressed in trophoblast cells of mouse placenta. Dev. Dyn., 216, 257-266.
    • (1999) Dev. Dyn , vol.216 , pp. 257-266
    • Chun, J.-Y.1    Han, Y.-J.2    Ahn, K.-Y.3
  • 36
    • 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
  • 38
    • 0141868916 scopus 로고    scopus 로고
    • R2D2, a bridge between the initiation and effector steps of the Drosophila RNAi pathway
    • Liu,Q., Rand,T.A., Kalidas,S., Du,F., Kim,H.-E., Smith,D.P. and Wang,Z. (2003) R2D2, a bridge between the initiation and effector steps of the Drosophila RNAi pathway. Science, 301, 1921-1925.
    • (2003) Science , vol.301 , pp. 1921-1925
    • Liu, Q.1    Rand, T.A.2    Kalidas, S.3    Du, F.4    Kim, H.-E.5    Smith, D.P.6    Wang, Z.7
  • 39
    • 0025876881 scopus 로고
    • Characterization of a human TAR RNA-binding protein that activates the HIV-1 LTR
    • Gatignol,A., Buckler-White,A., Berkhout,B. and Jeang,K.T. (1991) Characterization of a human TAR RNA-binding protein that activates the HIV-1 LTR. Science, 251, 1597-1600.
    • (1991) Science , vol.251 , pp. 1597-1600
    • Gatignol, A.1    Buckler-White, A.2    Berkhout, B.3    Jeang, K.T.4
  • 40
    • 0032480017 scopus 로고    scopus 로고
    • PACT, a protein activator of the interferon- induced protein kinase, PKR
    • Patel,R.C. and Sen,G.C. (1998) PACT, a protein activator of the interferon- induced protein kinase, PKR. EMBO J., 17, 4379-4390.
    • (1998) EMBO J , vol.17 , pp. 4379-4390
    • Patel, R.C.1    Sen, G.C.2
  • 41
    • 0037425583 scopus 로고    scopus 로고
    • Short-interfering-RNA-mediated gene silencing in mammalian cells requires Dicer and eIF2C translation initiation factors
    • Doi,N., Zenno,S., Ueda,R., Ohki-Hamazaki,H., Ui-Tei,K. and Saigo,K. (2003) Short-interfering-RNA-mediated gene silencing in mammalian cells requires Dicer and eIF2C translation initiation factors. Curr. Biol. 13, 41-46.
    • (2003) Curr. Biol , vol.13 , pp. 41-46
    • Doi, N.1    Zenno, S.2    Ueda, R.3    Ohki-Hamazaki, H.4    Ui-Tei, K.5    Saigo, K.6
  • 43
    • 0035863097 scopus 로고    scopus 로고
    • RNA interference is mediated by 21 and 22 nt RNAs
    • Elbashir,S.M., Lendeckel,W. and Tuschl,T. (2001) RNA interference is mediated by 21 and 22 nt RNAs. Genes Dev., 15, 188-200.
    • (2001) Genes Dev , vol.15 , pp. 188-200
    • Elbashir, S.M.1    Lendeckel, W.2    Tuschl, T.3
  • 45
    • 0036544755 scopus 로고    scopus 로고
    • Micro RNAs are complementary to 3′ UTR sequence motifs that mediate negative post-transcriptional regulation
    • Lai,E.C. (2002) Micro RNAs are complementary to 3′ UTR sequence motifs that mediate negative post-transcriptional regulation. Nat. Genet. 30, 363-364.
    • (2002) Nat. Genet , vol.30 , pp. 363-364
    • Lai, E.C.1
  • 48
    • 2142654329 scopus 로고    scopus 로고
    • MicroRNA-directed cleavage of HOXB8 mRNA
    • Yekta,S., Shih,I. and Bartel,D.P. (2004) MicroRNA-directed cleavage of HOXB8 mRNA. Science, 304, 594-596.
    • (2004) Science , vol.304 , pp. 594-596
    • Yekta, S.1    Shih, I.2    Bartel, D.P.3
  • 52
    • 22144489833 scopus 로고    scopus 로고
    • RNAi: The nuts and bolts of the RISC machine
    • Filipowicz,W. (2005) RNAi: The nuts and bolts of the RISC machine. Cell, 122, 17-20.
    • (2005) Cell , vol.122 , pp. 17-20
    • Filipowicz, W.1
  • 54
    • 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
  • 56
    • 33845755467 scopus 로고    scopus 로고
    • Illuminating the silence: Understanding the structure and function of small RNAs
    • Rana,T.M. (2007) Illuminating the silence: Understanding the structure and function of small RNAs. Nat. Rev. Mol. Cell. Biol., 8, 23-36.
    • (2007) Nat. Rev. Mol. Cell. Biol , vol.8 , pp. 23-36
    • Rana, T.M.1


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.