Silencing of gene expression in cultured cells using small interfering RNAs

Current Protocols in Cell Biology

Volumn , Issue SUPPL. 47, 2010, Pages

  Sakurai, Kumi ^a   Chomchan, Pritsana ^a   Rossi, John J ^a  

^a CITY OF HOPE NATIONAL MEDICAL CENTER   (United States)

Author keywords

gene silencing; mammalian cell culture; RNAi; small silencing RNAs; transfection

Indexed keywords

COMPLEMENTARY DNA; DEOXYRIBONUCLEASE I; DOUBLE STRANDED RNA; NUCLEOTIDE; SMALL INTERFERING RNA;

ALGORITHM; ANIMAL CELL; CELL CULTURE; EUKARYOTIC CELL; GENE CONTROL; GENE EXPRESSION; GENE FUNCTION; GENE SILENCING; GENETIC TRANSFECTION; HUMAN; HUMAN CELL; IMMUNOBLOTTING; MAMMAL CELL; NONHUMAN; PRIORITY JOURNAL; REAL TIME POLYMERASE CHAIN REACTION; REVIEW; RNA INTERFERENCE;

EUKARYOTA; MAMMALIA;

EID: 77953832371     PISSN: 19342500     EISSN: 19342616     Source Type: Journal    
DOI: 10.1002/0471143030.cb2701s47     Document Type: Review

References (32)

1. 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.
2. Bernstein, E., Caudy, A.A., Hammond, S.M., and, Hannon, G.J., 2001. Role for a bidentate ribonuclease in the initiation step of RNA interference. Nature 409: 363-366.
3. Bookout, A.L., Cummins, C.L., Kramer, M.F., Pesola, J.M., and, Mangelsdorf, D.J., 2006. High-throughput real-time quantitative reverse transcription PCR. Curr. Protoc. Mol. Biol. 73: 15.8.1-15.8.28.
4. Chalk, A.M., and, Sonnhammer, E.L., 2008. siRNA specificity searching incorporating mismatch tolerance data. Bioinformatics 24: 1316-1317.
5. Chalk, A.M., Warfinge, R.E., Georgii-Hemming, P., and, Sonnhammer, E.L., 2005. siRNAdb: A database of siRNA sequences. Nucleic Acids Res. 33: D131-134.
6. 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: W135-141.
7. Elbashir, S.M., Harborth, J., Lendeckel, W., Yalcin, A., Weber, K., and, Tuschl, T., 2001a. Duplexes of 21-nucleotide RNAs mediate RNA interference in cultured mammalian cells. Nature 411: 494-498.
8. Elbashir, S.M., Lendeckel, W., and, Tuschl, T., 2001b. RNA interference is mediated by 21-and 22-nucleotide RNAs. Genes Dev. 15: 188-200. (Pubitemid 32107664)
9. Elbashir, S.M., Martinez, J., Patkaniowska, A., Lendeckel, W., and, Tuschl, T., 2001c. Functional anatomy of siRNAs for mediating efficient RNAi in Drosophila melanogaster embryo lysate. EMBO J. 20: 6877-6888.
10. Fire, A., Xu, S., Montgomery, M.K., Kostas, S.A., Driver, S.E., and, Mello, C.C., 1998. Potent and specific genetic interference by double-stranded RNA in Caenorhabditis elegans. Nature 391: 806-811. (Pubitemid 28099681)
11. Gong, W., Ren, Y., Zhou, H., Wang, Y., Kang, S., and, Li, T., 2008. siDRM: An effective and generally applicable online siRNA design tool. Bioinformatics 24: 2405-2406.
12. Gregory, R.I., Chendrimada, T.P., Cooch, N., and, Shiekhattar, R., 2005. Human RISC couples microRNA biogenesis and posttranscriptional gene silencing. Cell 123: 631-640.
13. Heale, B.S., 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.
14. Kramer, M.F., and, Coen, D.M., 2001. Enzymatic amplification of DNA by PCR: Standard procedures and optimization. Curr. Protoc. Mol. Biol. 15.1.1-15.1.14.
15. 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.
16. Liu, Q., Rand, T.A., Kalidas, S., Du, F., Kim, H.E., Smith, D.P., and, Wang, X., 2003. R2D2, a bridge between the initiation and effector steps of the Drosophila RNAi pathway. Science 301: 1921-1925.
17. Meister, G., Landthaler, M., Patkaniowska, A., Dorsett, Y., Teng, G., and, Tuschl, T., 2004. Human Argonaute2 mediates RNA cleavage targeted by miRNAs and siRNAs. Molec. Cell 15: 185-197.
18. Owczarzy, R., Tataurov, A.V., Wu, Y., Manthey, J.A., McQuisten, K.A., Almabrazi, H.G., Pedersen, K.F., Lin, Y., Garretson, J., McEntaggart, N.O., Sailor, C.A., Dawson, R.B., and, Peek, A.S., 2008. IDT SciTools: A suite for analysis and design of nucleic acid oligomers. Nucleic Acids Res. 36: W163-W169.
19. Ren, Y., Gong, W., Zhou, H., Wang, Y., Xiao, F., and, Li, T., 2009. siRecords: A database of mammalian RNAi experiments and efficacies. Nucleic Acids Res. 37: D146-D149.
20. 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.
21. Rivas, F.V., Tolia, N.H., Song, J.J., Aragon, J.P., Liu, J., Hannon, G.J., and, Joshua-Tor, L., 2005. Purified Argonaute2 and an siRNA form recombinant human RISC. Nat. Struct. Molec. Biol. 12: 340-349.
22. Rose, S.D., Kim, D.H., Amarzguioui, M., Heidel, J.D., Collingwood, M.A., Davis, M.E., Rossi, J.J., and, Behlke, M.A., 2005. Functional polarity is introduced by Dicer processing of short substrate RNAs. Nucleic Acids Res. 33: 4140-4156.
23. Shah, J.K., Garner, H.R., White, M.A., Shames, D.S., and, Minna, J.D., 2007. sIR: siRNA Information Resource, a web-based tool for siRNA sequence design and analysis and an open access siRNA database. BMC Bioinformatics 8: 178.
24. Siolas, D., Lerner, C., Burchard, J., Ge, W., Linsley, P.S., Paddison, P.J., Hannon, G.J., and, Cleary, M.A., 2005. Synthetic shRNAs as potent RNAi triggers. Nat. Biotechnol. 23: 227-231.
25. 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.
26. Yiu, S.M., Wong, P.W., Lam, T.W., Mui, Y.C., Kung, H.F., Lin, M., and, Cheung, Y.T., 2005. Filtering of ineffective siRNAs and improved siRNA design tool. Bioinformatics 21: 144-151.
27. Zamore, P.D., Tuschl, T., Sharp, P.A., and, Bartel, D.P., 2000. RNAi: Double-stranded RNA directs the ATP-dependent cleavage of mRNA at 21 to 23 nucleotide intervals. Cell 101: 25-33.
28. http://genome.ucsc.edu/cgi-bin/hgGateway Source for mRNA sequences of genes.
29. http://www.idtdna.com/Scitools/Applications/RNAi/RNAi.aspx Site for assistance with RNAi design.
30. http://www1.infosci.coh.org/hpcdispatcher/Home of RNAi Site selector which considers secondary structure of target transcripts.
31. http://www.invitrogen.com Cell-type specific transfection protocols for stealth RNAi and siRNA.
32. http://www.promega.com/paguide/chap8.htm Protocols and applications guide.