Contact Us
800.227.0627

Articles of special interest on siRNA related journals and scientific texts

 
Print Print
02/11/2009

Articles of special interest on siRNA related journals and scientific texts

Articles of special interest on siRNA related journals and scientific texts.

The following articles describe important insights into the history and uses of RNAi.

RNAi in review: Many excellent reviews on RNAi can be found in the literature

  • Zamore, P. D. (2001) RNA interference: listening to the sound of silence. Nat Struct Biol 8, 746–750.
  • Tuschl, T. (2001). RNA Interference and Small Interfering RNAs. Chembiochem Europ J Chem Biol 2, 239-245
  • Hannon, G. J. (2002). RNA interference. Nature 418, 244-251. A thorough review of the underlying biology and mechanics of RNA interference
  • Agrawal, N., Dasaradhi, P. V. N., Mohmmed, A., Malhotra, P., Bhatnagar, R. K., and Mukherjee, S. K. (2003). RNA Interference: Biology, Mechanism, and Applications. Microbiol Mol Biol Rev 67, 657-685. A comprehensive review of the biology and proposed mechanism of RNA interference with over 200 references.
  • Bonetta, L. (2004) RNAi: Silencing never sounded better. Nature Methods. 1:79-86.
  • Gilmore, I., S. Fox, A. Hollins, M. Sohail and S. Akhtar. (2004) The design and exogenous delivery of siRNA for post-transcriptional gene silencing. J Drug Target. 12:315-40.
  • Sandy, P. V., Andrea. Jacks, Tyler. (2005) Mammalian RNAi: a practical guide. Bio Techniques. 39:1-10.
  • Dykxhoorn, D. and J. Lieberman. (2005) The silent revolution: RNA interference as basic biology, research tool, and therapeutic. Annu Rev Med. 56:401-23.

Milestones in siRNA Research

  • Early siRNA Research across the phyla (Petunia, Neurospora, and C. elegans)
  • Napoli, C., Lemieux, C., and Jorgensen, R. (1990). Introduction of a Chimeric Chalcone Synthase Gene into Petunia Results in Reversible Co-Suppression of Homologous Genes in trans. Plant Cell 2, 279-289.
  • Romano, N., and Macino, G. (1992). Quelling: transient inactivation of gene expression in Neurosporacrassa by transformation with homologous sequences. Mol Microbiol 6, 3343-3353.
  • 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. The fi rst report showing that double-stranded RNA (dsRNA)—comprising both sense and antisense strands—is far more potent than the individual antisense or sense strands alone in silencing gene targets.

Demonstrations of siRNA knockdown in 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. In this landmark publication, these authors demonstrate the utility of chemically synthesized siRNAs for targeted gene knockdown in vertebrates, effectively bypassing the interferon response.
  • Caplen, N. J., Parrish, S., Imani, F., Fire, A., and Morgan, R. A. (2001). Specific inhibition of gene expression by small double-stranded RNAs in invertebrate and vertebrate systems. PNAS 98, 9742-9747. This work provided independent support for the ability to achieve siRNA-mediated silencing in vertebrates cell culture.
  • Bantounas, I., L. A. Phylactou and J. B. Uney. (2004) RNA interference and the use of small interfering RNA to study gene function in mammalian systems. J. Mol. Endocrinol. 33:545-557.

Demonstration of siRNA silencing in vertebrates
Proof-of-principle studies demonstrating the utility of siRNA or shRNA-mediated silencing in animal models.

  • McCaffrey, A. P., Meuse, L., Pham, T. T., Conklin, D. S., Hannon, G. J., and Kay, M. A. (2002). Gene expression: RNA interference in adult mice. Nature 418, 38-39. This report demonstrates the utility of siRNAs and shRNAs as potential therapeutic agents whether delivered as chemical entities or expressed from vectors.
  • Lewis, D. L., Hagstrom, J. E., Loomis, A. G., Wolff, J. A., and Herweijer, H. (2002). Efficient delivery of siRNA for inhibition of gene expression in postnatal mice. Nat Genet 32, 107. This paper describes effi cient delivery of siRNAs via hydrodynamic tail injections and subsequent silencing of co-injected reporter plasmids in a dose dependent manner.

Demonstration of siRNA silencing in Plants, Pathogens, and Virus

  • Susi, P., M. Hohkuri, T. Wahlroos and N. J. Kilby. (2004) Characteristics of RNA silencing in plants: similarities and differences across kingdoms. Plant Mol Biol. 54:157-74. • Cottrell, T. and T. Doering. (2003) Silence of the strands: RNA interference in eukaryotic pathogens. Trends Microbiol. 11:37-43.
  • Tan, F. and J. Yin. (2004) RNAi, a new therapeutic strategy against viral infection. Cell Res. 14:460-6.

Considerations and Elements of siRNA Design Designing your experiment:
A list of references describing key parameters of siRNA design.

  • Editorial (2003) Whither RNAi? In Nat Cell Biol, pp. 489-490. A concise editorial proposing adoption of good experimental practices for RNAi research by academia and industry. These include the use of appropriate controls, biological replicates, confirmation of knockdown with multiple, independent RNAi effectors, and confirmation via distinct detection methods (mRNA levels, protein levels, and phenotype).
  • Huppi, K., Martin, S. E., and Caplen N.J. (2004) Defining and Assaying RNAi in Mammalian Cells. Mol Cell 17, 1-10. A review that reiterates good experimental practice with emphasis on attributes associated with expressed shRNA (i.e., confirming sequence fidelity, expression levels, regulation of expression, consideration of the mRNA target and its biological context—turnover rates, redundancy and feedback regulation).

Aspects of siRNA design

  • Schwarz, D. S., Hutvagner, G., Du, T., Xu, Z., Aronin, N., and Zamore, P. D. (2003). Unexpected Asymmetry in the assembly of the RNAi Enzyme Complex. Cell 115, 199-208. Biochemical studies that identifi ed a bias or asymmetry in functional siRNAs that was not present in non-functional duplexes.
  • Khvorova, A., Reynolds, A., and Jayasena, S. (2003). Functional siRNAs and miRNAs exhibit strand bias. Cell 115, 209-216. The authors compare closely related classes of small regulatory RNAs, microRNAs, and siRNAs to identify key attributes for effi cient processing by the RISC.
  • Kim, D-H, Behlke, M. A., Rose, S.D., Chang, M-S., Choi S., and Rossi, J.J. (2004) Synthetic dsRNA Dicer substrates enhance RNAi potency and efficacy. Nature Biotechnology Advanced Online Publication January 2004.
  • Despina Siolas, D., Lerner, C., Burchard, J., Ge, W., Linsley, P. S., Paddison, P.J. Hannon, G.J. and Cleary, M.A. (2004) Synthetic shRNAs as potent RNAi triggers. Nature Biotechnology Advanced Online Publication January 2004.
  • Saetrom, P. and O. Snove. (2004) A comparison of siRNA effi cacy predictors. Biochem Biophys Res Commun. 321:247-53.
  • Amarzguioui, M. and H. Prydz. (2004) An algorithm for selection of functional siRNA sequences. Biochem Biophys Res Commun. 316:1050-8.
  • Ui-Tei, K., Y. Naito, F. Takahashi, T. Haraguchi, H. Ohki-Hamazaki, A. Juni, R. Ueda and K. Saigo. (2004) Guidelines for the selection of highly effective siRNA sequences for mammalian and chick RNA interference. Nucleic Acids Res. 32:936-948.

Selected References Documenting In Vivo Studies

  • Soutschek, J., et al. (2004) Therapeutic silencing of an endogenous gene by systemic administration of modifi ed siRNAs. Nature. 432:173-8.
  • Watanabe, H., H. Saito, P. Rychahou, T. Uchida and B. M. Evers. (2005) Aging is Associated with Decreased Pancreatic Acinar Cell Regeneration and Phosphatidylinositol 3-kinase/Akt Activation. Gastroenterology. 128:1391-404.

For technical questions regarding the use of siRNA reagents, please contact Bio-Synthesis Products Technical Support at: biosyn@biosyn.com or call toll free 800.227.0627, 972.420.8505 (international).