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Designing Dual-Targeting siRNA Duplexes Having Two Active Strands that Combine siRNA and MicroRNA-Like Targeting

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siRNA Design

Part of the book series: Methods in Molecular Biology ((MIMB,volume 942))

Abstract

Short interfering RNAs (siRNAs) have become valued tools for knocking down specific genes. As such, siRNAs are routinely used to study gene function and are also being explored as therapeutic agents. Traditionally, siRNAs are designed to target one specific gene, but this chapter describes a procedure for designing dual-targeting siRNAs where the two strands in the siRNA duplex are both active and down-regulate different target genes through both siRNA and miRNA-like effects. The procedure can be used to create siRNAs that robustly target pairs of genes.

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References

  1. Birmingham A, Anderson EM, Reynolds A, Ilsley-Tyree D, Leake D, Fedorov Y, Baskerville S, Maksimova E, Robinson K, Karpilow J, Marshall WS, Khvorova A (2006) 3’ UTR seed matches, but not overall identity, are associated with RNAi off-targets. Nat Methods 3:199–204

    Article  CAS  Google Scholar 

  2. Jackson AL, Burchard J, Schelter J, Chau BN, Cleary M, Lim L, Linsley PS (2006) Widespread siRNA “off-target” transcript silencing mediated by seed region sequence complementarity. RNA 12:1179–1187

    Article  CAS  Google Scholar 

  3. Lin X, Ruan X, Anderson MG, McDowell JA, Kroeger PE, Fesik SW, Shen Y (2005) siRNA-mediated off-target gene silencing triggered by a 7 nt complementation. Nucleic Acids Res 33:4527–4535

    Article  CAS  Google Scholar 

  4. Tiemann K, Hohn B, Ehsani A, Forman SJ, Rossi JJ, Saetrom P (2010) Dual-targeting siRNAs. RNA 16:1275–1284

    Article  CAS  Google Scholar 

  5. Khvorova A, Reynolds A, Jayasena SD (2003) Functional siRNAs and miRNAs exhibit strand bias. Cell 115:209–216

    Article  CAS  Google Scholar 

  6. Schwarz DS, Hutvagner G, Du T, Xu Z, Aronin N, Zamore PD (2003) Asymmetry in the assembly of the RNAi enzyme complex. Cell 115:199–208

    Article  CAS  Google Scholar 

  7. Reynolds A, Leake D, Boese Q, Scaringe S, Marshall WS, Khvorova A (2004) Rational siRNA design for RNA interference. Nat Biotechnol 22:326–330

    Article  CAS  Google Scholar 

  8. Saetrom P (2004) Predicting the efficacy of short oligonucleotides in antisense and RNAi experiments with boosted genetic programming. Bioinformatics 20:3055–3063

    Article  CAS  Google Scholar 

  9. Saetrom P, Snove O Jr (2004) A comparison of siRNA efficacy predictors. Biochem Biophys Res Commun 321:247–253

    Article  CAS  Google Scholar 

  10. Hossbach M, Gruber J, Osborn M, Weber K, Tuschl T (2006) Gene silencing with siRNA duplexes composed of target-mRNA-complementary and partially palindromic or partially complementary single-stranded siRNAs. RNA Biol 3:82–89

    Article  CAS  Google Scholar 

  11. Karolchik D, Hinrichs AS, Furey TS, Roskin KM, Sugnet CW, Haussler D, Kent WJ (2004) The UCSC table browser data retrieval tool. Nucleic Acids Res 32:D493–496

    Article  CAS  Google Scholar 

  12. Hofacker IL (2003) Vienna RNA secondary structure server. Nucleic Acids Res 31:3429–3431

    Article  CAS  Google Scholar 

  13. Kim DH, Behlke MA, Rose SD, Chang MS, Choi S, Rossi JJ (2005) Synthetic dsRNA Dicer substrates enhance RNAi potency and efficacy. Nat Biotechnol 23:222–226

    Article  CAS  Google Scholar 

  14. Rose SD, Kim DH, Amarzguioui M, Heidel JD, Collingwood MA, Davis ME, Rossi JJ, Behlke MA (2005) Functional polarity is introduced by Dicer processing of short substrate RNAs. Nucleic Acids Res 33:4140–4156

    Article  CAS  Google Scholar 

  15. Halaas A, Svingen B, Nedland M, Saetrom P, Snove O, Birkeland OR (2004) A recursive MISD architecture for pattern matching. Ieee T Vlsi Syst 12:727–734

    Article  Google Scholar 

  16. Navarro G (2001) NR-grep: a fast and flexible pattern-matching tool. Software Pract Exper 31:1265–1312

    Article  Google Scholar 

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Acknowledgement

This work was supported by the Norwegian Functional Genomics Program of the Norwegian Research Council.

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Authors and Affiliations

  1. Departments of Computer and Information Science and Cancer Research & Molecular Medicine, Norwegian University of Science and Technology, Trondheim, Norway

    Pål Sætrom

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  1. Pål Sætrom
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Correspondence to Pål Sætrom .

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Editors and Affiliations

  1. , Lineberger Comprehensive Cancer Center, University of North Carolina, West Drive 450, Chapel Hill, 27599, North Carolina, USA

    Debra J. Taxman

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Sætrom, P. (2013). Designing Dual-Targeting siRNA Duplexes Having Two Active Strands that Combine siRNA and MicroRNA-Like Targeting. In: Taxman, D. (eds) siRNA Design. Methods in Molecular Biology, vol 942. Humana Press, Totowa, NJ. https://doi.org/10.1007/978-1-62703-119-6_9

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  • DOI: https://doi.org/10.1007/978-1-62703-119-6_9

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  • Publisher Name: Humana Press, Totowa, NJ

  • Print ISBN: 978-1-62703-118-9

  • Online ISBN: 978-1-62703-119-6

  • eBook Packages: Springer Protocols

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