Skip to main content

Thank you for visiting nature.com. You are using a browser version with limited support for CSS. To obtain the best experience, we recommend you use a more up to date browser (or turn off compatibility mode in Internet Explorer). In the meantime, to ensure continued support, we are displaying the site without styles and JavaScript.

  • Advertising Feature: Application Note
  • Published:

siRNA design including secondary structure target site prediction

Nature Methods volume 2, page 632 (2005)Cite this article

Abstract

When performing RNA interference (RNAi) experiments, the first critical challenge is the design of efficient small interfering RNAs (siRNAs). MWG Biotech has created an online design tool allowing researchers to analyze mRNA target sites.

This is a preview of subscription content, access via your institution

Access options

Buy this article

  • Purchase on SpringerLink
  • Instant access to the full article PDF.

USD 39.95

Prices may be subject to local taxes which are calculated during checkout

Figure 1
Figure 2
Figure 3: Examples of siRNA target sites (red) on the corresponding mRNA secondary structure predicted using RNAfold.

References

  1. Elbashir, S.M. et al. Duplexes of 21-nucleotide RNAs mediate RNA interference in cultured mammalian cells. Nature 411, 494–498 (2001).

    Article  CAS  Google Scholar 

  2. Reynolds, A. et al. Rational siRNA design for RNA interference. Nat. Biotechnol. 22, 326–330 (2004).

    Article  CAS  Google Scholar 

  3. Kim, D.H. et al. Synthetic dsRNA Dicer substrates enhance RNAi potency and efficacy. Nat. Biotechnol. 23, 222–226 (2005).

    Article  CAS  Google Scholar 

  4. Schubert, S., Grunweller, A., Erdmann, V.A. & Kurreck, J. Local RNA target structure influences siRNA efficacy: systematic analysis of intentionally designed binding regions. J. Mol. Biol. 348, 883–893 (2005).

    Article  CAS  Google Scholar 

  5. Heale, B.S., Soifer, H.S., Bowers, C. & Rossi, J.J. siRNA target site secondary structure predictions using local stable substructures. Nucleic Acids Res. 33, e30 (2005).

    Article  Google Scholar 

Download references

Author information

Authors and Affiliations

  1. MWG Biotech, Anzinger Strasse 7a, Ebersberg, 85560, Germany

    Gerrit Schramm & Rebecca Ramey

Authors
  1. Gerrit Schramm
    View author publications

    Search author on:PubMed Google Scholar

  2. Rebecca Ramey
    View author publications

    Search author on:PubMed Google Scholar

Corresponding author

Correspondence to Gerrit Schramm.

Additional information

Disclaimer

This article was submitted to Nature Methods by a commercial organization and has not been peer reviewed. Nature Methods takes no responsibility for the accuracy or otherwise of the information provided.

Rights and permissions

Reprints and permissions

About this article

Cite this article

Schramm, G., Ramey, R. siRNA design including secondary structure target site prediction. Nat Methods 2, 632 (2005). https://doi.org/10.1038/nmeth780

Download citation

  • Issue date:

  • DOI: https://doi.org/10.1038/nmeth780

This article is cited by

Search

Advanced search

Quick links

Nature Briefing

Sign up for the Nature Briefing newsletter — what matters in science, free to your inbox daily.

Get the most important science stories of the day, free in your inbox. Sign up for Nature Briefing