Short Hairpin RNA (shRNA): Design, Delivery, and Assessment of Gene Knockdown

  • Debra J. Taxman
  • Chris B. Moore
  • Elizabeth H. Guthrie
  • Max Tze-Han Huang
Part of the Methods in Molecular Biology book series (MIMB, volume 629)


Shortly after the cellular mechanism of RNA interference (RNAi) was first described, scientists began using this powerful technique to study gene function. This included designing better methods for the successful delivery of small interfering RNAs (siRNAs) and short hairpin RNAs (shRNAs) into mammalian cells. While the simplest method for RNAi is the cytosolic delivery of siRNA oligonucleotides, this technique is limited to cells capable of transfection and is primarily utilized during transient in vitro studies. The introduction of shRNA into mammalian cells through infection with viral vectors allows for stable integration of shRNA and long-term knockdown of the targeted gene; however, several challenges exist with the implementation of this technology. Here we describe some well-tested protocols which should increase the chances of successful design, delivery, and assessment of gene knockdown by shRNA. We provide suggestions for designing shRNA targets and controls, a protocol for sequencing through the secondary structure of the shRNA hairpin structure, and protocols for packaging and delivery of shRNA lentiviral particles. Using real-time PCR and functional assays we demonstrate the successful knockdown of ASC, an inflammatory adaptor molecule. These studies demonstrate the practicality of including two shRNAs with different efficacies of knockdown to provide an additional level of control and to verify dose dependency of functional effects. Along with the methods described here, as new techniques and algorithms are designed in the future, shRNA is likely to include further promising application and continue to be a critical component of gene discovery.

Key words

RNA interference (RNAi) small interfering RNA (siRNA) short hairpin RNA (shRNA) lentivirus design delivery ASC Porphyromonas gingivalis IL-1β ELISA THP1 



We thank Dr. David Baltimore for supplying us with FG12. We thank Dr. Jenny Ting for her support and guidance. These studies were supported by grants 1-RO1-DE016326 and 1-U54-AI057157.


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Copyright information

© Springer Science+Business Media, LLC 2010

Authors and Affiliations

  • Debra J. Taxman
    • 1
  • Chris B. Moore
    • 2
  • Elizabeth H. Guthrie
    • 1
  • Max Tze-Han Huang
    • 1
  1. 1.Department of Microbiology and Immunology, Lineberger Comprehensive Cancer CenterUniversity of North CarolinaChapel HillUSA
  2. 2.Department of Microbiology and ImmunologyUniversity of North CarolinaChapel HillUSA

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