Precise and efficient siRNA design: a key point in competent gene silencing

Cancer Gene Ther. 2016 Apr;23(4):73-82. doi: 10.1038/cgt.2016.4. Epub 2016 Mar 18.


RNA interference-related strategies have become appealing methods in various fields of research. Exact sequence design of these small molecules is an essential step in the silencing procedure. Numerous researchers have tried to define some algorithms in order to increase the chance of short interfering RNA's (siRNA's) success. In recent decades, online designing software has aimed at promoting the quality of siRNA designing based on the most cited algorithms. According to our previous experiments, a combination of different criteria would be helpful. That is, siRNAs suggested by a combination of tools seem to be more efficient. Furthermore, different factors such as distance of target region to transcription start site, nucleotide composition, absence of off-target effects and secondary structures in the target site and siRNA and the presence of asymmetry and energy valley within the siRNA will increase the efficiency of siRNAs. Despite application of different online tools and fulfilling the criteria, there is no guarantee for designing an effective siRNA. However, meticulous designing of siRNAs according to the suggested algorithms and scoring systems and using different siRNAs for targeting the same gene would lead to improved silencing outcome. In this review, we focus on common algorithms and online software, and introduce a new scoring system used in our experiments.

Publication types

  • Review

MeSH terms

  • Animals
  • Base Composition
  • Binding Sites
  • Computational Biology / methods
  • Gene Silencing*
  • Humans
  • RNA Interference*
  • RNA, Messenger / chemistry
  • RNA, Messenger / genetics
  • RNA, Small Interfering / chemistry
  • RNA, Small Interfering / genetics*
  • Software
  • Web Browser


  • RNA, Messenger
  • RNA, Small Interfering