DSIR: assessing the design of highly potent siRNA by testing a set of cancer-relevant target genes

PLoS One. 2012;7(10):e48057. doi: 10.1371/journal.pone.0048057. Epub 2012 Oct 30.


Chemically synthesized small interfering RNA (siRNA) is a widespread molecular tool used to knock down genes in mammalian cells. However, designing potent siRNA remains challenging. Among tools predicting siRNA efficacy, very few have been validated on endogenous targets in realistic experimental conditions. We previously described a tool to assist efficient siRNA design (DSIR, Designer of siRNA), which focuses on intrinsic features of the siRNA sequence. Here, we evaluated DSIR's performance by systematically investigating the potency of the siRNA it designs to target ten cancer-related genes. mRNA knockdown was measured by quantitative RT-PCR in cell-based assays, revealing that over 60% of siRNA sequences designed by DSIR silenced their target genes by at least 70%. Silencing efficacy was sustained even when low siRNA concentrations were used. This systematic analysis revealed in particular that, for a subset of genes, the efficiency of siRNA constructs significantly increases when the sequence is located closer to the 5'-end of the target gene coding sequence, suggesting the distance to the 5'-end as a new feature for siRNA potency prediction. A new version of DSIR incorporating these new findings, as well as the list of validated siRNA against the tested cancer genes, has been made available on the web (http://biodev.extra.cea.fr/DSIR).

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Algorithms
  • Base Pair Mismatch
  • Base Sequence
  • Gene Expression
  • Gene Knockdown Techniques
  • Genes, Neoplasm
  • HeLa Cells
  • Humans
  • RNA Interference*
  • RNA, Small Interfering / genetics
  • Software*
  • Transfection


  • RNA, Small Interfering

Grant support

This work is part of the national program called “Cartes d’Identité des Tumeurs” program (CIT) funded and developed by the Ligue Nationale Contre le Cancer. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.