Guidelines for the selection of effective short-interfering RNA sequences for functional genomics

Methods Mol Biol. 2007;361:201-16. doi: 10.1385/1-59745-208-4:201.


To avoid long-double-stranded-RNA-dependent interferon response, short-interfering RNAs (siRNAs) are widely used for RNA interference (RNAi) in mammalian cells. siRNA-based RNAi, however, may not be readily available for the large-scale gene silencing essential for systematic functional genomics, because only a limited fraction of siRNAs is capable of inducing effective mammalian RNAi. siRNAs correctly designed for the knockdown of a particular gene may also destroy the functions of unrelated genes. Here, we describe algorithms by which these serious setbacks can be eliminated in mammalian functional genomics using RNAi and a Web-based online software system for computing highly functional siRNA sequences with maximal target-specificity in mammalian RNAi.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Algorithms*
  • Animals
  • Cell Line
  • Genomics* / methods
  • Guidelines as Topic
  • Humans
  • RNA Interference*
  • RNA, Double-Stranded / genetics*
  • RNA, Small Interfering / genetics*
  • Software*


  • RNA, Double-Stranded
  • RNA, Small Interfering