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RNA interference

Eight steps to silence

Nature Reviews Drug Discovery volume 3, page 204 (2004)Cite this article

The criteria have been developed from a systematic analysis of 180 siRNAs that targeted every other position across two 197-nucleotide regions of firefly luciferase and human cyclophilin B mRNA. The authors found that the efficiency of siRNAs is determined by the siRNA sequence itself, rather than the mRNA content. This differs from gene knockdown by antisense methods, in which silencing is determined by the local mRNA conformation.

The small proportion of siRNAs that produced highly potent (>95%) gene silencing — 24.4% of luciferase siRNAs and 11.1% cyclophilin B siRNAs — confirms the necessity for rational siRNA design. In no order of importance, the eight criteria determined for effective siRNA design are: low G/C nucleotide content (30–52% G/C); three or more A/U nucleotides at the 3'-terminus of the sense strand (that is, the same sequence as mRNA target), in other words a bias towards low internal stability in this region; a lack of internal repeats that can form secondary structures; and sequence-specific preferences at the following positions on the sense strand — an A at position 19, an A at position 3, a U at position 10, and an absence of a G or C at position 19 and a G at position 13.

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References

ORIGINAL RESEARCH PAPER

  1. Reynolds, A. et al. Rational design for RNA interference. Nature Biotechnol. 1 February 2004 (DOI:10.1038/nbt936)

FURTHER READING

  1. Nature Reviews Journals web focus on RNA interference http://www.nature.com/focus/rnai

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Authors
  1. Simon Frantz
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Frantz, S. Eight steps to silence. Nat Rev Drug Discov 3, 204 (2004). https://doi.org/10.1038/nrd1340

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