siDirect 2.0: updated software for designing functional siRNA with reduced seed-dependent off-target effect
Open Access
- 30 November 2009
- journal article
- Published by Springer Science and Business Media LLC in BMC Bioinformatics
- Vol. 10 (1), 392
- https://doi.org/10.1186/1471-2105-10-392
Abstract
RNA interference (RNAi), mediated by 21-nucleotide (nt)-length small interfering RNAs (siRNAs), is a powerful tool not only for studying gene function but also for therapeutic applications. RNAi, requiring perfect complementarity between the siRNA guide strand and the target mRNA, was believed to be extremely specific. However, a recent growing body of evidence has suggested that siRNA could down-regulate unintended genes whose transcripts possess complementarity to the 7-nt siRNA seed region. This off-target gene silencing may often provide incongruous results obtained from knockdown experiments, leading to misinterpretation. Thus, an efficient algorithm for designing functional siRNAs with minimal off-target effect based on the mechanistic features is considered of value.This publication has 39 references indexed in Scilit:
- The promises and pitfalls of RNA-interference-based therapeuticsNature, 2009
- The art and design of genetic screens: RNA interferenceNature Reviews Genetics, 2008
- A three-dimensional view of the molecular machinery of RNA interferenceNature, 2008
- Argonaute proteins: key players in RNA silencingNature Reviews Molecular Cell Biology, 2008
- Argonaute2 Cleaves the Anti-Guide Strand of siRNA during RISC ActivationCell, 2005
- Passenger-Strand Cleavage Facilitates Assembly of siRNA into Ago2-Containing RNAi Enzyme ComplexesCell, 2005
- Guidelines for the selection of highly effective siRNA sequences for mammalian and chick RNA interferenceNucleic Acids Research, 2004
- Functional siRNAs and miRNAs Exhibit Strand BiasCell, 2003
- Asymmetry in the Assembly of the RNAi Enzyme ComplexCell, 2003
- RNA interference is mediated by 21- and 22-nucleotide RNAsGenes & Development, 2001