The design and exogenous delivery of siRNA for post-transcriptional gene silencing

siRNA target finder online tool (Ambion)

This tool employs the early, basic siRNA design guidelines first described by Tuschl and colleagues. In general, Ambion scientists find that ~50% of siRNAs designed using this tool will reduce target gene expression by >50%.

siRNA design center online tool (Dharmacon)

The siDESIGN® Center is an advanced, user-friendly siRNA design tool, which significantly improves the likelihood of identifying functional siRNA. One-of-a-kind options are now available to enhance target specificity and adapt siRNA designs for more sophisticated experimental design.

GenScript siRNA Target Finder (GenScript)

Instruction for using this online design tool:
1.Specify the length, GC%, range, and sequence region for each siRNA target site. Alternatively, you may use the default settings.
2.Specify the target mRNA nucleotide sequence by accession number or gene ID. Alternatively, you may copy/paste the cDNA sequence into the appropriate box below.
3.Specify the organism in which the RNA interference experiment is to be conducted. This is used to filter out non-unique sequences via BLAST/SmithWaterman search.
4.Check the box at the bottom to design multiple RT-PCR primer sets at the same time.
5.Click "Start." Our software will find siRNA target sites based on your specifications. The candidate sequences will be filtered to remove non-unique sequences by BLAST/SmithWaterman against a unique and comprehensive EST/mRNA collection. The BLAST/SmithWaterman search may take some time, so please be patient. The ranking of siRNA candidates is based on a proprietary algorithm using ?E parameters.

siRNA custom sequence design inquiry form (Molecula)

With this form you can check a product, then below let us know the species, accession number (if available), and any other information that will help us design the siRNA duplex for your specific applications.

The design and exogenous delivery of siRNA for post-transcriptional gene silencing. Gilmore IR, Fox SP, Hollins AJ, Sohail M, Akhtar S. J Drug Target. 2004 Jul;12(6):315-40.

Centre for Genome-based Therapeutics, The Welsh School of Pharmacy, Cardiff University, Redwood Building, King Edward VII Avenue, Cardiff CF10 3XF, UK.

RNA interference (RNAi) is a natural cellular process that effects post-transcriptional gene silencing in eukaryotic systems. Small interfering RNA (siRNA) molecules are the key intermediaries in this process which when exogenously administered can inhibit or "silence" the expression of any given target gene. Thus, siRNA molecules hold great promise as biological tools and as potential therapeutic agents for targeted inhibition of disease-causing genes. However, key challenges to the effective and widespread use of these polyanionic, macromolecular duplexes of RNA are their appropriate design and efficient delivery to cells in vitro and in vivo. This review highlights the current strategies used in the design of effective siRNA molecules and also summarises the main strategies being considered for the exogenous delivery of siRNA for both in vitro and in vivo applications.

Last update 10-Jan-2005, Rating n/a of 0 votes.