Protocol Online logo
Top : Forum Archives: : siRNA, microRNA and RNAi

shRNA design help - (Dec/04/2005 )

I would like to design shRNAs to a viral target. Can anyone recommend a good website where I can get good candidate target sequences? Different programs give different results and I don't know where to begin.

Thanks for helping!


Hi Kirsten,

Although Tom Tuschl once said that if you randomly pick a siRNA target, you will have 80-90% chance of silencing gene expression. That was the early days of RNAi. Now there are many validated siRNA targets for human genes and genes in other organisms and there are even cloned shRNA libraries for sale from Sigma. You can check places like Ambion, Qiagen, Darhmacon, Invitrogen or PubMed, etc. for validated targets for your gene. If no validated targets are found, design your own siRNAs by using design tools from any of those companies.

Hope that helps.


Hi Kirsten, there is a homepage for shRNA design in the internet.

best regards!