siRNA finder - (Jul/16/2005 )

Does anyone know what online siRNA Finder is the best? As a new-comer in siRNA techniques I realized that the results using the same query sequence are quite different. Besides, how can I establish siRNA by myself...Thanks for each response

Hi Gebhardt,

I don't think there is a "best" siRNA finder. In an article in Genome Technology, Philip Zamore said: "I don't know anybody who can't find one (siRNA) that works. It is a very stochastic thing. It's not that hard to find a good siRNA." Tom Tuschl said: "There are no stringent rules for design except they should be 21 nucleotide overhang. Essentially any sequence would qualify."

You can look into siRNA vendor's website such as Invitrogen, Qiagen, Dharmacon, Ambion, etc. They all provide free siRNA design tool. Or you can find a list here: http://www.protocol-online.org/prot/Resear...sign/index.html

You may not need to design your siRNA at all. Companies such as Qiagen, Ambion provide validated siRNAs known to work. You can order directly from them. It seems Qiagen give you the sequence for validated siRNAs while Ambion doesn't unless you order them from it.

Hi, when I designed shRNAs I used three different online tools and chose those sequences, which were present in all results which I got. most of the tools is based on Dharmacon rules and you can find them here: Rheynolds et al: Rational siRNA design for RNA interference. Nature Biotechnology 22, 3, March 2004

hi
pcrman is right. there is no strickly rules to design a siRNA. General advices, 21nt, 2 or 3nt overhang, no more than 3G repetition (GGGG is banned) and avoid 4T if you want to use siRNA transcription by a RNApol III system. Several online siRNA finders are available, and as mabacil said, you can perform mutiples tests and pick one or 2 sequences that can be find in both. But it is possible that with 3 different systems you don't get 2 same sequences. There is link to validated siRNA databases in this forum. You can eventually look at them if you want to do a siRNA assay against one designed target in those databases.
(link)

fred