I Need help in designing RNAi :?:

[julyy]

Hello,

How can I design an specific RNAi?
What is the protocol?

Thank you very much

Yuli

[jonmoulton]

Hi Yuli,

By its nature, RNAi is not very specific. See this blog post for a brief discussion and some citations on the topic of RNAi specificity: http://blogs.myspace.com/index.cfm?fuseaction=blog.view&blogId=496461710

There is software that scans an RNA sequence for regions where RNAi is more likely to target successfully (regions of less secondary structure). I've not used these packages, but looking for them is one avenue you might try. I expect some are freeware or open-source.

Alternatively, you can go directly to the companies that make siRNA. They might have validated oligos, which means the oligos have been shown to knock down their target mRNA (although "validated" does not mean "specific", the siRNA are likely modulating hundreds of off-target genes as well). At least most of these companies will help with siRNA design and likely have access to software that improves the probability of success of the siRNA.

Typically several RNAi sequences are screened to find one that produces a sufficiently strong knockdown.

Good luck!

- Jon