off target effects - (May/14/2015 )

Hello, I was wondering whether off taeget effects would be 'reproducible' or random. We are having troubles to reproduce results (siRNA knockdowns in ovarian cancer cells and invasion, colony formation and migration assays) - often the effects are reverse or simply disappear. Could this be off target effects ir would I then always have the same result but not in the right direction? Thanks a lot

I would think the off targeting for any specific siRNA to be non random. The siRNA is still base complementing, just that RNA can also form G:U base pairs in addition to the standard watson-crick base pairing. But this is just my opinion.

In your case, it could be that your transformation efficiency, and thus knockdown efficiency is not the same. As the protein being knockdown is not the same, so the phenotype is not reproducible. For some proteins you need to go below a threshold before you see a phenotype

Thank you so much for the helpful comment! I was actually thinking about testing another siRNA company and see whether they give better knockdown efficiency. I am currently using Dharmacon.