How to Design a Negative Control siRNA - (Sep/13/2010 )

Hey Everyone,

I would like to design a negative control siRNA. I've been told to basically just scramble the nucleotide sequence of my gene-specific siRNA.

The problem is, the genome for my model organism has not been sequenced. Therefore, I cannot search to see whether my scrambled control lacks homology with another gene. How can I prevent accidental knockdown of another gene with my control?

Thanks in advance for any suggestions!

Because the genome you are working with is not sequenced, the best control would be the scrambled sequence, alhtough the scrambling may create off-target, but is better than random sequences.