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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.