RNAi negative controls - (Nov/02/2005 )
Just wondering opinions on the best negative control for RNAi to use, as there are a number of them available, eg. scrambled oligo, mis-matched oligo, non-specific oligo???
What is the most widely/most sucessfully used?
i use scrambled RNAi sequence for my checkings.
Guidelines says that less than 13 following ntd without a mismatch is required for silencing. So if you want to do your own control, you may introduce mismtches every 10 ntd...
No matter how a constrol siRNA is designed scrambled, mis-matched, or non-specific, the most important thing is to minimize its homology with the gene of your interest and other sequences especially other coding sequences and regulatory sequence. Also remember that the 3' end of the siRNA duplex renders the siRNA specificity, so make sure there is even no partial perfect match between the 3' end and other sequences.