Tool for making scrambled control siRNA - (Mar/28/2006 )
hello everybody! can anyone give me advice on whether there's a tool (freeware) that generates nonsense DNA sequences (no homology to any organism)? I need it for making a control for my siRNA vector.
Thank you very much in advance!
I don't think there are such tools that can generate control siRNAs that lack homology with other sequences because the program has to first make a random sequence and then blast the sequence against genome database, and determine whether there are significant hits.
For RNAi, off-target effect is a big problem due to the fact that 1) only the 'seed' sequence is critical for sequence specificity and RNAi can tolerate mismatches between guide RNA's 3' end and mRNA target; 2) siRNA can bind to DNA targets and induce unexpected effects.
Alternatively you can search some vendors' site such as qiagen.com for control siRNA sequences which I believe has been validated.