Can I expect to see off target background when using d-siRNA for RNAi analysis?
It is important to take into consideration what target sequence will be used as a Dicer substrate. Dicer optimally works with long dsRNA of 500-1000 bp, although we’ve been successful in generating smaller siRNA duplexes (~200 bp) capable of blocking gene expression. It is important to select appropriate regions from a gene(s) of interest to amplify and transcribe. To avoid non-specific knockdown effects, avoid transcribing conserved regions and select a gene region that is specific to the gene of interest. Dicer is unique in that it also provides an opportunity to amplify conserved gene regions- and thus the expression of entire gene families can potentially be knocked out if desired.
