isoform specific knockwdown

Model Organism: Worms Methods & Reagents
1

Hi All,

Has anyone here designed or made constructs for isoform specific knockdown of a gene by RNAi? Isoforms for my gene of interest differ in the first exon. The exon lengths are betwwen 80-150 bp for the isoforms. Is this length sufficient to achieve isoform specific knockdown since most of the RNAi vectors I have studied or found contain at least 500bp of the coding sequence to knockdown gene of interest.
thanks

2

Isoform-specific RNAi has been reported multiple times: e.g., http://jcs.biologists.org/content/116/10/2073.short
and http://www.molbiolcell.org/content/19/3/785.long and http://www.sciencedirect.com/science/article/pii/S0012160603006973.

3

With the advent of CRISPR genome editing, I think we’re going to see a lot more isoform-specific knockouts. I’d recommend that on top of isoform-specific RNAi.