Design of shRNAs is still quite the voodoo (I do it for a living lol) contrary to siRNAs. If you can go with validated structures (stem plus loop is an important combination, the stem affects the processing efficacy of the loop for example) go from there.
Otherwise I usually use the DSir tool with not too bad results and go with the OpenBiosystems loop. But I have my constructs with the miR30 pre-miR structure too to impact loading bias of both strands (pre-miRNA do NOT act like shRNA in loading bias).
I've used this site - http://www.sirnawizard.com
as well as the shRNA design site for Clontech http://www.clontech.com/AU/Products/Inducible_Systems/Tetracycline-Inducible_Expression/xxclt_onlineToolsLoad.jsp?citemId=http://bioinfo.clontech.com/rnaidesigner/oligoDesigner.do?overhangs=on&restrictionSite=on&xxheight=750
The Life Technologies website has a very good general section on how to design your shRNA http://www.invitrogen.com/site/us/en/home/References/Ambion-Tech-Support/rnai-sirna/general-articles/-sirna-design-guidelines.html
Design of shRNAs is still quite the voodoo (I do it for a living lol) contrary to siRNAs. If you can go with validated structures (stem plus loop is an important combination, the stem affects the processing efficacy of the loop for example) go from there.
Otherwise I usually use the DSir tool with not too bad results and go with the OpenBiosystems loop. But I have my constructs with the miR30 pre-miR structure too to impact loading bias of both strands (pre-miRNA do NOT act like shRNA in loading bias).
I have used this for lentiviral vector based shRNA (cloning in mi30 backbone) and the lentiviral platform pSLICK and some of them were good (target are a nightmare even with commercial siRNA), inducible expression. But there are several ways to search.
http://cancan.cshl.edu/cgi-bin/Codex/Codex.cgi
I would also recommend Biosettia's design tool. We recently tried to knockdown a small target gene (less than 200 bp long). Biosettia's design only pulls out one shRNA sequence. We also tried two shRNAs based on Whitehead's design, two shRNAs based on Thermo Scientific's design. It turn out Biosetti designed shRNA displays the highest knockdown with lowest off-target effect. Maybe we're lucky with this particular shRNA but at least it gives me good confidence in Biosettia's design.
I have used this site..
https://portals.broadinstitute.org/gpp/public/
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