How to design the loop for shRNA? - (Oct/04/2006 )

I want to design siRNA that I will clone into a plasmid (pSilencer).
I got the sequence of the siRNA from a paper.
So, I have the sense, I converted into anti-sense, and now I need a linker (that will be the hair pin).
Dos anyone have experience with this sort of thing?
How long? What residues? Exec’
Thanks

Different loop sequences have been used in published literature. You can use Ambion's shRNA design tool to design your shRNA oligo template although you may not want to use their vector system.
http://www.ambion.com/techlib/misc/psilencer_converter.html

Also Ambion has a very good review on shRNA design in which some commonly used loop structures are given.
http://www.ambion.com/techlib/tb/tb_506.html

For the loop, u could use dif. ones.

In my old lab, we used to have 7bp loop, and in my present lab, we use 4bp.

But the other day heard someone say that its better to have 9bp loop.

The basic thing, is all of these do work. U have to make the choice.