Converting shRNA sequence to siRNA - (Jul/03/2012 )
I'm fairly new to using shRNA/siRNA. I've used both minimally but have never had to design or order either. I'm hoping ot use siRNA to transiently knockdown my target for a promoter assay. While searching for different sets that I could buy, I came accross two shRNA sequences that worked really well. Is it possible to convert the shRNA sequence to siRNA? If so, how? Or do different sequences work better for shRNA than siRNA and vise versa?
Lastly, do you have any suggestions about which siRNA company is more reliable or easy to work with based on experience.
Converting validated shRNA sequences to siRNA may not be that straight forward because the shRNA may contain more than 19 nt target sequence and has the loop. If you can identify the 19 nt target sequence next to the loop, the derived siRNA should work fine. a shRNA may have higher knockdown efficiency than its corresponding siRNA, and vice versa.
In terms of siRNA vender, if money is not an issue, go for big company like invitrogen, sigma. You can also shop around for a cheaper price.