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siRNA versus shRNA - (Jun/23/2005 )

Being new in the field of siRNAs, can someone please explain what the advantage/disadvantage is of having a siRNA (21nt) or an shRNA (50mer) oligo, anneal them and put them into a siRNA vector?


Here are things I can think of:

synthetic siRNAs are easy to make, for transient transfection.

shRNAs take time to build, for stable transfection, tend to cause interferon response.


shRNAs = only use if require stable-knockdown

siRNAs = preferred method for screening

shRNAs =
1) you have to clone
2) you have to verify insert
3) you should try to determine how much of the shRNA are the cells expressing
4) sometimes kills cells or IFN as pcrman indicated
5) recombination
6) more difficult to transfect
7) more difficult to control and understand rules for loop sequences

BUT, if you want STABLE knockdown then vectors is where you need to go. Look into viral-based vectors.

-Cali Girl-

just found this thread and i as i do not work on this field but being a student working on his diploma thesis have to give a presentation on RNAi i have wondered if shRNA more or less just works the same way as the ds si RNA by forming the hairpin structure. also does anyone have any site recommendations on where i can find additional information on the principle and methods in general?


the mechanism to which RNAi works in the cell is the same with shRNA and siRNA. Only the enzyme dicer will cleave the shRNA into an siRNA like oligo (removes the hairpin). The enzyme recognizes an oddly shaped hairpin structure and cleaves it.

A really good website that provides a great review on the mechanisms of RNAi is from Nature Reviews.

Best of Luck.