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shRNA versus siRNA

Discussion of all aspects of biological molecules, biochemical processes and laboratory procedures in the field.

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shRNA versus siRNA

Postby curious1 » Wed Jan 31, 2007 4:56 am

Hi hi,

I was wondering what the difference between using shRNA and siRNA really is. I have they both use the same mechanism for silencing except that shRNA contains an extra hairpin structure, but is that all? What is the advantage of using shRNA rather than siRNA? I read that shRNA is better for stable transfections but I thought siRNA can be used for stable transfections as well? What's the difference? Thankssss
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Postby sdekivit » Wed Jan 31, 2007 8:17 am

in siRNA already prepared double stranded RNA-molecules are transfected, so that is more difficult than shRNA. In shRNA a vector is made that contains a sequence that will result in the typical hairpin structure you already mentioned.

--> that vector can be tranfected in a viral/viral like delivery system which is much more efficient in targetting the shRNA in the nucleus.

Remember all the barriers the siRNA-molecule must overcome: first of all the extracellular spaces (can be overcome by ex vivo transfection), cell membrane, endosomes (low pH), high viscosity of the cytoplasm (relatively no diffusion possible), RNAses and other nucleases in the cytoplasm and the selective nuclear membrane.

--> viral systems can overcome these barriers, so shRNA is easier for targetting.
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Postby curious1 » Wed Jan 31, 2007 4:25 pm

O I see,

Does that mean shRNA is transcribed along with the genome while siRNA attacks the after double stranded RNA's have already been transcribed. Also, is it true that siRNA can only be used for transient transfections while shRNA for stable transfections since siRNA is not incorporated into the genome?
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Postby sdekivit » Wed Jan 31, 2007 9:59 pm

curious1 wrote:O I see,

Does that mean shRNA is transcribed along with the genome while siRNA attacks the after double stranded RNA's have already been transcribed. Also, is it true that siRNA can only be used for transient transfections while shRNA for stable transfections since siRNA is not incorporated into the genome?


true. shRNA can remain episomal as a plasmid or random recombination occurs so it's integrated in the host genome.

siRNA remains in the cytosol and has a shorter effect than shRNA.
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Postby curious1 » Thu Feb 01, 2007 9:58 pm

o i understand now, thanks!
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