What is difference between sirna and shrna?

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uday1
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What is difference between sirna and shrna?

Post by uday1 » Sun Jun 20, 2010 8:21 am

what is the difference between sirna and shrna? which technique is best to infect cell lines to get better knockdown of gene of my interest
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kolean
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Post by kolean » Sun Jun 20, 2010 11:57 pm

short interfering RNA is a RNA that is around 20+ nucleotides long, and is usually double stranded when you use it to infect your cell line (using the cell line's RNAi machinery to do your knockdown), while the short hairpin RNA is around 100 nucleotides long and a hairpin loop is formed, in which it looks like a pre-miRNA, and then uses the cell line's microRNA RNAi machinery to perform your knockdown (using Dosha/Pasha and Dicer enzyme complexes).
But alas, I have never worked with any of these for knockdown. So I do not know what one is more stable than the other, or which would be more cost effective, and if one works better than the other in the cell line you are going to use.

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JackBean
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Post by JackBean » Mon Jun 21, 2010 3:59 pm

what I have heared, the hairpin RNA should be more effective, probably due to longer half-life. I think I have somewhere seen some article, where they have compared different si/shRNAs with their efficiency.
But I don't have personnal experiences with that at all.
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Post by sorin » Mon Jun 21, 2010 5:37 pm

Hey guys,
usually shRNA works better. one reason is that you generally transfect your cells with a construct encoding for (inducible) shRNA, so you get a stable knockdown upon expression...
second reason is that in contrast to siRNA it goes through the whole drosha/dicer/... pathway and can usually be utilized by the cell in a better way than pre-formed siRNA.
but siRNA could also work fine (if it is the right sequence...) and it is faster and easy to order.

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