Hi all,
I want to order one siRNA from one publication. In the publication, they used 3 siRNAs and I want to order the most efficient one first. This is a 19nt siRNA. But when I do the blast, besides the aim mRNA, the first 14nt (from 5' to 3') will 100% match another mRNA. Does this mean there is a high chance that this siRNA will knock down that gene too?
Which part of the siRNA sequence matters most for the knock down, the 5', 3' or the middle? There is no way to 100% avoid off target effect, right?
Thanks!
The 5′ end of the guide strand, called the seed region, is important for silencing if I understand correctly. It is likely that the siRNAs you mentioned also targets another mRNA. I don't think there is a way to avoid off-target completely (well, maybe there is), but you might want to check papers such as http://www.nature.com/nrd/journal/v9/n1/full/nrd3010.html
Good luck
It would always be good try two siRNA to validate our target gene. As mentioned by Tomyasu it is difficult to avoid off target effects since your siRNA has a complimentary sequence with another mRNA
Hi Pramod,
I'm totally new to siRNA but if I'm not wrong, it's the anti-sense strand that targets mRNA right?
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