Antagomir design tool - (Mar/13/2012 )
I need to design some antagomirs for my experiments to knock-down some miRNAs of interest. Is there any antagomir designing software/too that is freely available? I came across this tool in IDT website. It says antisense design. Can I use the same for my need also?
Thanks a lot.
The most important part of antagomir design is chemical modification of the oligo which is complementary to the entire mature miRNA sequence. So there is no much room for tweaking the sequence. I would suggest that you order premade antagomir from vendors. A cheaper way other than buying antagormirs from company is to design siRNA to target the loop sequence of pre-miRNA. Sometimes we can have better knockdown efficiency using siRNA than any antagomir.
I am consider buying from vendors as the last option I guess. If I have to design it for myself do you know of any tools that can be of help in this regard? And also, which one - mature sequence or the stem loop sequence- you have to take so that you can desing antagomirs against them? I think it is the mature sequences. Right?
I can't speak for the cholesterol-modified phosphorothioate oligos, but for Morpholinos we like to target across the guide and slightly into the loop. For specificity controls we'll target across the star and into the loop. There is more on that strategy in this paper:
Kloosterman WP, Lagendijk AK, Ketting RF, Moulton JD, Plasterk RH. Targeted Inhibition of miRNA Maturation with Morpholinos Reveals a Role for miR-375 in Pancreatic Islet Development. PLoS Biol. 2007 Jul 24;5(8):e203