What program can I use to design an RNA Antisense Oligonucleotide?

I tried Primer3, but could only figure out how to design regular (forward and reverse) DNA primers for PCR.





What computer program can I use to design an Antisense Oligo?

What program can I use to design an RNA Antisense Oligonucleotide?
It depends. What do you want to target. For how long? In what cell type? Do you only want a single sequence? You probably should test at least 3 different targets in an mRNA as silencing is so variable.





Deqor is a place to cut down on off target effects.





You can get all sorts of modifications too such as antagomirs, 2'-O-methyl or LNA depending on your needs.





An alternative to picking a single sequence is to use the esiRNA system. It works as well as siRNAs and has fewer off target effects. But, it's kind of a lot of work up front, especially if you only need to knock down a few genes.

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