RNAi questions from a bioinformatician

[shazzle]

Hi guys,

I have a few questions. Pardon me if I sound as if I'm just starting out in RNAi studies (which I am ).

1. Is there a consensus that miRNA will only bind to the 3' UTR region only for interference, and does siRNA and shRNA exhibit the same action of binding to 3' UTR for interference?

2. If 1. is true, can miRNA and si/shRNA bind to other regions besides the 3' UTR and also degrades/inhibits the mRNA?

3. For off-target effects, can the un-intended target become degraded as a result of the off-target binding?

Thanks!

[krobison]

You really should find a good, recent & in depth review of the subject (try Reviews in... or Nature Reviews) for your first 2; I've been out of the field too long to answer those. It may also not be a question of absolutes but efficiency; certain locations in the mRNA may be more efficient than others.

Your #3 is the major mode of off-target effects nowadays (if experiments are performed correctly).

More generic off-target effects can come from either (a) overloading the processing machinery or (b) triggering an anti-viral response. Both are controlled by minimizing the dose of siRNA.