How to design siRNAs for RNAi - (Mar/02/2006 )

I have a horrendous fear of molecular biology but have come to the stage in my PhD where I can no longer hide this...

....so can someone explain to me the rules of designing a primer, and either give me an example of how one is done or point me to a website that can?

I'm sure this is very simple, and I have looked it up on the net, but I just can't get to grips with it.

Many, many thanks, any help is very much appreciated.

hi
hiding a misknowledge under PhD reason is not the best. Googling drives you to dedicates sites. But instead to give you those sites, i'll tell you beginning of answer... and it's you to find the rest. post it and we'll correct it if wrong. Ok?


basically, primers are designated to amplify a specific sequence. So they're supposed to be specific. Generally done under a small complex DNA, specificity is quite easy to obtain.
As you do PCR in same tube, annealing temp should not that differ between the two primers. they're not supposed to form strong hairpin structures (supposed by intra complementarity)...


For designing siRNA, just surf on google or in this forum and you'll find the answer... Go to forum siRNA...

yea, same Tm for both primers, ending with C or G, no hairpins or go to the invitrogen page and introduce the sequence that you want to amplify. interesting calculator u can find there