RNA interference

[tgk]

In plants for getting a hairpin loop structure in pHannibal vector people normally use cDNA as the starting material from which to amplify the gene of interest. My question is whether one can start with the genomic DNA? What happens if introns are present in the region which will form ds RNA after transcription? The basic idea being that cDNA preparation can be avoided.

[JackBean]

Hi,
there are several modes of RNA interference, one of them is the binding to DNA thus blocking transcription. Unfortunately, I don't remember, whether this is plant's or animal's case...
If it was possible, then using gDNA would be fine. If it worked classicaly through binding to mRNA and it's digest, then your RNAi would have non-complementar part and probably would not work

[tgk]

Thank you. You are right. Since the interference is by binding of antisense RNA strand of 21-24 nt in RISC to mRNA, if introns are present they will not have complementary sequence in mRNA. In short, there is no short cut. It has to be cDNA.

[JackBean]

well, I didn't say exactly that, but you're rigth