HI, I do transient transfections of HEK293T cells using Fugene. I would like to quantify my target gene expression after the transfection by RT-PCR. However using the standard RNA isolation protocol using Trizol, followed by DNAse treatment is not enough to get rid off the plasmid DNA.. So when I make cDNA and PCR I have false amplification of the product coming from the vector construct. Does anybody have a solution for that?

I assume you know it is contamination by the input vector because a no-RT control has PCR products?

You might try tossing in a 4 base cutter restriction enzyme prior to the DNase step. If the plasmid is really supper-coiled the DNase might not be able to access. Alternatively the amount of genomic DNA is going to be much greater than the plasmid DNA. In which case you might try more or longer DNase treatment.