mniku

Here's another confused beginner... I'm still not 100% sure I understand the talk about "strand-specific" primers. Isn't this just like "traditional" PCR primer design, except that one of course uses a bisulfate converted sequence?

I mean, I usually use just the sense strand sequence as the design template and use something like Primer3 to pick the primers. If I now use the bisulfate-converted sense sequence, I will obviously get a reverse (antisense) primer that is fully complementary to the sense strand, and a forward (sense) primer that is NOT complementary to the antisense strand because of the bisulfate conversion. So during the first round of the PCR, only the sense strand will be amplified. And after that, the forward primer will bind to the new products and the rest is exponential amplification of the original sense strand. Is this what the strand specificity means?

I just don't see what else could I do. I mean, if I did design the primers fitting to both of the converted strands, they would amplify the original templates all right, but not the products, so the amplification would be only linear.