I'm hermawan, I am a new member here. I'm doing a research dealing with MSP.
I have 2 primer for methylated and 1 primer for unmethylated.
I'm still doing optimization for MSP. For this optimization, I use DNA template for methylated and unmethylated using Methylated and Unmethylated DNA control from Qiagen respectively.
I got a good result (clear band) in unmethylated primer. For methylated primer, I got a band in the right place (in accordance with its amplicon size), but the intensity of brightness is still less than unmethylated primer, it is still faint. I don't know why.
For this MSP, I have done temperature gradient PCR to choose the best annealling temperature based on Tm Forward and reverse primer given by company where I order those primer (eurogentec ait, singapore)
Please give me any suggestion, what should I do next to get a better result in MSP for my methylated primer?