1. Bisulfite Treatment: DNA is treated with sodium bisulfite, converting unmethylated cytosines to uracil. 2. PCR Amplification: Two sets of primers are usedâone specific for methylated DNA and the other for unmethylated DNA. 3. Gel Electrophoresis: The PCR products are separated on an agarose gel to determine the presence of methylated or unmethylated DNA.