What is methylation-specific PCR used to detect?

• A. Gene expression levels in RNA
• B. Chromosome banding patterns
• C. The methylation status of CpG sites in DNA
• D. Protein folding dynamics

Answer: (C)

The key idea is identifying whether CpG sites in DNA are methylated or not. Methylation-specific PCR is built to distinguish methylated from unmethylated DNA sequences at CpG dinucleotides. After treating DNA with bisulfite, unmethylated cytosines are converted to uracil (read as thymine in PCR), while methylated cytosines stay cytosine. Primers are then designed to match either the methylated or the unmethylated sequence, so PCR amplification indicates the presence or absence of methylation at those CpG sites. This technique specifically targets DNA methylation status, not RNA expression, chromosome banding, or protein folding. Thus, methylation-specific PCR is used to detect the methylation status of CpG sites in DNA.