How does bisulfite conversion affect methylated cytosine residues?

The process of bisulfite conversion is designed specifically to differentiate between methylated and unmethylated cytosine residues in DNA. When DNA is treated with bisulfite, unmethylated cytosines are converted into uracils, while methylated cytosines remain unchanged. This is fundamentally important for applications such as quantitative methylation analysis and cloning of methylated sequences.

Thus, the effect of bisulfite conversion on methylated cytosine residues is that they are left unaffected. This allows researchers to identify which cytosines are methylated in the original DNA by comparing the bisulfite-treated DNA's sequence to a reference sequence. The unchanged methylated cytosines can later be identified because they will remain as cytosines, while the unmethylated cytosines will have been converted to uracil and then typically read as thymine during PCR amplification.

In terms of the other options, converting methylated cytosines into uracil is incorrect because only unmethylated cytosines undergo this change. The option stating that it alters their sequence entirely is also inaccurate since only the unmethylated residues are affected, not the methylated ones. Finally, targeting only specific genes is misleading; bisulfite conversion does