When people talk about DNA methylation at CpG sites, I keep seeing CpG spelled out as "cytosine-phosphorothioate-guanine"… isn’t it all wrong? I thought CpG just means a cytosine and a guanine containing deoxyribonucleotide bonded with a normal phosphodiester bond, and "p" just stands for phosphodiester. I looked it up, "phosphorothioate" would mean that an oxygen was replaced within the phosphodiester bond with a sulfur atom. But that is not what CpG should originally mean, right? In the normal human body, we don’t have sulfur in our DNA, right? Please clarify.
I see only phosphorothioates in chemically modified DNA oligonucleotides used as antisense oligonucleotides. Phosphorothioate render DNA oligonucleotides less subject to degradation by nucleases and still allow RNAse H to cleave mRNA hybridized to the phosphorothioate DNA oligonucleotide. CpG sequence in DNA is Cytosine phosphate Guanine. It is indeed a privileged site of DNA methylation.