![](http://sciencenotes.files.wordpress.com/2008/04/dna-helix-w-methyl.jpg)
Take a good look at where the methylation is located. It is not "outside" the double helix but inside. It is not "substituted" for anything - it is added to the nucleic acid base inside the double helix phosphate backbones. Neither is it a system "outside" of DNA - it is a system for regulating the expression of DNA.