Based on my limited knowledge of genetics the DNA is contained in the nucleus of the cell. The mRNA does not penetrate into the nucleus of the cell, so I am not sure how the DNA itself is changed. mRNA is transcribed from DNA but then leaves the nucleus. The article states that the operating system is changed; I don't doubt that. The cell is intricate and is made up of many parts that are all part of the "operating system."
Some things can change DNA such as HIV virus (and retroviruses in general). If I was worried about DNA modification I'd be worried about vaccines containing pathogens from these type of viruses.