Variable presence of 5-methylcytosine in commercial RNA and DNA

Its presence in DNA is a widely accepted epigenetic mark for transcription inactivation. In RNA, its appearance in different coding as well as non-coding RNA implies multiple functions, with regulation of gene expression as a common denominator.

Here we report on the serendipitous discovery of m 5 C in synthetic oligonucleotides, which prompted a systematic quantification in synthetic DNA and RNA of academic as well as of commercial origin. For both types of oligonucleotides, m 5 C was identified by comparison of fragmentation pattern and retention time with authentic standards by highly sensitive LC-MS/MS analysis with limit-of-quantification values in the attomol range.