Synthesis of RNA Containing 5-Hydroxymethyl-, 5-Formyl-, and 5-Carboxycytidine

Chemistry. 2017 Nov 13;23(63):15894-15898. doi: 10.1002/chem.201704216. Epub 2017 Oct 20.


5-Hydroxymethyl-, 5-formyl-, and 5-carboxy-2'-deoxycytidine are new epigenetic bases (hmdC, fdC, cadC) that were recently discovered in the DNA of higher eukaryotes. The same bases (5-hydroxymethyl-, 5-formyl-, and 5-carboxycytidine; hmC, fC, and caC) have now also been detected in mammalian RNA with a high abundance in mRNA. While DNA phosphoramidites (PAs) that allow the synthesis of xdC-containing oligonucleotides for deeper biological studies are available, the corresponding silyl-protected RNA PAs for fC and caC have not yet been disclosed. Here, we report novel RNA PAs for hmC, fC, and caC that can be used in routine RNA synthesis. The new building blocks are compatible with the canonical PAs and also with themselves, which enables even the synthesis of RNA strands containing all three of these bases. The study will pave the way for detailed physical, biochemical, and biological studies to unravel the function of these non-canonical modifications in RNA.

Keywords: RNA epigenetics; cytidine modifications; mRNA modifications; oligonucleotides; phosphoramidites.

MeSH terms

  • Animals
  • Deoxycytidine / analogs & derivatives*
  • Oligonucleotides / chemical synthesis
  • Oligonucleotides / chemistry
  • Organophosphorus Compounds / chemical synthesis
  • Organophosphorus Compounds / chemistry
  • RNA / chemical synthesis*
  • RNA / chemistry
  • Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization


  • Oligonucleotides
  • Organophosphorus Compounds
  • phosphoramidite
  • Deoxycytidine
  • RNA