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A role for modified synthetic RNA oligos in structural studies

How synthetic oligos can be used as a convenient and reliable RNA source for your experiment.

RNA fulfills a variety of roles in cells, from acting as a structural scaffold to carrying genetic information. Although it was originally believed that the key to this structural and functional diversity was sequence oriented, current research suggests a part is also played by a variety of over 140 chemical modifications that have been identified on mRNA and non-coding RNA molecules1. Among these modifications of interest is 5-formylcytosine, or f5C. One example of an f5C-containing RNA is tRNAMet. In a number of species, f5C is found in the wobble position of the anticodon loop -- allowing one tRNA the ability to interpret multiple codons of the genetic code. However, a clear understanding of how this modified base might affect duplex stability, and thus allow a phenomenon such as decoding expansion, had remained elusive.

In Wang et al.2 the authors used a series of synthetic RNA oligos containing 5-formylcytosine or natural cytosine to undertake a detailed study of the structural properties specific to f5C. Using thermodynamic and spectroscopic analysis the authors were able to demonstrate a number of differences in properties due to the 5-formyl group, such as increase of melting temperature and enhanced base pairing specificity. Further crystallographic analysis of these duplexes using a series of conditions revealed hydration patterns which may result in greater rigidity of the RNA and thus higher stability of f5C-modified duplexes.

Custom RNA synthesis of modified oligos for any experiment

Chemical synthesis methods allow researchers the ultimate control in creation of RNA substrates for their experiments. Since 1995 Dharmacon has been a leader in RNA synthesis technology. Our novel 2’-ACE chemistry allows routine synthesis of oligos of unprecedented length, quality and yield.

In addition to creating standard ssRNA oligos, we also offer numerous modifications. These standard modifications can be easily ordered online, and paired with custom purification and processing, so your oligos arrive ready for use. If your modification of interest is not already listed on our website (such as the f5C mentioned above), just contact tech support. Our custom synthesis and chemistry teams can also work together to create custom phosphoramidites, specialized chemical modifications, and modified bases.


  1. Machnicka,M.A., Milanowska,K., Osman Oglou,O., Purta,E., Kurkowska,M., Olchowik,A., Januszewski,W., Kalinowski,S., Dunin-Horkawicz,S., Rother,K.M. et al. MODOMICS: a database of RNA modification pathways–2013 update. (2013) Nucleic Acids Res., 41, D262–D267.
  2. Rui Wang, Zhipu Luo, Kaizhang He, Michael O. Delaney, Doris Chen, Jia Sheng. Base pairing and structural insights into the 5-formylcytosine in RNA duplex. (2016) Nucleic Acids Res., 44, 4968-4977.

Additional resources