RNA structure determination can be performed by liquid state nuclear magnetic resonance (NMR) spectroscopy that requires millimolar amounts of isotopically labeled RNA to obtain well-resolved signals.

A successful approach to generate sufficient isotopically labeled RNA amounts is the in vitro transcription-mediated synthesis of 19F-labeled RNA using fluorinated NTPs[1]. 2F-ATP or 5F-UTP are incorporated instead of their natural counterparts in a non-perturbing way (intact base-pairing properties) and simultaneously function as a sensitive NMR reporter group (larger chemical shift dispersion than 1H)[1].

Selected References

[1] Graber et al. (2008) 19F NMR Spectroscopy for the Analysis of RNA Secondary Structure Populations. J. Am. Chem. Soc. 130 (51):17230.
[2] Sochor et al. (2016) S(19)F-labeling of the adenine H2-site to study large RNAs by NMR spectroscopy. J. Biomol. NMR 64 (1):63.
[3] Scott et al. (2004) Enzymatic synthesis and 19F NMR studies of 2-fluoroadenine-substituted RNA. J. Am. Chem. Soc. 126 (38):11776.