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Nucleotides for Structure Determination by NMR

RNA plays a fundamental role in biological processes (e.g. translation or gene regulation). Therefore, the biophysical properties of RNA molecules such as their three dimensional shape or secondary structure distribution gained increasing importance.

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] Roth et al. (2011) RNA Structure Determination by NMR: Combining Labeling and Pulse Techniques. Advances in Biomedical Spectroscopy 3:205.