Synthesis of 5-Fluoropyrimidine Nucleotides as Sensitive NMR Probes of RNA Structure

• Published in: Journal of the American Chemical Society Vol. 129; no. 48; pp. 14911 - 14921
• Main Authors: Hennig, Mirko, Scott, Lincoln G, Sperling, Edit, Bermel, Wolfgang, Williamson, James R
• Format: Journal Article
• Language: English
• Published: 01.01.2007
• Subjects: Human immunodeficiency virus 2
• ISSN: 1272-7863; 1520-5126
• DOI: 10.1021/ja073825iPII:S0002-7863(07)03825-5

Enzymatic synthesis methods for the fluorinated 5'-triphosphate analogues 5F-UTP and 5F-CTP have been developed to facilitate super(19)F-labeling of RNAs for biophysical studies. HIV-2 TAR RNAs were synthesized using these analogues by in vitro transcription reactions using T7 RNA polymerase. The uniform incorporation of 5F-U or 5F-C analogues into HIV-2 TAR RNA transcripts does not significantly alter the RNA structure or thermodynamic stability. Fluorine observed homonuclear super(19)F- super(19)F and heteronuclear super(19)F- super(1)H NOE experiments providing selective distance information are presented and discussed. The availability of efficient synthesis of 5F-UTP, and for the first time, 5F-CTP, will facilitate the use of 5F-labeled RNAs in structural, ligand binding, and dynamic studies of RNAs using the advantages of super(19)F-labeling.