title: Synthesis of 5-fluoropyrimidine nucleotides as sensitive NMR probes of RNA structure.
abstract: Enzymatic synthesis methods for the fluorinated 5'-triphosphate analogues 5F-UTP and 5F-CTP have been developed to facilitate 19F-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 19F-19F and heteronuclear 19F-1H 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 19F-labeling.
authors.affiliation: Department of Biochemistry and Molecular Biology, Medical University of South Carolina, 173 Ashley Avenue, P.O. Box 250509, Charleston, South Carolina 29425, USA. hennig@musc.edu
authors.forename: Mirko
authors.initials: M
authors.lastname: Hennig
authors.forename: Lincoln G
authors.initials: LG
authors.lastname: Scott
authors.forename: Edit
authors.initials: E
authors.lastname: Sperling
authors.forename: Wolfgang
authors.initials: W
authors.lastname: Bermel
authors.forename: James R
authors.initials: JR
authors.lastname: Williamson
mesh_terms: D016325:HIV Long Terminal Repeat; D015498:HIV-2 / Q000235:genetics; D009682:Magnetic Resonance Spectroscopy / Q000379:methods*; D008958:Models, Molecular; D009690:Nucleic Acid Conformation; D009711:Nucleotides / Q000138:chemical synthesis* / Q000737:chemistry; D010710:Phosphates / Q000737:chemistry; D011743:Pyrimidines / Q000138:chemical synthesis* / Q000737:chemistry* / Q000378:metabolism; D012313:RNA / Q000737:chemistry* / Q000235:genetics; D015347:RNA Probes / Q000138:chemical synthesis* / Q000737:chemistry / Q000235:genetics; D012680:Sensitivity and Specificity; D013696:Temperature; D044366:Transition Temperature
chemical_list: D009711:Nucleotides; D010710:Phosphates; D011743:Pyrimidines; D015347:RNA Probes; D012313:RNA; C029269:5-fluoropyrimidine