Measurement of long-range 1H-19F scalar coupling constants and their glycosidic torsion dependence in 5-fluoropyrimidine-substituted RNA

Monitoring of duplex and triplex formation by 19F NMR using oligodeoxynucleotides possessing 5-fluorodeoxyuridine unit as 19F signal transmitter

We prepared oligodeoxynucleotides (ODNs) possessing a 5-fluorodeoxyuridine (5-FU) unit as a 19F-signal transmitter, and characterized their structures including single strand, duplex, and triplex using 19F NMR. The change in chemical shift induced by incorporation of 5-FU into the ODNs and the formation of higher order structures allowed monitoring of structural changes. Data from UV melting experiments and CD spectra were consistent with the spectral changes in the NMR studies. These 19F-labeled ODNs may be promising molecular probes for the identification of DNA structures in complicated biological conditions.

5-Fluoro pyrimidines: labels to probe DNA and RNA secondary structures by 1D 19F NMR spectroscopy

¹⁹F NMR spectroscopy has proved to be a valuable tool to monitor functionally important conformational transitions of nucleic acids. Here, we present a systematic investigation on the application of 5-fluoro pyrimidines to probe DNA and RNA secondary structures. Oligonucleotides with the propensity to adapt secondary structure equilibria were chosen as model systems and analyzed by 1D ¹⁹F and ¹H NMR spectroscopy. A comparison with the unmodified analogs revealed that the equilibrium characteristics of the bistable DNA and RNA oligonucleotides were hardly affected upon fluorine substitution at C5 of pyrimidines. This observation was in accordance with UV spectroscopic melting experiments which demonstrated that single 5-fluoro substitutions in double helices lead to comparable thermodynamic stabilities. Thus, 5-fluoro pyrimidine labeling of DNA and RNA can be reliably applied for NMR based nucleic acid secondary structure evaluation. Furthermore, we developed a facile synthetic route towards 5-fluoro cytidine phosphoramidites that enables their convenient site-specific incorporation into oligonucleotides by solid-phase synthesis.

Long-range through-bond heteronuclear communication in platinum complexes

Four analogous platinum stilbene- and stilbazole-based complexes exhibit unusual long-range heteronuclear spin-spin coupling in solution. Single crystal analysis and NMR experiments show that the (19)F, (31)P, and (195)Pt nuclei communicate over large distances (0.9-1.3 nm) through bond rather than through space. Spin-spin couplings between (195)Pt and (19)F over seven bonds and between (31)P and (19)F over eight bonds are observed with (7)J(PtF) = 2.9 Hz and (8)J(PF) = 11.8 Hz. Remarkably, a very large spin coupling between (195)Pt and (19)F over six bonds ((6)J(PtF) = 40.1 Hz) is also observed in a structurally related pyridinium complex. Experimental and gNMR (version 5.0) simulated (19)F{(1)H}, (31)P{(1)H}, and (195)Pt{(1)H} spectra of the complexes reveal a three-spin AMY system (A = (31)P, M = (31)P, Y = (19)F) or a five-spin AMY(3) flanked by a four-spin AMXY or a six-spin AMXY(3) system (X = (195)Pt), respectively. Density functional theory calculations at the PBE0/SDD level of theory show a pi-conjugated metal-ligand network, which may contribute to the experimentally observed spin-spin interactions.

A nonafluoro nucleoside as a sensitive 19f NMR probe of nucleic acid conformation

A nucleoside carrying a perfluorinated tert-butyl group ( 4) was prepared by a Sonogashira coupling of 5-iodo-2'-deoxyuridine with 4,4,4-trifluoro-3,3-bis(trifluoromethyl)-1-butyne in nearly quantitative yield and subsequently incorporated into DNA oligomers. Thermal denaturation studies showed that 4 had a negligible effect on duplex stability when compared to thymidine. Transition from single strand to duplex was monitored by (19)F NMR spectroscopy at micromolar concentrations of oligomers, demonstrating the sensitivity of 4 as an NMR reporter nucleoside.

Synthesis of 5-fluoropyrimidine nucleotides as sensitive NMR probes of RNA structure

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.