Structural Comparison of Oligoribonucleotides and Their 2′-Deoxy-2′-fluoro Analogs by heteronuclear NMR spectroscopy

1-(2′-Deoxy-2′-fluororibofuranosyl)pyrimidines were synthesized and incorporated into an RNA oligonucleotide to give 5′-r[C_fGC_f(U_fU_fC_fG)GC_fG]-3′ (C_f: short form of C = 2′-deoxy-2′-fluorocytidine; U_f: short form of U = 2′-deoxy-2′-fluorouridine). The oligomer was investigated by means of UV, CD, and NMR spectroscopy to address the question of how F-labels can substitute ¹³C-labels in the ribose ring. Through-space (NOE) and through-bond (scalar couplings) experiments were performed that make use of the ameliorated chemical-shift dispersion induced by ¹⁹F as an alternative heteronucleus. A comparison of the structures of fluorinated vs. unmodified oligomer is given. It turns out that the fluorinated oligonucleotide exists in a 14:3 equilibrium between a hairpin and a duplex conformation, in contrast to the unmodified oligonucleotide which predominantly adopts the hairpin conformation. Furthermore, the fluorinated hairpin structure adopts two distinct conformations that differ in the sugar conformation of the U and C nucleoside units, as detected by the ¹⁹F-NMR chemical shifts. The role of the 2′-OH group as stabilizing element in RNA secondary structure is discussed.