STRUCTURAL COMPARISON OF OLIGORIBONUCLEOTIDES AND THEIR 2'-DEOXY-2'-FLUORO ANALOGS BY HETERONUCLEAR NMR-SPECTROSCOPY

1-(2'-Deoxy-2'-fluororibofuranosyl)pyrimidines were synthesized and in corporated into an RNA oligonucleotide to give 5'-r[C(f)GC(f)(U(f)U(f) C(f)G)GC(f)G]-3' (C-f:short form of C-d2'f2 = 2'-deoxy-2'-fluorocytidi ne; U-f:short form of U-d2'f2 = 2'-deoxy-2'-fluorouridine). The oligom er was investigated by means of UV, CD, and NMR spectroscopy to addres s the question of how F-labels can substitute C-13-labels in the ribos e ring. Through-space (NOE) and through-bond (scalar couplings) experi ments were performed that make use of the ameliorated chemical-shift d ispersion induced by F-19 as an alternative heteronucleus. A compariso n of the structures of fluorinated vs. unmodified oligomer is given. I t turns out that the fluorinated oligonucleotide exists in a 14:3 equi librium between a hairpin and a duplex conformation, in contrast to th e unmodified oligonucleotide which predominantly adopts the hairpin co nformation. Furthermore, the fluorinated hairpin structure adopts two distinct conformations that differ in the sugar conformation of the U- f(5) and C-f(6) nucleoside units, as detected by the F-19-NMR chemical shifts. The role of the 2'-OH group as stabilizing element in RNA sec ondary structure is discussed.