A 6′-Fluoro-Substituent in Bicyclo-DNA Increases Affinity to Complementary RNA Presumably by CF–HC Pseudohydrogen Bonds

The
synthesis of a novel bicyclic thymidine analogue carrying a β-fluoro
substituent at C6′ (6′F-bcT) has been achieved. Key
steps of the synthesis were an electrophilic fluorination/stereospecific
hydrogenation sequence of a bicyclo sugar intermediate, followed by
an N-iodo-succinimide-induced stereoselective nucleosidation.
A corresponding phosphoramidite building block was then prepared and
used for oligonucleotide synthesis. Tm measurements of oligonucleotides with single and double incorporations
showed a remarkable stabilization of duplex formation particularly
with RNA as complement without compromising pairing selectivity. Increases
in Tm were in the range of +1–2
°C compared to thymidine and +1–3 °C compared to
a standard bc-T residue. Structural investigations of the 6′F-bcT
nucleoside by X-ray crystallography showed an in-line arrangement
of the fluorine substituent with H6 of thymine, however, with a distance
that is relatively long for a nonclassical CF–HC hydrogen bond.
In contrast, structural investigations in solution by 1H and 13C NMR clearly showed scalar coupling of fluorine
with H6 and C6 of the nucleobase, indicating the existence of at least
weak electrostatic interactions. On the basis of these results, we
put forward the hypothesis that these weak CF–HC6 electrostatic
interactions increase duplex stability by orienting and partially
freezing torsion angle χ of the 6′F-bcT nucleoside.