Backbone FC-H···O hydrogen bonds in 2'F-substituted nucleic acids.

Stabilization of nucleic acid secondary structures results from a subtle balance of multiple interactions. Base pairing, base stacking, and cation binding have been extensively studied for decades, whereas the role of other interactions remains poorly understood. Among them, nonconventional C H···O hydrogen bonds are especially interesting. The importance of these interactions in proteins was recognized more than 40 years ago, and during the last few years, several studies have shown their relevance in multiple biological structures. In nucleic acids, most studies have focused on aromatic C H···O interactions, and in particular, on the effect of nonconventional hydrogen bonds in base pairing and in base– sugar interactions. Backbone C H···O hydrogen bonds have received less attention, although they have been proposed to play a role in the stabilization of four stranded i-motif structures, and in tight packing of RNA and DNA elements. Although these interactions are considered weak in natural nucleic acids, their strength can be increased through chemical modifications. Fluorine substitutions are particularly relevant, since fluorine provokes significant charge polarization effects in geminal and vicinal protons, an effect that has been well-characterized in small molecular systems. Recently, Kakshoor et al. have observed fluorineenhanced aromatic C H···N interactions that significantly affect the strength of 2,4-difluorotoluene–adenine base pairs. The prevalence of 2’-fluorinated oligonucleotides in nucleic acids research motivated us to examine the role of enhanced nonconventional hydrogen bonding in duplex stability. Effects contributing to the enhanced thermal stability of 2’-deoxy-2’-fluororibonucleic acid (2’F-RNA) duplexes have been the subject of recent studies. Recently, work by Egli and co-workers has demonstrated that 2’F-RNA duplex stabilization is primarily enthalpic in origin, through enhanced base stacking and pairing arising from long-range fluorine inductive effects on the nucleobases. Stabilizing effects arising from fluorine have also been observed in the 2’ epimer of 2’F-RNA, 2’-deoxy-2’-fluoroarabinoonucleic acids (2’F-ANA). The geometry of 2’F-ANA:RNA duplexes are such that close 2’F···purine (H8) contacts are provoked, providing a very favorable geometry for hydrogen bond formation. Herein, we identify an additional stabilizing factor in Aform duplexes modified with 2’F-ANA and 2’F-RNA. Results demonstrate that fluorine-enhanced FC H···O backbone interactions can have a strong stabilizing effect on oligonucleotide duplexes. Although close FC H2’···O interactions have gone largely unnoticed, we propose that these interactions exist in other recently reported fluorinated duplexes, and complement the enhanced base stacking and pairing effects stabilizing 2’F-RNA duplexes. Two chimeric self-complementary duplexes containing continuous tracts (duplex H) and alternating regions (duplex S) of 2’F-ANA and 2’F-RNA residues (Figure 1A and B) were used to carry out these structural, thermodynamic, and computational studies. Self-complementary duplex formation and melting was monitored by UVabsorbance at 260 nm and H and F NMR (Supporting Information, Figure S1 and S2). Melting temperature (Tm) values are shown in Table 1, showing that the Tm of H is over 20 8C greater than that of S, a trend in agreement