2'-Fluoro substituents can mimic native 2'-hydroxyls within structured RNA

Abstract

The ability of fluorine in a C-F bond to act as a hydrogen bond acceptor is controversial. To test such ability in complex RNA macromolecules, we have replaced native 2'-OH groups with 2'-F and 2'-H groups in two related systems, the Tetrahymena group I ribozyme and the ΔC209 P4-P6 RNA domain. In three cases the introduced 2'-F mimics the native 2'-OH group, suggesting that the fluorine atom can accept a hydrogen bond. In each of these cases the native hydroxyl group interacts with a purine exocyclic amine. Our results give insight about the properties of organofluorine and suggest a possible general biochemical signature for tertiary interactions between 2'-hydroxyl groups and exocyclic amino groups within RNA.

Figure 1

Schematic representation of the interactions made by the base of the guanosine nucleophile in the closed complex of the Tetrahymena group I ribozyme. The hydrogen bond between G and residue A261 is shown in red.

Figure 2

ΔC209 P4-P6 secondary structure with histogram indicating the 2′-F/2′-H interference profile at 0.45 mM MgCl₂. Sites of 2′-F and 2′-H interference are represented by the green and red bars, respectively. Sites of unique 2′-F interference correlate with residues that adopt a 2′-endo conformation in the structural models, as previously observed for the hairpin ribozyme (Ryder and Strobel, 1999), and are omitted for clarity. Interference values were calculated as described by Ryder et al. (Ryder et al., 2000). Only sites with interference values >1.5 are shown to take into account the experimental errors. See also Table S2 and Figure S2.