NMR solution structure of an oligonucleotide hairpin with a 2'F-ANA/RNA stem: Implications for RNase H specificity toward DNA/RNA hybrid duplexes

The first structure of a 2'-deoxy-2'-fluoro-D-arabinose nucleic acid (2'F-A NA)/RNA duplex is presented. We report the structural characterization by N MR spectroscopy of a small hybrid hairpin, r(GGAC)-d(TTCG)2 'F-a(GTCC), con taining a 2 'F-ANA/RNA stem and a four-residue DNA loop. Complete H-1,C-13, F-19. and P-31 resonance assignments, scalar coupling constants, and NOE c onstraints were obtained from homonuclear and heteronuclear 2D spectra. In the chimeric duplex, the RNA strand adopts a classic A-form structure havin g C3 ' endo sugar puckers. The 2'F-ANA strand is neither A-form nor B-form and contains O4 ' endo sugar puckers. This contrasts strongly with the dyna mic sugar conformations previously observed in the DNA strands of DNA/RNA h ybrid duplexes. Structural parameters for the duplex, such as minor groove width, x-displacement, and inclination, were intermediate between those of A-form and B-form duplexes and similar to those of DNA/RNA duplexes. These results rationalize the enhanced stability of 2 'F-ANA/RNA duplexes and the ir ability to elicit RNase H activity. The results are relevant for the des ign of new antisense drugs based on sugar-modified nucleic acids.