Conformations of nucleoside analogue 1-(2′-deoxy-β-D-ribofuranosyl)-1,2,4-triazole-3-carboxamide in different DNA sequence contexts

The concept of using a dynamic base-pairing nucleobase as a mode for degenerate recognition presents a unique challenge to analysis of DNA structure. Proton and phosphorus NMR studies are reported for two nine-residue DNA oligodeoxyribonucleotides, d(CATGGGTAC)·d(GTACNCATG) (1) and d(CATGTGTAC)·(GTACNCATG) (2), which contained 1-(2′-deoxy-β-D-ribofuranosyl)-1,2,4-triazole3-carboxamide (N) in the center of the helix at position 14. The duplexes were compared to the canonical Watson-Crick duplexes, d(CATGGGTAC)·d(GTACCCATG) (3) and d(CATGTGTAC)·d(GTACACATG) (4). Two-dimensional NOESY spectra of 1-4 in H₂O and D₂O solutions collected at 5°C allowed assignment of the exchangeable and nonexchangeable protons for all four oligodeoxyribonucleotides. Thermodynamic and circular dichroism data indicated that 1-4 formed stable, B-form duplexes at 5°C. Two-dimensional ¹H-³¹P correlation spectra indicated that there were minor perturbations in the backbone only near the site of the triazole base. Strong NOESY cross-peaks were observed between the H5 and H1′ of N14 in 1 and, unexpectedly, 2, which indicated that, in both duplexes, N14 was in the syn_χ conformation about the glycosidic bond. NOESY spectra of 1 and 2 recorded in 95% H₂O, 5% D₂O indicated that the imino proton of the base opposite N14, G5, or T5, formed a weak hydrogen bond with N14. These conformations place the polar carboxamide functional group in the major groove with motional averaging on the intermediate time scale.