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 synχ 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.
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