Conformations of nucleoside analogue 1-(2 '-deoxy-beta-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 degene rate recognition presents a unique challenge to analysis of DNA structure. Proton and phosphorus NMR studies are reported for two nine-residue DNA oli godeoxyribonucleotides, d(CATGGGTAC).d(GTACNCATG) (1) and d(CATGTGTAC).(GTA CNCATG) (2), which contained l-(2'-deoxy-beta -D-ribofuranosyl)- 1,2,4-tria zole-3-carboxamide (N) in the center of the helix at position 14. The duple xes were compared to the canonical Watson-Crick duplexes, d(CATGGGTAC).d(GT ACCCATG) (3) and d(CATGTGTAC).d(GTACACATG) (4). Two-dimensional NOESY spect ra of 1-4 in H2O and D2O solutions collected at 5 degreesC allowed assignme nt of the exchangeable and nonexchangeable protons for all four oligodeoxyr ibonucleotides. Thermodynamic and circular dichroism data indicated that 1- 4 formed stable, B-form duplexes at 5 OC. Two-dimensional H-1-P-31 correlat ion spectra indicated that there were minor perturbations in the backbone o nly near the site of the triazole base. Strong NOESY cross-peaks were obser ved between the H5 and H1' of N14 in 1 and, unexpectedly, 2, which indicate d that, in both duplexes, N14 was in the syn(x) conformation about the glyc osidic 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 h ydrogen bond with N14. These conformations place the polar carboxamide func tional group in the major groove with motional averaging on the intermediat e time scale.