Conformations of Nucleoside Analogue 1-(2‘-Deoxy-β-d-ribofuranosyl)-1,2,4-triazole-3-carboxamide in Different DNA Sequence Contexts

• Published in: Biochemistry (Easton) Vol. 40; no. 6; pp. 1518 - 1527
• Main Authors: Klewer, Douglas A, Zhang, Peiming, Bergstrom, Donald E, Davisson, V. Jo, LiWang, Andy C
• Format: Journal Article
• Language: English
• Published: United States American Chemical Society 13-02-2001
• Subjects: 1-(2'-Deoxy-^b-D-ribofuranosyl)-1,2,4-triazole-3-carboxamide; Amides - chemistry; Base Pairing; Circular Dichroism; Glycosides - chemistry; Hydrogen Bonding; Nuclear Magnetic Resonance, Biomolecular; Nucleic Acid Conformation; Nucleic Acid Heteroduplexes - chemistry; nucleoside analogs; Oligodeoxyribonucleotides - chemistry; Phosphorus Isotopes; Protons; Ribavirin - analogs & derivatives; Ribavirin - chemistry; Sequence Analysis, DNA; Temperature; Thermodynamics
• ISSN: 0006-2960; 1520-4995
• DOI: 10.1021/bi001448f

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-triazole-3-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.