α-DNA-III. Characterization by high field1H-NMR, anti-parallel self-recognition and

Abstract

High field 2-D-¹H-NMR techniques permitted the assignment of all non-exchangeable protons of the unnatural deoxyribonucleotides α-[d(CpApTpGpCpG)] and α-[d(CpGpCpApTpG)]. 1-D and 2-D NOESY experiments show strong H₆H₈-H₄, dipolar interactions for all nucleotides in both sequences. These data, together with COSY and J-reseolved spectra, indicate that these two α-oligomers adopt 3'-exo conformations of the sugar moieties in solution with anti conformations of the glycosyl linkages. Both ¹H-NMR data, and hypochromicity comparison.of α-CATGCG and β-CATGCG, demonstrate a higher degree of base stacking in the case of the α-sequence. The UV hyperchromicity at 260 run, and symmetry considerations in the imino proton NMR experiments reveal antiparallel self-recognition and duplex annealing at positions 1–4 for α-[d(CATGCG)] and positions 3–6 for α-[d(CGCATG)] The temperature variation of the imino proton NMR signals suggests that the hydrogen bonding in self-recognition is comparable in strength with that in a β-DNA duplex, and NOE data are in accord with Watson-Crick rather than Hoogsteen base pairing.