α-DNA-V. Parallel annealing, handedness and conformation of the duplex of the unnatural α-hexadeoxyribonucleotide α-[d(CpApTpGpCpG)] with its β-complement β-[d(GpTpApCpGpC)] deduced from high field1H-NMR

Abstract

The β-complementary hexamer, β-d[GTACGC], to the α-sequence, α-d[CATGCG], was synthesized by the phosphotriester method. The non-exchangeable proton assignments were obtained using 1D- and 2D-NMR techniques, including NOE, COSY and NOESY. The β-strand exists as a random coil at 21°C, however, at 4°C, it forms an antiparallel self-recognition duplex annealing at positions 1–4. The β-strand was annealed to the α-strand, and confirmation of complete annealing was obtained by detection and assignment of the six base pair imino protons in H²O/D²O solution at 21°C. 1D-NOE experiments of the α, β duplex d [ α- (CATGCG) β- (GTACGC) ] reveal that (i) it exists in aqueous solution in a conformation that belongs to the B family, (ii) it is 70±10% right-handed, (iii) the sugar-base orientations of the β-strand are anti, and the deoxyribose units exist predominantly in the 2'-endo-3'-exo conformation, NOE measurements of the imino proton signals in the α, β duplex reveal that the duplex exhibits parallel polarity.