"Alternating B-DNA" conformation for the oligo(dG-dC) duplex in high-salt solution.

Abstract

The high resolution 1H and 31P NMR spectra of the (dG-dC)8 duplex were recorded in low- and high-salt solutions to evaluate the structural aspects of the salt-induced transition of oligo(dG-dC) in solution. The NMR data require that the (dG-dC)8 duplex in 4 M NaCl adopt an alternating B-DNA conformation for which the symmetry unit repeats every 2 base pairs. The oligomer duplex in low-salt solution is of the regular B-DNA type in solution. The chemical shift parameters for oligo(dG-dC) in high-salt solution show that every other glycosidic torsion angle and phosphodiester linkage adopts a different conformation from that observed in regular B-DNA structure is facilitated by introduction of halogen atoms at the 5 position of pyrimidine; this probably reflects the greater overlap of this position with adjacent base pairs in high salt solution. An alternating B-DNA model was recently proposed for alternating deoxy purine-deoxy pyrimidine polynucleotides based on the X-ray structure of pdA-dT-dA-dT.