Pure absorption phase, proton two-dimensional nuclear Overhauser effect (2D NOE) and double-quantum-filtered COSY (DQF-COSY) spectra were recorded for d(AC)4.d(GT)4. A full proton resonance assignment was made, except for the 5' and 5" protons. A new semiautomatic method for improved quantitation of 2D NOE peak intensities was developed, and its limitations and usefulness were examined. With this new method, 2D NOE intensity sets at several mixing times were obtained. Simulations of the 1'2', 1'2", and 2'3' DQF-COSY cross-peaks were compared with experimental data, establishing an alternating sugar pucker for the alternating purine-pyrimidine sequence. Scalar coupling constants for the sugar ring protons, derived from the fitting of the simulated spectra, are reported. Complete relaxation matrix analysis of the 2D NOE spectrum verified this alternating structure for all NOE interactions between nonexchangeable protons. Both the DQF-COSY and the 2D NOE results qualitatively indicate that the structure of d(AC)4.d(GT)4 resembles wrinkled D-DNA in aqueous solution.