A series of dideoxyribonucleoside methylphosphonates, d-ApA, d-ApT, d-TpA, and TpT, were synthesized chemically and the diastereoisomers of each dimer were separated [Miller, P. S., Yano, J., Yano, E., Carroll, C., Jayaraman, K., & Ts'o, P. O. P. (1979) Biochemistry 18, 5134]. The 1H NMR spectra of these compounds are similar to those of their parent diester compounds. Specifically, the assignments of the 1H resonances of the two diastereoisomers of d-ApA (designated as 1 and 2) were reaffirmed by comparing with the unmodified, parent d-ApA. The absolute configuration of the phosphonate methyl group of the two isomers (d-ApA)1 and (d-ApA)2 was determined by the NOE technique. The 1H NMR spectra of the diastereoisomers of d-ApA, as well as the corresponding monomer components dAp and CH3pdA, and TpT were analyzed by spectrum simulation techniques. Thus, all the coupling constants and chemical shifts of the proton resonances of the deoxyribofuranose ring and the phosphonate methyl group could be precisely determined. These data provide the information for an analysis of the sugar puckering and backbone conformations of these novel nonionic nucleic acid analogues. It was found that the conformations of the sugar-phosphate backbones of each isomer are similar to each other and are similar to the conformations of the parent dinucleoside monophosphates. The average adenine stacking conformations of (d-ApA)1 and (d-ApA)2 were described in numerical coordinates derived from a computer analysis which included both ring-current magnetic anisotropy and atomic diamagnetic anisotropy effects. The two computer-derived conformational models are similar to those derived from the graphic approximation based only on the ring-current effects. For each pair of dimer analogues, the base stacking mode of isomer 1 is similar to that of its parent diester while the extent of base overlap in isomer 2 is less than that in isomer 1. The results of the conformational analysis based on NMR data are consistent with the results obtained from ultraviolet and circular dichroism measurements on these dimers.