Bilayers of palmitoyl-oleoylphosphatidylnucleoside derivatives (1-palmitoyl-2-oleoyl-phosphatidyl-adenosine and 1-palmitoyl-2-oleoyl-phosphatidyl-uridine) were synthesized and investigated in the low-water content regime by a combination of neutron diffraction and Fourier transform infrared linear dichroism (LD-FTIR). Attention was focused on the modulation of structural properties operated by the presence of nucleic acid bases (either adenosine or uridine, a purine and a pyrimidine that are complementary in RNA). Base substitution causes major differences in phase behavior of the phospholipids, i.e., water sorption from a controlled humidity atmosphere and smectic periodicity. The profile of scattering length density can be inferred from five diffraction orders for 1-palmitoyl-2-oleoyl-phosphatidyl-uridine lamellar phase. 1-Palmitoyl-2-oleoyl-phosphatidyl-adenosine is characterized by lower and less ready hydration, giving rise to a powder-like sample. A linear dichroism FTIR investigation on the same lamellar phases was undertaken with the purpose of gathering details at the submolecular level on different portions of the molecule. 1-Palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine bilayers were also investigated with the same technique for the sake of comparison. Besides a confirmation of the diffraction data interpretation, FTIR has provided evidence that the same chemical groups at the bilayer interface (namely the sugar-phosphate) have a different orientation depending on whether the base is a purine or a pyrimidine. A very simple geometrical optimization agrees with this observation. This indicates that a different pattern of base interaction is operating in the two cases and that base substitution acts as a modulator of the phase properties.