Phosphatidyl-nucleosides are a class of functional amphiphiles, where a nucleic acid monomer is conjugated to a lipid skeleton. These derivatives self-organize in aqueous solution as assemblies of various size, shape, and interfacial curvature. This paper presents a comparison of the aggregation behavior of different 1-R,2R-sn-glycero-3-phosphatidyl-nucleosides, where R = 8 (DiC(8)PN) or R = 12 (DLPN) and N is either adenosine (a purine) or uridine (a pyrimidine), a complementary pair in RNA. Surface tension, small angle neutron scattering, cryo-TEM, and circular dichroism are used to highlight and distinguish the impact of the hydrophobic assembler and of the base substitution on the solution phase behavior. Our main conclusion is that the nucleic functionalization provides an additional parameter to control self-assembly through specific interactions among the polar heads. Further nonideal effects are induced by mixing nucleolipids with complementary base substitution. We show that these contributions alter the aggregation thresholds and modulate properties of the aggregates on the mesoscale.