This article focuses on reactions performed in nanostructured environments where the pair of complementary nucleotides, 5¢-AMP and 5¢-UMP, are converted into their amphiphilic derivatives. The synthesis is carried out by using the hydrophobic reactant dodecyl epoxide (DE) dispersed in a micellar solution based on the cationic surfactant cetyltrimethylammoniumbromide (CTAB). Novel nucleo-lipids monomers and CTAB molecules give rise to the spontaneous self-assembly of catanionic supramolecular structures in water, showing typical Maltese crosses in optical microscopy. In the final colloidal suspensions, mono- and dichained derivatives have been identified in the system incubated with 5¢-UMP through LC-QqTOF-MS analysis, whereas only mono-alkylated adducts are found in the analogue reaction with 5¢-AMP. A new di-alkylated 5¢-UMP adduct is obtained from the 1:1 mixture of both complementary nucleotides, in addition to the nucleo-lipids found in separate systems. Time-resolvedDLSmeasurements reveal very different kinetic processes for aggregates’ formation when 5¢-UMP, 5¢-AMP, or their equimolar combination are used in the reaction mixture. This system as a whole represents a potential experimental model where the effect of both intermolecular interactions and self-association processes can be investigated by tuning the type of nucleobases in the reaction mixtures.