Herein, we report the preparation of nucleobase-containing synthetic amphiphilic diblock copolymers using RAFT polymerization. Well-defined spherical micelles can be formed in aqueous solutions through the self-assembly of the amphiphilic copolymers, with the nucleobase functionality sequestered in the core of the particles. Following assembly, copolymers with the complementary nucleobase were introduced into the preformed micellar solutions. This addition induced a change in nanostructure size and morphology and this reorganization was fully characterized by DLS, TEM, SLS and SAXS analysis. The insertion of copolymers with the complementary nucleobase into formed micelles was also confirmed by 1H NMR and UV-vis spectroscopy. For micelles consisting of moderately short hydrophobic blocks, upon the addition of complementary nucleobase copolymer a decrease in size was observed but without any accompanying morphological change. For micelles formed from longer hydrophobic blocks, a morphological transition from spheres to cylinders and then to smaller spheres was observed upon increasing the amount of the complementary copolymer. This work highlights how complementary nucleobase interactions can be used to induce nanostructure reorganization and through a simple mixing process provide access to different nanostructure sizes and morphologies.