A novel difunctional alkoxyamine initiator, DEPN2, was synthesized and utilized as an efficient initiator in nitroxide-mediated controlled radical polymerization of triblock copolymers. Complementary hydrogen-bonding triblock copolymers containing adenine (A) and thymine (T) nucleobase-functionalized outer blocks were synthesized. These thermoplastic elastomeric block copolymers contained short nucteobase-functionalized outer blocks (M-n similar to 1K-4K) and n-butyl acrylate rubber blocks of variable length (M-n similar to 14K-70K). Hydrogen-bonding interactions were observed for blends of the complementary nucleobase-functionalized block copolymers in terms of increased specific viscosity as well as higher scaling exponents for specific viscosity as a function of solution concentration. In the solid state, the blends exhibited evidence of a complementary A-T hard phase, which formed upon annealing, and dynamic mechanical analysis (DMA) revealed higher softening temperatures. Morphological development of the block copolymers was studied using SAXS and AFM, which revealed intermediate interdomain spacings and surface textures for the blends compared to the individual precursors. Hydrogen-bonding interactions enabled the compatibilization of complementary hydrogen-bonding guest molecules such as 9-octyladenine.