This work describes the synthesis and characterization of a new family of DNA amphiphiles containing modified nucleobases. The hydrophobicity was imparted by the introduction of a dodec-1-yne chain at the 5-position of the uracil base, which allowed precise and simple tuning of the hydrophobic properties through solid-phase DNA synthesis. The micelles formed from these modified DNA sequences were characterized by atomic force microscopy, dynamic light scattering, and polyacrylamide gel electrophoresis. These experiments revealed the role of the quantity and location of the hydrophobic units in determining the morphology and stability of the micelles. The effects of hybridization on the physical characteristics of the DNA micelles were also studied; these results showed potential for the sequence-specific noncovalent functionalization of the self-assembled aggregates.