Peptide nucleic acid amphiphiles (PNAA) are a promising set of materials for sequence-specific separation of nucleic acids from complex mixtures. To implement PNAA in micellar separations, the morphology and size of PNAA micelles in the presence and absence of a sodium dodecyl sulfate (SDS) cosurfactant have been studied by small-angle X-ray scattering and dynamic light scattering. We find that a 6-mer PNAA with a 12-carbon n-alkane tail forms ellipsoidal micelles (a = 5.15 nm; b = 3.20 nm) above its critical micelle concentration (CMC) of 110.9 mu M. On addition of a stoichiometric amount of complementary DNA, PNAA hybridizes to DNA, suppressing the formation of PNAA micelles. At a ratio of 19:1 SDS/PNAA (total concentration = 20 mM), spherical micelles are formed with outer radius R-s = 2.67 nm, slightly larger than spherical micelles of pure SDS. Capillary electrophoresis studies show that PNAA/DNA duplexes do not comicellize with SDS micelles. No such effects are observed using noncomplementary DNA. The shape and size of the PNAA micelles is also verified by dynamic light scattering (DLS) studies. These results provide an interesting case study with competing electrostatic, hydrophobic, and hydrogen-bonding interactions in micellar systems and make possible the use of PNAA in micellar separations of DNA oligomers.