Improved DNA vaccine plasmids are disclosed. The improved plasmids eliminate all extraneous sequences, and have superior eukaryotic expression, improved yield and stability during bacterial production, facilitate flexible targeting of antigens to various intracellular destinations, and novel RNA-based functionality. These vectors are utilized in novel immunization methods wherein combinations of immunostimulatory DNA vaccine plasmids that target antigens to various intracellular destinations are used to elicit improved immune response.