Formulation of nanoparticulate DNA vaccines requires the assessment of stability and integrity of the components implicated. Stability of cationic nanoparticles made of N-trimethyl chitosan and chondroitin sulfate (TMC nanoparticles) was investigated in aqueous solution and after freeze-drying by characterization of their size, polydispersity index (PDI), and zeta potential. Furthermore, the structural integrity of plasmid DNA (pDNA) on adsorption to the nanoparticle surface was investigated. Agarose gel electrophoresis showed DNA retention when applied with the nanocarrier, suggesting that pDNA adsorption on nanoparticles took place. In circular dichroism (CD) spectra, ellipticity of pDNA decreased at 280 nm and increased at 245 nm, and the maximum wavelength shifted from 275 nm to 285 nm when nanoparticles were present. Once released from the particles, the secondary structure of the plasmid was retained in its native form. pDNA release from pDNA-TMC nanoparticles was indicated by a rise in zeta potential from initially -32 mV (pDNA adsorbed to particles) to 14 mV during one hour, and to 36 mV after 24 hours. Unloaded TMC nanoparticles remained stable in suspension for 24 hours, maintaining diameters of around 200 nm, and zeta potential values of approximately 38 mV. Freeze-drying with sucrose could ensure storage for 30 days, with minimal increase in size (291 nm) and charge (62 mV). In conclusion, TMC nanoparticles may potentially be freeze-dried in the presence of sucrose to be stored for prolonged periods of time. Furthermore, pDNA was successfully adsorbed to the cationic nanoparticles and remained intact after being released.