Gene therapy using non viral vectors remains a challenging problem of maximizing efficiency while minimizing risks due to the multiple biological hurdles for a carrier agent to deliver its genetic cargo. The precise connection between the physical properties of the vectors and their transfection behaviors remains to be fully realized. We have used atomic force microscopy as well as dynamic light scattering and zeta potential measurements in order to image and characterize DNA complexes with polyethylenimine (PEI), histidine-lysine (HK) peptide, and triethylenetetramine (TETA)-functionalized gold nanoparticles. The resulting complex structures are analyzed as a function of amine to phosphate (N/P) ratios and as a function of sample preparation protocols. This work aims to not only characterize these specific complexes, but to aid in the general understanding of complex formation and how it relates to transfection observations to promote a more rational design of future gene delivery agents.