A novel nanostructure was constructed using two different generations of polyamidoamine (PAMAM) dendrimers and three sets of complementary oligonucleotides (34, 50, and 66 bases in length). The oligonucleotides were covalently conjugated to partially acetylated generation 5 and 7 PAMAM dendrimers, and these conjugates were characterized by agarose gel electrophoresis. The agarose gel electrophoresis appearance of these covalently linked oligonucleotide dendrimers was also compared to electrostatically bound oligonucleotide-dendrimer complexes. Equimolar amounts of the G5 and G7 conjugates were then hybridized together to allow for the DNA-directed self-assembly of supramolecular clusters. Dynamic light scattering (DLS) analysis indicated that the overall size of the DNA-linked dendrimer clusters tended to increase according to the length of the oligonucleotide used ranging from 30 to 50 nm, which agreed with the diameter of dendrimer nanoclusters predicted by molecular modeling. The DNA-linked novel dendrimer nanoclusters were also examined with tapping-mode atomic force microscopy (AFM) to distinguish the DNA-linked structure from a nonlinked simple G7/G5 dendrimer mixture. AFM image analysis suggested that the distance between the DNA-linked dendrimers was significantly larger than what was seen after simple mixing of G7/G5 dendrimers. The mixture showed a few dendrimers physically in contact with an interdendrimer distance of 8-10 nm. The interdendrimer distance of the nanoclusters linked with the 50-base-long oligonucleotide pairs was measured to be 21 ± 2 nm, which is in agreement with the theoretical length of the oligonucleotides duplex. These results suggest that PAMAM dendrimers can be self-assembled via complementary oligonucleotides to form supramolecular nanoclusters.