DNA-based nanotechnology has been propelled by the use of DNA molecules as the building blocks or the templates for controllable nanostructures. To control the higher-level organization of DNA molecules remains to be a challenge in nanotechnology. DNA condensation induced by the presence of multivalent cations is considered as an approach to attain ordered DNA structures.
In this study, PAMAM dendrimer was used as the condensing agent. The self-assembly behavior of the complexes of DNA with fully surface-protonated poly(amidoamine) (PAMAM) dendrimer of generation four as a function of the overall complex composition. The complex composition (x) was expressed by the molar ratio of the positively charged ammonium groups in the dendrimer to the DNA base pairs. The complexation was found to result in DNA condensation through which the dendrimer-bound DNA chains aggregated significantly to form ordered structures. A condensed nematic phase in which the locally oriented DNA chains did not exhibit coherent positional order formed at x = 2. Although the numbers of positive and negative charges were identical at this composition, the charge matching was frustrated by the DNA-DNA repulsion which limited the number of DNA chains surrounding each dendrimer molecule. Therefore, the nematic mesophase was built up by the irregularly packed square columnar cells (with each dendrimer molecule surrounded by four DNA chains in each cell), yielding defective DNA networks with the average interhelical distance of 4.2 nm. A significant fraction of the phosphate groups on the DNA chains in the network remained unbound to the dendrimer due to limited supply of dendrimer molecules. The condensed DNA structure transformed into a long-range ordered square columnar phase with the interhelical distance of 4.25 nm at x = 4.0. Here the number of dendrimer became abundant enough to maximize the charge matching for the DNA chains, and the interconnection of the square columnar unit cells led to a long-range ordered lattice.
We also demonstrate the coupling between the phenomenon of DNA condensation and the concept of DNA-templated NP assembly to prepare spatially organized nanowires with pearl-chain morphology. Electrostatic complexation of gold NP-embedded dendrimers with DNA brought about the condensation of the dendrimer on DNA and a spontaneous aggregation and ordering of the DNA chains, yielding nanowires with nematic order in thin film and bulk state. The present study revealed a bio-templating approach for fabricating nanostructured materials exhibiting special properties.
Finally, a highly ordered dense DNA array on rubbed polyimide film was prepared. AFM images showed two-dimensional dense arrays for both linear and calf thymus DNA. We attributed the ordering to be driven by the condensation of DNA on rubbed polyimide. However, only DNA molecules on polyimide film within ca. 1.0 nm in thickness could be aligned. DNA molecules distant from the interface could hardly be affected by the rubbed polyimide. In addition to stretched DNA molecules on the substrate, DNA bundles were also visible. These DNA bundles were mechanically stronger and they could provide more binding and nucleation sites for the assembly of NPs toward nanowire structure.

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