Programmed Self-Assembly of Functional DNA Nanostructures

Zhiyu Liu, Purdue University


Since the first introduction by Seeman in the early 1980s, structural DNA nanotechnology has been rapidly developed over the past three decades. Many advanced DNA self-assembly strategies are invented, which has been successful utilized for the construction of various one, two and three dimensional DNA nanostructures. Comparing to the considerably mature self-assembly methodology, the functionalities of DNA nanostructures are relatively underdeveloped. Hence, for the work of this thesis, we have focused more towards the integration of responsive functions with DNA nanostructures. Besides, we also have devoted effort to obtaining sub-nanometer level information on DNA double-crossover molecule, which is beneficial to the overall development of structural DNA nanotechnology. Firstly, we incorporated the idea of DNA nano-motor into DNA nanoparticles, which leaded to the construction and characterization of a “smart” DNA nanocage that could isothermally assemble/dissociate upon pH changes. This reversible assembly/dissociate strategy could be readily adapted for other DNA nanocages, for instance, DNA octahedron and icosahedron. The environment-responsive behavior would be important for potential applications of DNA nanocages, such as on-demand drug release. Secondly, we developed a step-wised strategy to assemble ATP-responsive, Russian doll-like, multi-layered DNA nanocages. The layer-by-layer assembly method provided a generally compatible solution for achieving high structural complexity. It could also be readily applied to other DNA nanostructures, including DNA origami and single-stranded-tile structures. Additionally, the ATP-responsive ability of the DNA nanocages was demonstrated to function efficiently at biologically relevant ATP concentration. Hence, such stimuli-responsive property suggested a way for controllable release of cargos enclosed in nanocages. Thirdly, we came up with a method to report transient molecular events by specialized DNA strand displacement. DNA triplexes are involved in some biological processes, for example, gene expression activity. Yet, the C-containing DNA triplex exists at low concentration with a short lifetime in the cells, making its detection a great challenge. We addressed such issue by applying the strategy of conditioned strand displacement, which coupled the triplex formation with a DNA strand displacement reaction. The developed method was proved to be able to detect DNA triplex formation at wide pH range. Lastly, we assembled and characterized a rationally designed DNA crystal which used double-crossover (DX) motif as basic building block. Upon successfully solving the X-ray crystal structure, we were able to obtain sub-nanometer level structural information of DX motif. Such information provided the field with better understanding of DX motif, which was useful for the development of advanced DNA self-assembly strategies. For instance, a super-helical feature hidden in the network of DNA lattice was first identified, which helped explain how DNA molecules compromised internal stress.




Mao, Purdue University.

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