Self-assembly of Geometrically Well-defined 3D DNA Nanotubes: Stimuli-triggered Conformation Changes and Aptamers-derived Multiplex Detection


Student thesis: Doctoral Thesis

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Award date27 Feb 2018


DNA, as the main carrier of genetic information, has been exploited extensively in the field of nanotechnology. The specific molecular recognition between bases, the predictable and programmable hybridization between complementary strands and the ease in chemical synthesis and modification have made DNA an extremely attractive building block in the bottom-up fabrication of advanced 3D nanostructures. Besides, through the introduction of stimuli-responsive components into DNA strands, self-assembled DNA nanostructures exhibited controllable responsiveness to various external stimuli, such as pH, metal ions, small molecules, DNA strands and proteins. However, those conventional stimuli suffered from drawbacks such as the accumulation of waste in systems, which finally would hamper or halt the functioning of the system. Light, as a clean stimulus, could overcome the above drawbacks. Here, we demonstrated in our work that the morphology or conformation changes of self-assembled well-defined DNA nanotubes could be finely controlled by light. This was realized through the incorporation of light-responsive moieties into DNA strands which were further used to assemble DNA nanotubes. By introducing o-nitrobenzyl moieties, we could use two-photon excitation to trigger the conformation changes of DNA nanotubes. This process was irreversible. However, if we incorporated azobenzene moieties into the DNA nanotubes, we could reversibly switch the morphologies of the assembled DNA nanotubes with light of different wavelengths. Here, light was an ideal stimulus as it would not introduce exogenous materials into systems or interrupt the function of systems. On the other hand, introducing other functionalities into DNA nanostructures usually brought about separation and purification problems. DNA aptamers were free from those hurdles because they were intrinsically fragments of short DNA strands. Meanwhile, DNA aptamers also had the advantages of high specificity and affinity for targets. Thus, the integration of DNA aptamers into DNA nanostructures was naturally a desirable choice in many tasks, including detection, sensing and delivery. We integrated three different DNA aptamer sequences into the same DNA nanotubes, and achieved the simultaneous detection of three different molecular targets which included thrombin, insulin and ATP. We demonstrated the platform was sensitive and accurate in discriminating different targets and easy for fabrication and generalization. We believe, our work added credits to the rapidly developed field of DNA nanotechnology and their implementation in performing multiple delicate tasks.