Browsing by Author "Kuzyk, Anton, Assoc. Prof., Aalto University, Department of Neuroscience and Biomedical Engineering, Finland"
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Item DNA-BASED STIMULI-RESPONSIVE NANOTECHNOLOGY AND MATERIALS(Aalto University, 2023) Ryssy, Joonas; Neurotieteen ja lääketieteellisen tekniikan laitos; Department of Neuroscience and Biomedical Engineering; Molecular Nanoengineering; Perustieteiden korkeakoulu; School of Science; Kuzyk, Anton, Assoc. Prof., Aalto University, Department of Neuroscience and Biomedical Engineering, FinlandThis thesis is a study of various stimuli-responsive DNA-based systems. The systems presented here take advantage of the advances in DNA nanotechnology to provide plasmonic outputs due to structural reconfiguration in response to external stimuli. DNA is a versatilebiomolecule with responsiveness to specific environmental cues. We utilized three different environmental cues, pH, light, and small molecules, to induce structural changes in the designed system that led to changes in the gold nanorod-based plasmonic outputs. First, the inherent pH-responsiveness of DNA was used in the form of Hoogsteen bonding and triplex self-assembly. The triplex self-assembly was coupled with a structural reconfiguration of DNA origami-based chiral plasmonic metamolecules. When formed, the triplex acted as a bridge to bring forth an intense chiral plasmonic state. The state of the triplex was controlled through a photoresponsive medium containing protonated merocyanine, MCH+. Therefore, a DNA-based chiral plasmonic system could be rapidly actuated with external visible-light stimulus without any light-responsive modifications on the DNA itself. Next, we brought DNA nanotechnology towards macro-scale applications by conjugating DNA-functionalized gold nanorods into synthetic polymer networks to create a hybrid DNA hydrogel. Here, gold nanorods did not only act as plasmonic optical reporters but also as stimuli-responsive elements. The gold nanorods were designed to absorb light in the visible-light spectrum's red region and act as heating elements. The inherent thermoresponsiveness of DNA was used to implement dynamic reversible light responses into the hydrogel system. The external visible-light stimulus provided an inexpensive, robust, spatial, and waste-free method to trigger structural changes. The hybrid hydrogel exhibited reversible plasmonic optical output in the form of visible colors. Third, we introduced DNA origami-based chiral plasmonic metamolecules functionalized with DNA aptamer bridges between the origami arms as a sensing platform. The binding of a target to the duplexed aptamer bridge brought structural changes that affected the gold nanorod-mediated chiral plasmonic signal. By adequately screening the reference analytes and complementary strand designs, the platform was utilized to characterize aptamer-target affinity. Overall, this thesis highlights the utility of DNA for the fabrication of nanostructures and materials with programmable stimuli responses.Item Nucleic Acid Nanostructures - Design, Reconfigurability, and Applications(Aalto University, 2023) Natarajan, Ashwin Karthick; Kuzyk, Anton, Assoc. Prof., Aalto University, Department of Neuroscience and Biomedical Engineering, Finland; Neurotieteen ja lääketieteellisen tekniikan laitos; Department of Neuroscience and Biomedical Engineering; Molecular Nanoengineering group; Perustieteiden korkeakoulu; School of Science; Kuzyk, Anton, Assoc. Prof., Aalto University, Department of Neuroscience and Biomedical Engineering, FinlandSelf-assembly with near-atomic precision forms the basis for synthesizing biological structures found in living cells. These self-assembled structures retain the accuracy across sizes ranging from nanometers to macroscopic scale by exploiting the information encoded in the biomolecules. The fabrication of complex 3D synthetic molecular structures with such precision and controllability is cumbersome. Nucleic acid nanotechnology eases this process by enabling bottom-up construction of well-defined nanoscale objects through the predictability and programmability of interactions within DNA and RNA. The design, reconfigurability and a potential application of such nucleic acid nanostructures are presented in this thesis, which is based on three publications. Publication I presents a highly general and automated approach for the design and assembly of 3D RNA wireframe polyhedral nanostructures. Grounded on the principles of spanning tree-based strand routing, the method renders the target 3D wireframe structure as a single-stranded RNA. The output RNA sequence can be readily transcribed from the corresponding DNA template and assembled into the intended shape. As case examples, the design of three RNA polyhedral models: a tetrahedron, a triangular bipyramid, and a triangular prism were experimentally realized. The developed design pipeline is not restricted to polyhedral models and can be used to render arbitrary straight-line 3D meshes as RNA strands. Publication II and Publication III focus on the DNA origami approach to fabricate dynamic nanostructures. Publication II presents a reconfigurable chiral plasmonic molecule (CPM) that can be modulated remotely using visible light. The native CPMs are non-responsive to light but can change their spatial configuration by forming DNA triplex locks upon a decrease in the solution pH. To this end, a merocyanine-based photoacid was utilized as a photoresponsive medium that decreases the pH upon exposure to visible light. The chiral response from the CPMs was thus modulated by the intensity of the incident light, which alters the pH. By tuning the intensity, distinct steady out-of-equilibrium states were achieved, both in the pH and in the chiral response. In Publication III, the precise positioning capability and reconfigurability of the DNA origami technique were exploited. A DNA-origami-based device was fabricated to investigate DNA bending induced by TATA-binding protein. This bending was translated into an angular change in the DNA origami structures directly observable using a transmission electron microscope. Further, the role of transcription factors II A and II B in DNA bending was investigated. Our approach can be readily expanded to other DNA-distorting proteins with careful design considerations.Overall, this thesis contributes to various facets of nucleic acid nanotechnology from design to reconfigurability to applications. In essence, the findings presented in the individual sections illustrate that nucleic acid nanotechnology still has a large unexplored design space, novel switching mechanisms, and under-explored applications.