DNA barrel nanostructure - a programmable building block for hierarchical self-assembly

Abstract

DNA nanostructures with complex structures and functions are emerging as promising tools for realising new applications, such as nanorobotics and advanced materials. To date, the complexity achieved is still limited, due to shortcomings associated with current self-assembly methods. This thesis presents a new assembly scheme to build more complex nanostructures. DNA barrel nanostructures were used as 3D voxels to build up superstructures. A literature nanostructure design was adopted and improved for use in the proposed hierarchical assembly strategy. Modified barrel nanostructures (referred to as DNA origami brick or DOB) have two-barrel subunits connected laterally. An additional lateral connection motif was developed to assemble DOBs in 2D x-y dimensions. An assembly line (AL) was developed to build arbitrary superstructures using DOB building blocks. The designed lateral motif was used for all x-y connections, while assembly in the z-direction was accomplished utilising a literature connection motif. The proposed AL comprised three integrated modules: 1/shape design, 2/sequence design, and 3/assembly protocol design. Arbitrary 2D and 3D assemblies were successfully built using the proposed AL. Additional analysis (such as particle averaging) was carried out to validate structural features of built superstructures against AL predictions. Structural switching was integrated into DOB units for potentially achieving even more complex superstructures. A motif was designed to reversibly transform DOB units between coaxial and lateral stage upon triggering using strand displacement reactions. The transformation was successfully facilitated by DNA dissociation and hybridisation, to disrupt and form different connections, respectively. An additional stimulation was proposed based on nanoparticle heating effects when iron oxide or gold nanoparticles were exposed to radio-frequency (RF) fields or waves. Preliminary results showed RF energy from an alternating magnetic field is a potential trigger stimulus.