Design of DNA Origami Machines and Mechanisms

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This research award provides funding for the development of a systematic design framework for nanoscale machines and mechanisms using DNA origami nanotechnology. DNA origami enables construction of two and three-dimensional nanoscale shapes with unprecedented geometric complexity via molecular self-assembly. The majority of DNA origami research focuses on assembly of static 2D or 3D structures. The goal of this work is to incorporate functional dynamic parts with directed motion into the DNA origami design toolbox. To achieve this goal, a kinematics approach will be implemented to design DNA origami machines and mechanisms that are comprised of links and joints, similar to macroscale machines. A catalogue of various DNA origami links and joints will be designed and fabricated, and their mechanical properties will be characterized experimentally and by molecular simulation. These links and joints will be implemented in the design of prototype mechanisms for proof-of-principle studies. A new theory called projection kinematics will be developed to evaluate the three-dimensional motion of these prototype mechanisms from two-dimensional electron microscopy snapshots. To facilitate future application of DNA origami machines, a computer aided design and simulation program will be developed that facilitates conceptual mechanism design and automates the integration of DNA origami links and joints from the previously developed part catalogues. If successful, this research will greatly advance the fields of DNA nanotechnology, nanoscale design, and nano-robotics. The machines and mechanisms developed in this work together with nanoactuators and controllers will enable design of future nanorobots for applications in numerous fields such as self-assembling computers and chemical compounds, nano-manufacturing, molecular transport in bio-reactors, and drug delivery. This work also opens the door for applying kinematic design to DNA nanotechnology. The computer design automation software developed in this research will greatly facilitate the widespread use of DNA origami mechanisms and machines.