Design of DNA Origami Machines and Mechanisms

This research introduces DNA origami as a viable approach to design and fabricate nanoscale mechanisms and machines. DNA origami is a recently developed nanotechnology that has enabled the construction of objects with unprecedented nanoscale geometric complexity via self-assembly. These objects are made up of thousands of DNA base-pairs packed into 3D structures with typical dimensions of 10–100nm. The majority of DNA origami research to date focuses on assembly of static 2D or 3D structures. In this work, we aim to extend the scope of DNA origami to include design of objects with kinematically constrained moving parts. Borrowing concepts from macro-scale kinematic mechanisms, we propose the concept of DNA Origami Mechanisms and Machines (DOMM) comprised of multiple links connected by joints. The links are designed by bundling double stranded DNA (dsDNA) helices to achieve the desired geometry and stiffness. The joints are designed by combining links with strategic placement flexible single stranded DNA (ssDNA) to enable motion in specific degrees of freedom. We detail design approaches for links and common joints including revolute, prismatic, and spherical, and discuss their integration into higher order mechanisms. As a proof of concept, we built a nanoscale hinge (revolute joint) and integrated four of these hinges into a prototype DOMM, namely a Bennett 4-bar linkage, which can be completely folded into a closed bundle geometry and unfolded into an open square geometry with a specified kinematic motion path. A kinematic analysis shows that the DNA Bennett linkage closely follows the 3D motion path of the rigid body counterpart. Our results demonstrate that DNA origami has high potential for the design and assembly of nanoscale machines. The ultimate goal of this work is to develop a library of nanoscale DNA-based links and joints that can be widely used in the design and assembly of higher order mechanisms and machines. We anticipate that, in the future, these components can be used to build nanorobots for useful applications including drug delivery, nanomanufacturing, and biosensing.