Design and fabrication of DNA origami mechanisms and machines

Abstract

The goal of this paper is to introduce scaffolded DNA origami as a viable approach to the design of nanoscale mechanisms and machines. Resembling concepts of links and joints in macro scale mechanisms and machines, we propose the concept of DNA Origami Mechanisms and Machines (DOMM) that are comprised of multiple links connected by joints. Realization of nanoscale machines would pave the way for novel devices and processes with potential to revolutionize medicine, manufacturing, and environmental sensing. The realization of nanoscale machines and robots will enable scientists to manipulate and assemble nano objects in a more precise, efficient and convenient way at the molecular scale. For example, DNA nanomachinery could potentially be used for nano manufacturing, molecular transport in bioreactors, targeting cancer cells for drug delivery, or even repairing damaged tissue. As a proof of concept, we build a nanoscale spatial Bennett 4-bar mechanism that can be completely folded and unfolded with a specified kinematic motion path. The links comprise a 16 double stranded DNA (dsDNA) helices bundled in a 4 by 4 square cross-section yielding a high mechanical stiffness. The joints (in this case hinges) are designed using single strand DNA (ssDNA) connections between the links. This DOMM was designed within caDNAno, a recently developed computer-aided DNA origami design software, and then fabricated via a molecular self-assembly process. The resulting structure was imaged by transmission electron microscopy to identify structural conformations. Our results show that the designed DNA origami Bennett mechanism closely follows the kinematics of their rigid body counterparts. This research has the potential of opening a new era of design, analysis and manufacture of nanomechanisms, nanomachines and nanorobots. © Springer-Verlag 2012.