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DNA Origami Machines and Mechanisms (DOMM)

Scaffolded DNA origami has enabled the fabrication of nanoscale objects with unprecedented geometric complexity via programmed molecular self-assembly with DNA. For an overview of the scaffolded DNA origami approach see Dr. Castro's paper. While this approach has been used to develop nanostructures for drug delivery, biosensing, and material templating applications, research to date has largely focused on fabrication of static (no motion) structures. In collaboration with the lab of Dr. Haijun Su, our lab is combining DNA-based design with macroscopic engineering approaches to make DNA origami machines and mechanisms. Similar to macroscopic machines, systems with complex motion can be constructed by combining joints and links into precisely designed mechanisms. We are first developing individual joints with constrained degrees of freedom. We have currently built revolute joints (hinges) with a single angular degree of freedom and prismatic joints (linear joints) with a single translational degree of freedom.

 A series of static TEM snapshots demonstrating the rotational motion of unconstrained DNA origami hinges Slider joint demonstrating linear motion. Scale bar = 50 nm

Using the joint designs from above, we have developed prototype mechanisms combining multiple joints for more complex motion. We created a mechanism with four hinges and four links, called a Bennett Linkage, that moves through a well-defined 3D motion path between a closed bundle and open frame configuration. In the absence of actuation, the mechanism passively fluctuates along the constrained motion path due to thermal fluctuation. The videos below shows a series of transmission electron microscopy (TEM) snapshots of the joints and mechanisms in several configurations along the motion path illustrating the motion.  We also created a crank slider mechanism coupling linear and rotational motion using hinges and linear joints. This mechanism moves freely in 2D and is demonstrated below. 

 

Crank slider mechanism coupling linear and rotational motion. Scale bar = 50 nm

We have further developed a method to actively control the motion of the mechanisms. Using single-stranded DNA overhangs (black) distributed across the mechanism, we add "closing" strands (green) to bind the overhangs and close the mechanism. We can open the mechanism again by adding "opening" strands (orange), which will remove the closing strands via strand displacement. Using a fluorescence quenching assay, we measured actuation times on ~minute timescales. Our work is establishing a foundation for the design of complex nanoscale machines with controllable motion that could be implemented for example in nanomanufacturing systems to assemble nanoscale objects.

Actuating DNA origami Bennett linkages using DNA hybridization and strand displacement. Controlled closing and opening occur on minute timescales. Scale bars = 100 nm. (PNAS, 2015)

 

Research Team: Alex Marras, Lifeng Zhou, collaboration with Dr. Haijun Su

 

For more info see:

Marras, A., Zhou, L., Su, H., and Castro, C.E. Programmable motion of DNA origami mechanisms in PNAS 2015 link. (pdf)

Castro, C.E., Su, H., Marras, A.E., Zhou, L., Johnson, J. "Mechanical Design of DNA nanostructures." Nanoscale 2015. link.

Marras, A.E., Zhou, L., Kolliopoulos, V., Su, H., Castro, C.E., "Directing folding pathways for multi-component DNA origami nanostructures with complex topology." New Journal of Physics. link.

Support - NSF Engineering and Systems Design (ESD) program

 

Also check out our related work on designing DNA origami compliant mechanisms