(295e) DNA Origami Tubes with Reconfigurable Cross-Sections | AIChE

(295e) DNA Origami Tubes with Reconfigurable Cross-Sections


Kucinic, A. - Presenter, Ohio State University
Castro, C. E., The Ohio State University
Huang, C. M., Duke University
Wang, J., Ohio State University
DNA nanotechnology has emerged over the last decades as a promising approach for various biological, mechanical, and environmental applications. The programmable nature of DNA bases provides a framework to construct nanoscale devices with complex geometry, precise motion, and controlled dynamic and mechanical properties. Dynamic devices in particular have emerged as promising tools for various biological, mechanical, and environmental applications such as biophysical measurement devices, nanorobotic components, triggered drug delivery vehicles, and nanobiosensors. The unique properties of DNA nanostructures also make them highly attractive for bottom-up assembly of materials with dynamically programmable properties. Hence, coupling across length scales, i.e. using individual devices on the molecular scale to make larger assemblies including microscale robotic systems and materials, is an exciting avenue for DNA nanotechnology. There have been major advances over the last decade in higher order assembly of DNA structures, including recent efforts to make reconfigurable arrays and lattices; however, the dynamic behavior of these assemblies remains limited compared to the major advances in complexity of individual devices. Here our goal is to provide an approach using dynamic DNA devices capable of reconfigurable higher order assembly to advance the complexity of reconfigurable arrays and lattices on a larger scale.

We leverage scaffolded DNA origami (DO), which is a molecular self-assembly approach where many short single-stranded DNA (ssDNA) oligos, referred to as “staples,” bind with a long ssDNA strand of a known sequence called a “scaffold.” The staples bind to the scaffold using Watson-Crick complementary base-pairing in precise locations to create double-stranded DNA (dsDNA) regions that fold into precisely designed shapes. Early work on DO structures focused on static structures and shapes, whereas more recent work on dynamic DO structures include motion or actuation to increase complexity. Advanced 3D dynamic devices include objects with 1D motion such as hinges or pistons, and mechanisms with more complex motion such as crank-sliders or Bennet linkages with programmed kinematic motion or actuation capabilities. A number of recent efforts have expanded DO to larger scales through hierarchical assemblies that integrate many individual structures in a controlled way, and prior efforts have demonstrated integration of reconfigurable constructs into arrays. However, the reconfiguration of higher order assemblies remains quite simple to 1D rotation and only open-to-close reconfiguration. Therefore, we developed a reconfigurable 6-component DNA origami mechanism, the 6-bar, that can be reconfigured into multiple shapes (Figure 1A) and assembled into linear arrays (Figure 1C) with different cross-sections. Our goal is to demonstrate the reconfiguration of DO shapes into a variety of stiff cross-sections and demonstrating the reconfiguration of DO tubes between several distinct cross-section shapes.

The 6-bar consists of 6 arms or links, consisting of 12 double-stranded DNA (dsDNA) helices arranged in a 3x4 square lattice cross section. These 6 bundles are connected via ssDNA hinges to form a closed-loop mechanism. The “free” state is flexible and contains 172 nucleotide (nt) scaffold loops on each bundle. These scaffold loops are present to enable the formation of struts that connect neighboring components at a specific angle to determine the shape of the mechanism. The struts can create bundle angles of 60°, 90°, 120°, and 180° (Figure 1A). Each folded configuration contains three full struts, and all the staples comprising the struts contain overhanging ssDNA extensions to serve as toe-holds for toe-hold mediated strand displacement (TMSD). Each configuration can thus reconfigure back to the free (i.e. no strut) state with the use of TMSD, and then to a different geometry through the addition of new strut strands. Figure 1B illustrates a transition between an open rectangle to a flat closed geometry with high efficiency of reconfiguration. Reconfiguring the individual 6-bar devices provides a basis for reconfiguring higher-order assemblies. We expand the reconfiguration to polymer “tubes” with the same reconfigurable cross-sections. We can assemble these DO polymers into several different cross-section shapes (Figure 1C). These polymers allow us to bridge the gap between individual device reconfiguration to multi-device reconfiguration.

In addition to demonstrating reconfiguration of individual devices and tubes, the 6-bar provides an interesting platform to study free energy differences of the various conformations that only vary by the composition of the struts. Introducing different sets of strut staples to the free (i.e no strut) state allows us to analyze the preferred, or stable, configurations. Exhibiting reconfiguration between multi-states also allows us to study the energetics between the open to closed loop structures. We expanded this idea to structural tuning of the interactions as an approach to control formation of higher order assemblies such as tubes with varying cross-sections across the length. Studying the energetics of the higher order assemblies may provide new ways to control assembly to create more complex reconfigurable DO structures.

This work expands upon molecular motors and machines to include nanoscale and micron-scale mechanisms. The 6-bar mechanism and 6-bar polymers could be used to organize components over a micron length-scale or create assemblies with inhomogeneous properties. DNA origami includes many applications such as drug delivery, signal transmission, and biological mechanisms, however has expanded broadly to many different fields outside of biology. Using DNA as a material to construct mechanisms studied in fields such as chemical, mechanical, and bio-engineering has been an amazing advancement provided the biological nature and application of DNA.

Figure 1: A. (left) Course-grain molecular dynamic simulations of 6-bar mechanism. (right) Transmission electron microscope (TEM) image averages of each 6-bar configuration (scale bar = 50nm). B. (left) Reconfiguration schematic. (right) TEM images at each step of reconfiguration with image average insets (scale bar = 50nm). C (top) 6-bar polymer schematics and (bottom) TEM images of the rectangular and compact configurations (scale bar = 100nm).