(563c) Reconfiguration, Manipulation, and Control of Higher Order Dynamic DNA Origami Assemblies

Over the last few decades DNA has garnered interest as a material for bottom-up- self-assembly of new devices and materials for various biological, mechanical, and chemical applications. DNA nanotechnology, specifically DNA origami, provides a platform that leverages Watson-Crick complementary base-pairing to design nanoscale devices with a pre-defined geometry capable of precise motion and controlled mechanical properties. The self-assembly process and tunable mechanical properties of DNA nanostructure components provides a framework to design dynamic nano devices capable of higher order assembly and reconfiguration. Methods have also been developed to reconfigure individual nanodevices into many different states, but to date the actuation of higher order assemblies is limited to simple reconfiguration like opening or closing of hinge joints. The most common approach to actuate reconfiguration in these devices is toe-hold mediated strand displacement, which relies on the formation or dissociation of specific DNA interactions that control the device conformation. While strand displacement is a robust method of actuation, limitations include the slow response time (minutes or greater) and the need to introduce strands into solution. To overcome these limitations recent efforts have established methods that leverage externally applied fields to manipulate structures. For example, recent efforts developed an approach to integrate magnetic microbeads for direct real-time manipulation of devices with sub-second time scales, tunable applied forces, and precise spatial resolution. However, actuating DNA devices with external fields has been limited to simple systems such as levers and hinges. This work seeks to enable direct manipulation of complex DNA nanodevice assemblies, in particular demonstrating actuation into many different states (i.e. assembly configurations), using DNA strand displacement, magnetic fields, and optical traps.

We employ scaffolded DNA origami (DO) for the fabrication of DNA assemblies. We designed these DO assemblies in the custom software MagicDNA, which enables the design of complex 3D assemblies on the order of minutes. Advanced 3D dynamic DO devices have expanded to larger scales through hierarchical assemblies that integrate many individual structures in a controlled way. Here, we present two reconfigurable higher order DO assemblies: 1) The 6-bar DO assembly demonstrates reconfiguration into many different conformations using DNA strand displacement and 2) the lattice DO assembly to demonstrate real-time assembly actuation with magnetic fields and optical tweezers.

The 6-bar DO assembly is a device comprised of 6-links with multiple strut regions that may lock the structure into pre-defined shapes. The struts may be displaced via DNA strand displacement and replaced to form a new shape. The free energies are explored to understand shape preference and used to guide the development of reconfiguration schemes. These shapes can polymerize into DO-tubes with stiff cross-sections using the same DNA strand displacement scheme as the individual devices. This work demonstrates higher order reconfiguration of a complex DO device is possible with DNA strand displacement understanding free energy of various states to guide tuning of structure and mechanical properties, which could enable tailoring of DNA assemblies for a variety of biological, chemical, or mechanical applications.

The latter portion of this work expands on the reconfiguration of higher order DO assemblies through external inputs. The primary lattice DO assembly is comprised of 4-links of a 3x4 cross-section of dsDNA helices with 16 ssDNA joint connections (4 per link) and a secondary lattice DO assembly comprised of 7-links with 6-links of a 3x4 cross-section of dsDNA helices and 1-link of a 2x6 cross-section with 32 ssDNA joint connections amongst the 7-links. Both lattice devices are designed with ssDNA overhangs in the corners of the joints that allow for actuation of the lattice, producing a more compact lattice structure. The actuation strands can also be decorated with fluorescent molecules and quenchers to provide a readout of the assembly configuration. Fluorometer results of the single-scaffold lattice show high efficiency of quenching of actuation strands resulting in successful actuation. Both lattice constructs are designed to polymerize into arrays when ssDNA polymerization strands are added. Our goal is to create micron-scale reconfigurable constructs that can be actuated via magnetic fields or optical trapping to expand the dynamic capabilities to DO to long-range micron-scale devices.

The reconfiguration and actuation of higher order DO assemblies provides tools for a variety of applications in the biological, chemical, and mechanical spaces. Creating bio-based tools for controlling more complex devices serving a foundation for nano-or micro-scale robotic systems provides platforms for multiplexing the control of nanomachines or molecular interactions. DNA strand displacement amongst large-scale DO assemblies shows local interactions among stiff DNA cross-sections can cause shape changes and external micron-bead actuation on DO lattice assemblies shows a level of spatiotemporal control for real-time manipulation of molecular systems. Investigating these actuation methods on higher order dynamic DO assemblies provides a basis for future actuation methods for nanoscale and micron-scale DNA constructs. Increased complexity of current actuation capabilities in the DNA nanotechnology space provides tools and methods spanning across multiple disciplines in engineering.