Programmable Assembly of Nano-architectures through Designing Anisotropic DNA Origami Patches

Programmable assembly of nanoparticles (NPs) into well-defined architectures has attracted attention because of tailored properties resulting from coupling effects. However, general and precise approaches to control binding modes between NPs remain a challenge owing to the difficulty in manipulating the accurate positions of the functional patches on the surface of NPs. Here, a strategy is developed to encage spherical NPs into pre-designed octahedral DNA origami frames (DOFs) through DNA base-pairings. The DOFs logically define the arrangements of functional patches in three dimensions, owing to the programmability of DNA hybridization, and thus control the binding modes of the caged nanoparticle with designed anisotropy. Applying the node-and-spacer approach that was widely used in crystal engineering to design coordination polymers, patchy NPs could be rationally designed with lower symmetry encoded to assemble a series of nano-architectures with high-order geometries.     

Tunable DNA Origami Motors Translocate Ballistically Over μm Distances at nm/s Speeds

Inspired by biological motor proteins, that efficiently convert chemical fuel to unidirectional motion, there has been considerable interest in developing synthetic analogues. Among the synthetic motors created thus far, DNA motors that undertake discrete steps on RNA tracks have shown the greatest promise. Nonetheless, DNA nanomotors lack intrinsic directionality, are low speed and take a limited number of steps prior to stalling or dissociation. Herein, we report the first example of a highly tunable DNA origami motor that moves linearly over micron distances at an average speed of 40 nm/min. Importantly, nanomotors move unidirectionally without intervention through an external force field or a patterned track. Because DNA origami enables precise testing of nanoscale structure-function relationships, we were able to experimentally study the role of motor shape, chassis flexibility, leg distribution, and total number of legs in tuning performance. An anisotropic rigid chassis coupled with a high density of legs maximizes nanomotor speed and endurance.     

Nanoparticle-Assisted Alignment of Carbon Nanotubes on DNA Origami

Aligning carbon nanotubes (CNTs) is a key challenge for fabricating CNT-based electronic devices. Herein, we report a spherical nucleic acid (SNA) mediated approach for the highly precise alignment of CNTs at prescribed sites on DNA origami. We find that the cooperative DNA hybridization occurring at the interface of SNA and DNA-coated CNTs leads to an approximately five-fold improvement of the positioning efficiency. By combining this with the intrinsic positioning addressability of DNA origami, CNTs can be aligned in parallel with an extremely small angular variation of within 10°. Moreover, we demonstrate that the parallel alignment of CNTs prevents incorrect logic functionality originating from stray conducting paths formed by misaligned CNTs. This SNA-mediated method thus holds great potential for fabricating scalable CNT arrays for nanoelectronics.     

Cuboid Vesicles Formed by Frame‐Guided Assembly on DNA Origami Scaffolds

We describe the use of a frame‐guided assembly (FGA) strategy to construct cuboid and dumbbell‐shaped hetero‐vesicles on DNA origami nanostructure scaffolds. These are achieved by varying the design of the DNA origami scaffolds that direct the distribution of the leading hydrophobic groups (LHG). By careful selection of LHGs, different types of amphiphiles (both polymer and small‐molecule surfactants) were guided to form hetero‐vesicles, demonstrating the versatility of the FGA strategy and its potential to construct asymmetric and dynamic hetero‐vesicle assemblies with complex DNA nano‐scaffolds.     

Docking of Antibodies into the Cavities of DNA Origami Structures

Immobilized antibodies are extensively employed for medical diagnostics, such as in enzyme‐linked immunosorbent assays. Despite their widespread use, the ability to control the orientation of immobilized antibodies on surfaces is very limited. Herein, we report a method for the covalent and orientation‐selective immobilization of antibodies in designed cavities in 2D and 3D DNA origami structures. Two tris(NTA)‐modified strands are inserted into the cavity to form NTA–metal complexes with histidine clusters on the Fc domain. Subsequent covalent linkage to the antibody was achieved by coupling to lysine residues. Atomic force microscopy (AFM) and transmission electron microscopy (TEM) confirmed the efficient immobilization of the antibodies in the origami structures. This increased control over the orientation of antibodies in nanostructures and on surfaces has the potential to direct the interactions between antibodies and targets and to provide more regular surface assemblies of antibodies.     

Single‐Molecule Observation of the Photoregulated Conformational Dynamics of DNA Origami Nanoscissors

We demonstrate direct observation of the dynamic opening and closing behavior of photocontrollable DNA origami nanoscissors using high‐speed atomic force microscopy (HS‐AFM). First the conformational change between the open and closed state controlled by adjustment of surrounding salt concentration could be directly observed during AFM scanning. Then light‐responsive moieties were incorporated into the nanoscissors to control these structural changes by photoirradiation. Using photoswitchable DNA strands, we created a photoresponsive nanoscissors variant and were able to distinguish between the open and closed conformations after respective irradiation with ultraviolet (UV) and visible (Vis) light by gel electrophoresis and AFM imaging. Additionally, these reversible changes in shape during photoirradiation were directly visualized using HS‐AFM. Moreover, four photoswitchable nanoscissors were assembled into a scissor–actuator‐like higher‐order object, the configuration of which could be controlled by the open and closed switching induced by irradiation with UV and Vis light.     

DNA Origami Post‐Processing by CRISPR‐Cas12a

Customizable nanostructures built through the DNA‐origami technique hold tremendous promise in nanomaterial fabrication and biotechnology. Despite the cutting‐edge tools for DNA‐origami design and preparation, it remains challenging to separate structural components of an architecture built from—thus held together by—a continuous scaffold strand, which in turn limits the modularity and function of the DNA‐origami devices. To address this challenge, here we present an enzymatic method to clean up and reconfigure DNA‐origami structures. We target single‐stranded (ss) regions of DNA‐origami structures and remove them with CRISPR‐Cas12a, a hyper‐active ssDNA endonuclease without sequence specificity. We demonstrate the utility of this facile, selective post‐processing method on DNA structures with various geometrical and mechanical properties, realizing intricate structures and structural transformations that were previously difficult to engineer. Given the biocompatibility of Cas12a‐like enzymes, this versatile tool may be programmed in the future to operate functional nanodevices in cells.     

Reversible Covalent Stabilization of Stacking Contacts in DNA Assemblies

Stacking bonds formed between two blunt‐ended DNA double helices can be used to reversibly stabilize higher‐order complexes that are assembled from rigid DNA components. Typically, at low cation concentrations, stacking bonds break and thus higher‐order complexes disassemble. Herein, we present a site‐specific photochemical mechanism for the reversible covalent stabilization of stacking bonds in DNA assemblies. To this end, we modified one blunt end with the 3‐cyanovinylcarbazole (^cnvK) moiety and positioned a thymine residue (T) at the other blunt end. In the bound state, the two blunt‐ended helices are stacked together, resulting in a co‐localization of ^cnvK and T. Such a configuration induces the formation of a covalent bond across the stacking contact upon irradiation with 365 nm light. This bond can also be cleaved upon irradiation with 310 nm light, allowing repeated formation and cleavage of the same covalent bond on the timescale of seconds. Our system will expand the range of conditions under which stacking‐bond‐stabilized objects may be utilized.