Planar 2D wireframe DNA origami

Diverse applications of DNA origami as a cross-disciplinary tool

As knowledge from a single discipline is no longer sufficient to keep pace with the growing complexity of technological advancements, interdisciplinary collaboration has become a crucial driver of innovation. DNA nanotechnology exemplifies this integration, serving as a field where cross-disciplinary communication is particularly prominent. Since its introduction by Rothemund in 2006, DNA origami has proved to be a powerful tool for interdisciplinary research, offering exceptional structural stability, programmability, and addressability. This review provides an overview of the development of DNA origami technology, highlights its major advances, and explores its innovative applications across various disciplines in recent years, showcasing its vast potential and future prospects. We believe DNA origami is poised for even broader applications, driving progress across multiple fields.

Structural stability of wireframe DNA origami: The role of nanocomponent modifications

Wireframe DNA origami nanostructures hold immense potential for diverse applications in nanotechnology. The design of wireframe DNA origami structures traditionally follows a top-down approach. This study introduces a complementary bottom-up approach to investigate the nano-components constituting these nanostructures and their impact on structural stability. To this end, modifications to edge staple crossovers, poly-T bulges, and staple sequences were examined through coarse-grained molecular dynamics. The results reveal that reducing the number of edge staple crossovers slightly alters the distance between the two double-stranded DNA helices forming the edges but maintains adequate structural stability. The removal of poly-T bulges, however, leads to edge opening under specific thermal conditions, whereas structures containing poly-T bulges remain intact, highlighting their critical role in edge stability. Furthermore, changes to the staple sequences, achieved by repositioning the scaffold nick, showed negligible effects on the overall stability of the wireframe DNA origami structures. The incorporation of a bottom-up approach in designing wireframe DNA origami structures can enable the creation of nanostructures with tailored properties for specific applications. These modifications can be adapted for a variety of wireframe DNA origami structures, broadening their potential uses in nanotechnology.

Wireframe DNA Origami Capable of Vertex-protruding Transformation

Regulating dynamic behavior of the designed molecular structures provides a foundation for the construction of functional molecular devices. DNA nanotechnology allows conformational changes in two-dimensional and three-dimensional DNA origami nanostructures by introducing flexibility between the faces of the structures. However, dynamic transformations in wireframe DNA origami, composed solely of vertices and edges, remain challenging due to vertex-specific flexibility. We report a wireframe DNA origami capable of vertex-protruding transformation between the open- and closed-form with eight protruding vertices. This reversible transformation is driven by DNA hybridization and a toehold-mediated strand displacement reaction. Spacer strands between vertices and edges were designed to introduce flexibility. Coarse-grained molecular dynamics simulations demonstrated that a longer spacer increases conformational flexibility and can achieve the narrow angles required for the vertex-protruding transformation. The experimental results showed the successful assembly of the open-form structure under optimized salt conditions, as visualized through transmission electron microscopy images. Furthermore, the transformation between the open- and closed-form structures was demonstrated by the sequential addition of signal strands. This vertex-protruding transformation mechanism will expand the design approach of dynamic DNA nanostructures and help develop functional molecular devices for artificial molecular systems.

Toward Precise Fabrication of Finite-Sized DNA Origami Superstructures

DNA origami enables the precise construction of 2D and 3D nanostructures with customizable shapes and the high-resolution organization of functional materials. However, the size of a single DNA origami is constrained by the length of the scaffold strand, and since its inception, scaling up the size and complexity has been a persistent pursuit. Hierarchical self-assembly of DNA origami units offers a feasible approach to overcome the limitation. Unlike periodic arrays, finite-sized DNA origami superstructures feature well-defined structural boundaries and uniform dimensions. In recent years, increasing attention has been directed toward precise control over the hierarchical self-assembly of DNA origami structures and their applications in fields such as nanophotonics, biophysics, and material science. This review summarizes the strategies for fabricating finite-sized DNA origami superstructures, including heterogeneous self-assembly, self-limited self-assembly, and templated self-assembly, along with a comparative analysis of the advantages and limitations of each approach. Subsequently, recent advancements in the application of these structures are discussed from a structure design perspective. Finally, an outlook on the current challenges and potential future directions is provided, highlighting opportunities for further research and development in this rapidly evolving field.

Hairygami: Analysis of DNA Nanostructures' Conformational Change Driven by Functionalizable Overhangs

DNA origami is a widely used method to construct nanostructures by self-assembling designed DNA strands. These structures are often used as "pegboards" for templated assembly of proteins, gold nanoparticles, aptamers, and other molecules, with applications ranging from therapeutics and diagnostics to plasmonics and photonics. Imaging these structures using atomic force microscopy (AFM) or transmission electron microscope (TEM) does not capture their full conformation ensemble as they only show their shape flattened on a surface. However, certain conformations of the nanostructure can position guest molecules into distances unaccounted for in their intended design, thus leading to spurious interactions between guest molecules that are designed to be separated. Here, we use molecular dynamics simulations to capture a conformational ensemble of two-dimensional (2D) DNA origami tiles and show that introducing single-stranded overhangs, which are typically used for functionalization of the origami with guest molecules, induces a curvature of the tile structure in the bulk. We show that the shape deformation is of entropic origin, with implications for the design of robust DNA origami breadboards as well as a potential approach to modulate structure shape by introducing overhangs. We then verify experimentally that the DNA overhangs introduce curvature into the DNA origami tiles under divalent as well as monovalent salt buffer conditions. We further experimentally verify that DNA origami functionalized with attached proteins also experiences such induced curvature. We provide the developed simulation code implementing the enhanced sampling to characterize the conformational space of DNA origami as open source software.

Supramolecular assembly of phenanthrene-DNA conjugates into light-harvesting nanospheres

The self-assembly of highly functionalized phenanthrene-DNA conjugates into supramolecular nanostructures is presented. DNA oligomers modified with phenanthrene residues at the 3'-end and internal positions self-assemble into spherical nanostructures. The nanospheres exhibit light-harvesting properties. Upon irradiation of phenanthrene, the excitation energy is transferred along phenanthrene units, resulting in phenanthrene-pyrene exciplex formation.

Binding Site Programmable Self-Assembly of 3D Hierarchical DNA Origami Nanostructures

DNA nanotechnology has broad applications in biomedical drug delivery and programmable materials. Characterization of the self-assembly of DNA origami and quantum dots (QDs) is necessary for the development of new DNA-based nanostructures. We use computation and experiment to show that the self-assembly of 3D hierarchical nanostructures can be controlled by programming the binding site number and their positions on DNA origami. Using biotinylated pentagonal pyramid wireframe DNA origamis and streptavidin capped QDs, we demonstrate that DNA origami with 1 binding site at the outer vertex can assemble multimeric origamis with up to 6 DNA origamis on 1 QD, and DNA origami with 1 binding site at the inner center can only assemble monomeric and dimeric origamis. Meanwhile, the yield percentages of different multimeric origamis are controlled by the QD:DNA-origami stoichiometric mixing ratio. DNA origamis with 2 binding sites at the αγ positions (of the pentagon) make larger nanostructures than those with binding sites at the αβ positions. In general, increasing the number of binding sites leads to increases in the nanostructure size. At high DNA origami concentration, the QD number in each cluster becomes the limiting factor for the growth of nanostructures. We find that reducing the QD size can also affect the self-assembly because of the reduced access to the binding sites from more densely packed origamis.

A computational model for structural dynamics and reconfiguration of DNA assemblies

Recent advances in constructing a structured DNA assembly whose configuration can be dynamically changed in response to external stimuli have demanded the development of an efficient computational modeling approach to expedite its design process. Here, we present a computational framework capable of analyzing both equilibrium and non-equilibrium dynamics of structured DNA assemblies at the molecular level. The framework employs Langevin dynamics with structural and hydrodynamic finite element models that describe mechanical, electrostatic, base stacking, and hydrodynamic interactions. Equilibrium dynamic analysis for various problems confirms the solution accuracy at a near-atomic resolution, comparable to molecular dynamics simulations and experimental measurements. Furthermore, our model successfully simulates a long-time-scale close-to-open-to-close dynamic reconfiguration of the switch structure in response to changes in ion concentration. We expect that the proposed model will offer a versatile way of designing responsive and reconfigurable DNA machines.

Ultrafast dense DNA functionalization of quantum dots and rods for scalable 2D array fabrication with nanoscale precision

Scalable fabrication of two-dimensional (2D) arrays of quantum dots (QDs) and quantum rods (QRs) with nanoscale precision is required for numerous device applications. However, self-assembly-based fabrication of such arrays using DNA origami typically suffers from low yield due to inefficient QD and QR DNA functionalization. In addition, it is challenging to organize solution-assembled DNA origami arrays on 2D device substrates while maintaining their structural fidelity. Here, we reduced manufacturing time from a few days to a few minutes by preparing high-density DNA-conjugated QDs/QRs from organic solution using a dehydration and rehydration process. We used a surface-assisted large-scale assembly (SALSA) method to construct 2D origami lattices directly on solid substrates to template QD and QR 2D arrays with orientational control, with overall loading yields exceeding 90%. Our fabrication approach enables the scalable, high fidelity manufacturing of 2D addressable QDs and QRs with nanoscale orientational and spacing control for functional 2D photonic devices.

Advanced applications of DNA nanostructures dominated by DNA origami in antitumor drug delivery

DNA origami is a cutting-edge DNA self-assembly technique that neatly folds DNA strands and creates specific structures based on the complementary base pairing principle. These innovative DNA origami nanostructures provide numerous benefits, including lower biotoxicity, increased stability, and superior adaptability, making them an excellent choice for transporting anti-tumor agents. Furthermore, they can considerably reduce side effects and improve therapy success by offering precise, targeted, and multifunctional drug delivery system. This comprehensive review looks into the principles and design strategies of DNA origami, providing valuable insights into this technology's latest research achievements and development trends in the field of anti-tumor drug delivery. Additionally, we review the key function and major benefits of DNA origami in cancer treatment, some of these approaches also involve aspects related to DNA tetrahedra, aiming to provide novel ideas and effective solutions to address drug delivery challenges in cancer therapy.

Honeycomb Biosilica in Sponges: From Understanding Principles of Unique Hierarchical Organization to Assessing Biomimetic Potential

Structural bioinspiration in modern material science and biomimetics represents an actual trend that was originally based on the bioarchitectural diversity of invertebrate skeletons, specifically, honeycomb constructs of natural origin, which have been in humanities focus since ancient times. We conducted a study on the principles of bioarchitecture regarding the unique biosilica-based honeycomb-like skeleton of the deep-sea glass sponge Aphrocallistes beatrix. Experimental data show, with compelling evidence, the location of actin filaments within honeycomb-formed hierarchical siliceous walls. Principles of the unique hierarchical organization of such formations are discussed. Inspired by poriferan honeycomb biosilica, we designed diverse models, including 3D printing, using PLA-, resin-, and synthetic-glass-prepared corresponding microtomography-based 3D reconstruction.

Toehold-Mediated Shape Transition of Nucleic Acid Nanoparticles

We introduce a toehold-mediated strand displacement strategy for regulated shape-switching of nucleic acid nanoparticles (NANPs) enabling their sequential transformation from triangular to hexagonal architectures at isothermal conditions. The successful shape transitions were confirmed by electrophoretic mobility shift assays, atomic force microscopy, and dynamic light scattering. Furthermore, implementation of split fluorogenic aptamers allowed for monitoring the individual transitions in real time. Three distinct RNA aptamers─malachite green (MG), broccoli, and mango─were embedded within NANPs as reporter domains to confirm shape transitions. While MG "lights up" within the square, pentagonal, and hexagonal constructs, the broccoli is activated only upon formation of pentagon and hexagon NANPs, and mango reports only the presence of hexagons. Moreover, the designed RNA fluorogenic platform can be employed to construct a logic gate that performs an AND operation with three single-stranded RNA inputs by implementing a non-sequential polygon transformation approach. Importantly, the polygonal scaffolds displayed promising potential as drug delivery agents and biosensors. All polygons exhibited effective cellular internalization followed by specific gene silencing when decorated with fluorophores and RNAi inducers. This work offers a new perspective for the design of toehold-mediated shape-switching nanodevices to activate different light-up aptamers for the development of biosensors, logic gates, and therapeutic devices in the nucleic acid nanotechnology.

Recent Advances in DNA Origami-Engineered Nanomaterials and Applications

DNA nanotechnology is a unique field, where physics, chemistry, biology, mathematics, engineering, and materials science can elegantly converge. Since the original proposal of Nadrian Seeman, significant advances have been achieved in the past four decades. During this glory time, the DNA origami technique developed by Paul Rothemund further pushed the field forward with a vigorous momentum, fostering a plethora of concepts, models, methodologies, and applications that were not thought of before. This review focuses on the recent progress in DNA origami-engineered nanomaterials in the past five years, outlining the exciting achievements as well as the unexplored research avenues. We believe that the spirit and assets that Seeman left for scientists will continue to bring interdisciplinary innovations and useful applications to this field in the next decade.

Center backbone-rigidified DNA polygonal nanostructures and bottom face-templated polyhedral pyramids with structural stability in a complex biological medium

Due to the sequence programmability, good biocompatibility, versatile functionalities and vast sequence space, DNA oligonucleotides are considered to be ideal building blocks for the assembly of diverse nanostructures in one, two and three dimensions that are capable of engineering of multiple functional nucleic acids into a useful tool to implement intended tasks in biological and medical field. However, the construction of wireframe nanostructures consisting of only a few DNA strands remains quite challenging mainly because of the molecular flexibility-based uncontrollability of size and shape. In this contribution, utilizing gel electrophoretic analysis and atomic force microscopy, we demonstrate the modeling assembly technique for the construction of wireframe DNA nanostructures that can be divided into two categories: rigid center backbone-guided modeling (RBM) and bottom face-templated assembly (BTA) that are responsible for the construction of DNA polygons and polyhedral pyramids, respectively. The highest assembly efficiency (AE) is about 100%, while the lowest AE is not less than 50%. Moreover, when adding one edge for polygons or one side face for pyramids, we only need to add one oligonucleotide strand. Especially, the advanced polygons (e.g., pentagon and hexagon) of definite shape are for the first time constructed. Along this line, introduction of cross-linking strands enables the hierarchical assembly of polymer polygons and polymer pyramids. These wireframe DNA nanostructures exhibit the substantially enhanced resistance to nuclease degradation and maintain their structural integrity in fetal bovine serum for several hours even if the vulnerable nicks are not sealed. The proposed modeling assembly technique represents important progress toward the development of DNA nanotechnology and is expected to promote the application of DNA nanostructures in biological and biomedical fields. STATEMENT OF SIGNIFICANCE: DNA oligonucleotides are considered to be ideal building blocks for the assembly of diverse nanostructures. However, the construction of wireframe nanostructures consisting of only a few DNA strands remains quite challenging. In this contribution, we demonstrate the modeling technique for the construction of different wireframe DNA nanostructures: rigid center backbone-guided modeling (RBM) and bottom face-templated assembly (BTA) that are responsible for the assembly of DNA polygons and polyhedral pyramids, respectively. Moreover, cross-linking strands enables the hierarchical assembly of polymer polygons and polymer pyramids. These wireframe DNA nanostructures exhibit the substantially enhanced resistance to nuclease degradation and maintain their structural integrity in fetal bovine serum for several hours, promoting the application of DNA nanostructures in biological and biomedical fields.

Dynamics of DNA Origami Lattices

Hierarchical assembly of programmable DNA frameworks─such as DNA origami─paves the way for versatile nanometer-precise parallel nanopatterning up to macroscopic scales. As of now, the rapid evolution of the DNA nanostructure design techniques and the accessibility of these methods provide a feasible platform for building highly ordered DNA-based assemblies for various purposes. So far, a plethora of different building blocks based on DNA tiles and DNA origami have been introduced, but the dynamics of the large-scale lattice assembly of such modules is still poorly understood. Here, we focus on the dynamics of two-dimensional surface-assisted DNA origami lattice assembly at mica and lipid substrates and the techniques for prospective three-dimensional assemblies, and finally, we summarize the potential applications of such systems.