Hierarchical Assembly of Super-DNA Origami Based on a Flexible and Covalent-Bound Branched DNA Structure

DNA/RNA Origami Based on Different Scaffolds and Their Biomedical Applications

Nucleic acids, including DNA and RNA, have been used extensively as building blocks to construct sophisticated nanostructures through complementary base pairing with predetermined shapes and sizes. With remarkable biocompatibility, spatial addressability, and structural programmability, self-assembled nucleic acid biomaterials have found widespread applications in various biomedical researches, including drug delivery, bioimaging, or disease diagnosis. Notably, as one of the representative nanostructures, DNA origami has drawn much attention. In this review, we summarize the latest developments in DNA/RNA origami design based on single-stranded DNA (ssDNA), double-stranded DNA (dsDNA), and single-stranded RNA (ssRNA) scaffolds for a range of biomedical applications, including drug delivery, gene regulation, immunomodulation, and receptor recognition. Additionally, the challenges and future opportunities of DNA/RNA origami in biomedical applications will be discussed.

Genetically Encoded Nucleic Acid Nanostructures for Biological Applications

Nucleic acid, as a carrier of genetic information, has been widely employed as a building block for the construction of versatile nanostructures with pre-designed sizes and shapes through complementary base pairing. With excellent programmability, addressability, and biocompatibility, nucleic acid nanostructures are extensively applied in biomedical researches, such as bio-imaging, bio-sensing, and drug delivery. Notably, the original gene-encoding capability of the nucleic acids themselves has been utilized in these structurally well-defined nanostructures. In this review, we will summarize the recent progress in the design of double-stranded DNA and mRNA-encoded nanostructures for various biological applications, such as gene regulation, gene expression, and mRNA transcription. Furthermore, the challenges and future opportunities of genetically encoded nucleic acid nanostructures in biomedical applications will be discussed.

DNA‑Directed Assembly of Photonic Nanomaterials for Diagnostic and Therapeutic Applications

DNA-directed assembly has emerged as a versatile and powerful approach for constructing complex structured materials. By leveraging the programmability of DNA nanotechnology, highly organized photonic systems can be developed to optimize light-matter interactions for improved diagnostics and therapeutic outcomes. These systems enable precise spatial arrangement of photonic components, minimizing material usage, and simplifying fabrication processes. DNA nanostructures, such as DNA origami, provide a robust platform for building multifunctional photonic devices with tailored optical properties. This review highlights recent progress in DNA-directed assembly of photonic nanomaterials, focusing on their applications in diagnostics and therapeutics. It provides an overview of the latest advancements in the field, discussing the principles of DNA-directed assembly, strategies for functionalizing photonic building blocks, innovations in assembly design, and the resulting optical effects that drive these developments. The review also explores how these photonic architectures contribute to diagnostic and therapeutic applications, emphasizing their potential to create efficient and effective photonic systems tailored to specific healthcare needs.

Tuning the Stability of DNA Tetrahedra with Base Stacking Interactions

DNA nanotechnology uses the programmable assembly of DNA to create nanoscale objects. Recent work from our laboratory suggested that terminal stacking interactions between adjacent strands could be a design parameter for DNA nanotechnology. Here, we explore that idea by creating DNA tetrahedra with sticky ends containing identical base pairing interactions but different stacking interactions. Testing all 16 stacking combinations, we found that the melting temperature of DNA tetrahedra varied by up to 10 °C from altering a single base stack in the design. We also show that a 4 bp sticky end with weak stacking does not form stable tetrahedra, while strengthening the stacks confers high stability with a 46.8 ± 1.2 °C melting temperature, comparable to that of a 6 bp sticky end with weak stacking (49.7 ± 2.9 °C). The results likely apply to other DNA nanostructures and suggest that stacking interactions play a role in the formation and stability of DNA nanostructures.

Tuning the stability of DNA tetrahedra with base-stacking interactions

DNA nanotechnology relies on programmable anchoring of regions of single-stranded DNA through base pair hybridization to create nanoscale objects such as polyhedra, tubes, sheets, and other desired shapes. Recent work from our lab measured the energetics of base-stacking interactions and suggested that terminal stacking interactions between two adjacent strands could be an additional design parameter for DNA nanotechnology. Here, we explore that idea by creating DNA tetrahedra held together with sticky ends that contain identical base pairing interactions but different terminal stacking interactions. Testing all 16 possible combinations, we found that the melting temperature of DNA tetrahedra varied by up to 10 °C from altering a single base stack in the design. These results can inform stacking design to control DNA tetrahedra stability in a substantial and predictable way. To that end, we show that a 4 bp sticky end with weak terminal stacking does not form stable tetrahedra, while strengthening the stacks confers high stability with a 46.8 ± 1.2 °C melting temperature, comparable to a 6 bp sticky end with weak stacking (49.7 ± 2.9 °C). The results likely apply to other types of DNA nanostructures and suggest that terminal stacking interactions play an integral role in formation and stability of DNA nanostructures.

Dependencies between effective parameters in coarse-grained models for phase separation of DNA-based fluids

DNA is now firmly established as a versatile and robust platform for achieving synthetic nanostructures. While the folding of single molecules into complex structures is routinely achieved through engineering basepair sequences, very little is known about the emergence of structure on larger scales in DNA fluids. The fact that polymeric DNA fluids can undergo phase separation into dense fluid and dilute gas opens avenues to design hierachical and multifarious assemblies. Here, we investigate to which extent the phase behavior of single-stranded DNA fluids can be captured by a minimal model of semiflexible charged homopolymers while neglecting specific hybridization interactions. We first characterize the single-polymer behavior and then perform direct coexistence simulations to test the model against experimental data. While low-resolution models show great promise to bridge the gap to relevant length and time scales, obtaining consistent and transferable parameters is challenging. In particular, we conclude that counterions not only determine the effective range of direct electrostatic interactions but also contribute to the effective attractions.

Toward Automated DNA Nanoprinting: Advancing the Synthesis of Covalently Branched DNA

Covalently branched DNA molecules are hybrid structures where a small molecule core is covalently linked to different DNA strands. They merge the programmability of DNA nanotechnology with synthetic molecules' functionality, offering enhanced stability over their non-covalent counterparts like double-crossover tiles. They enable the efficient assembly of stable DNA nanostructures with new geometries and functionalities. These motifs can be prepared through "DNA printing", which uses a DNA nanostructure as a temporary template to covalently transfer specific DNA strands to a small molecule core. Here, the "printing" process is streamlined with DNA-immobilized polystyrene microspheres, laying the foundation for future automated DNA printing devices. First, the DNA template hybridizes with reactive complementary strands, which are then crosslinked using a small molecule. Second, beads with fully complementary molecules capture the "daughter" products by strand displacement. This ensures high product yields and high recovery of the "mother" template for reuse. This method allows the precise transfer of different DNA strands onto various small molecules, including aromatics and functional porphyrins. Notably, these branching motifs exhibit remarkable stability toward nucleases without any specialized modifications. Moreover, they can serve as robust building blocks for precise assembly of 3D structures, such as an addressable tetrahedron from only two components.

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.

miR-21 Responsive Nanocarrier Targeting Ovarian Cancer Cells

In recent years, DNA origami-based nanocarriers have been extensively utilized for efficient cancer therapy. However, developing a nanocarrier capable of effectively protecting cargos such as RNA remains a challenge. In this study, we designed a compact and controllable DNA tubular origami (DTO) measuring 120 nm in length and 18 nm in width. The DTO exhibited appropriate structural characteristics for encapsulating and safeguarding cargo. Inside the DTO, we incorporated 20 connecting points to facilitate the delivery of cargoes to various ovarian and normal epithelial cell lines. Specifically, fluorescent-labeled DNA strands were attached to these sites as cargoes. The DTO was engineered to open upon encountering miR-21 through RNA/DNA strand displacement. Significantly, for the first time, we inhibited fluorescence using the compact DNA nanotube and observed dynamic fluorescent signals, indicating the controllable opening of DTO through live-cell imaging. Our results demonstrated that the DTO remained properly closed, exhibited effective internalization in ovarian cancer cells in vitro, showcasing marked differential expression of miR-21, and efficiently opened with short-term exposure to miR-21. Leveraging its autonomous behavior and compact design, the DTO emerges as a promising nanocarrier for various clinically relevant materials. It holds significant application prospects in anti-cancer therapy and the development of flexible biosensors.

Stepwise Assembly of DNA Nanostructures in a Surface-Based Method

Hierarchical assembly of DNA nanostructures has already led to superstructures of ever-increasing level of complexity. Processing control in building nanostructures hierarchically is desirable but remains underexplored. Here, we present the stepwise assembly of DNA origami nanostructures by a surface-based method. With solid support of magnetic beads or glass slides, we demonstrate hierarchical assembly of preformed DNA origami units to a number of superstructures. The anchoring of DNA constructs on the surface results in better programmability and controllability for DNA self-assembly, suggesting a potential for our surface-based strategy to become a general and standardized assembly methodology of DNA nanostructures and beyond.

Phase Behavior Modulation of a Unary DNA Origami System through Allosteric Stimuli

A unary system is the most conceptually concise design for conducting self-assembly. However, in most DNA-guided self-assembly schemes, a unary system has rarely been adopted because of the inherent challenge of strictly decoupling the monomer synthesis process from the assembly process, which may directly lead to the inaccurate control over assembly. Herein, we provide a multi-stimulus-triggered assembly strategy based on the DNA origami structure, which allows the unary system to realize controllable crystallization and phase transition by exerting allosteric stimuli. We intentionally introduced a specific DNA stimulus to convert the self-aggregation of functionalized groups into the connection of nearby monomers, thus producing multidimensional high-quality crystals. Furthermore, this unary system can undergo a phase transition from simple cubic to face-centered cubic with the introduction of more cation stimuli. We believe that this dynamic stimulation strategy can offer a novel solution for fabricating materials with on-demand modulation.

A modular DNA origami nanocompartment for engineering a cell-free, protein unfolding and degradation pathway

Within the cell, chemical reactions are often confined and organized through a modular architecture. This facilitates the targeted localization of molecular species and their efficient translocation to subsequent sites. Here we present a cell-free nanoscale model that exploits compartmentalization strategies to carry out regulated protein unfolding and degradation. Our synthetic model comprises two connected DNA origami nanocompartments (each measuring 25 nm × 41 nm × 53 nm): one containing the protein unfolding machine, p97, and the other housing the protease chymotrypsin. We achieve the unidirectional immobilization of p97 within the first compartment, establishing a gateway mechanism that controls substrate recruitment, translocation and processing within the second compartment. Our data show that, whereas spatial confinement increases the rate of the individual reactions by up to tenfold, the physical connection of the compartmentalized enzymes into a chimera efficiently couples the two reactions and reduces off-target proteolysis by almost sixfold. Hence, our modular approach may serve as a blueprint for engineering artificial nanofactories with reshaped catalytic performance and functionalities beyond those observed in natural systems.

Efficient one-pot assembly of higher-order DNA nanostructures by chemically conjugated branched DNA

Chemically conjugated branched DNA was successfully synthesized by a copper-free click reaction to construct sophisticated and higher-order polyhedral DNA nanostructures with pre-defined units in one pot, which can be used as an efficient nanoplatform to precisely organize multiple gold nanoparticles in predesigned patterns.

Ratiometric electrochemical biosensor based on lateral movement of multi-pedal DNA tetrahedron machine on biomimetic interface

In this work, a lateral moving multi-pedal DNA tetrahedron machine (MTM) is designed and coupled with dual-signal output system to construct a biomimetic electrochemical ratiometric strategy for ultrasensitive target DNA analysis. The tetrahedral structure provided rigid support for the pedal, ensuring efficient replacement of the rail chain modified with ferrocene. By conjugating cholesterol molecules to one vertex of MTM, it is decorated on a lipid bilayer. This molecular architecture confers lateral movement of MTM on an electrode surface while prevents its detachment from the system. The methylene blue tagged hairpin probe provides constant power to support MTM swim on lipid bilayer. Compared with the conventional motion mode, the lateral moving mechanism has the fastest reaction rate and the highest signal-to-noise ratio. Additionally, the dual-signal reporting system further improves the accuracy of target detection on the basis of ensuring motion efficiency. The work improved movement efficiency and shortened time fragment. A linear relationship between the ratio value of two reporters and target DNA concentration was observed from 0.5 fM to 50 pM with a detection limit of 28 aM. The lateral motion mode of DNA machine coalescing with ratiometric system made this sensing platform ultrasensitive and accurate, which holds new avenue of early diagnosis.

Chemically Conjugated Branched Staples for Super-DNA Origami

DNA origami, comprising a long folded DNA scaffold and hundreds of linear DNA staple strands, has been developed to construct various sophisticated structures, smart devices, and drug delivery systems. However, the size and diversity of DNA origami are usually constrained by the length of DNA scaffolds themselves. Herein, we report a new paradigm of scaling up DNA origami assembly by introducing a novel branched staple concept. Owing to their covalent characteristics, the chemically conjugated branched DNA staples we describe here can be directly added to a typical DNA origami assembly system to obtain super-DNA origami with a predefined number of origami tiles in one pot. Compared with the traditional two-step coassembly system (yields <10%), a much greater yield (>80%) was achieved using this one-pot strategy. The diverse superhybrid DNA origami with the combination of different origami tiles can be also efficiently obtained by the hybrid branched staples. Furthermore, the branched staples can be successfully employed as the effective molecular glues to stabilize micrometer-scale, super-DNA origami arrays (e.g., 10 × 10 array of square origami) in high yields, paving the way to bridge the nanoscale precision of DNA origami with the micrometer-scale device engineering. This rationally developed assembly strategy for super-DNA origami based on chemically conjugated branched staples presents a new avenue for the development of multifunctional DNA origami-based materials.

Geometry guided crystallization of anisotropic DNA origami shapes

Three-dimensional assembly based on DNA origami structures is an ideal method to precisely fabricate nano-scale materials. Additionally, applying an anisotropic assembly unit facilitates constructing complex materials with extraordinary structure. However, it still remains challenging to crystallize anisotropic DNA nano-structures using simple design, because the assembly of low-symmetry monomers often requires harsh auxiliary conditions and more complicated crystallization processes. In this work, we managed to crystallize the anisotropic elongated octahedral DNA origami frames by non-specific connections, and acquired two kinds of highly ordered superlattices purely by conducting multiple annealing processes and increasing the rigidity of the connection parts. In the case where the connection parts were composed of soft DNA sticky ends, we obtained the theoretically inaccessible simple cubic superlattices by this anisotropic DNA origami shape. Through characterization by small-angle X-ray scattering and scanning electron microscopy, we found that the DNA monomers are arbitrarily arranged due to the stress buffering of the soft DNA SEs, while in the stiffer case, simple tetragonal superlattices with translational arrangement of most anisotropic DNA origami shapes were synthesized as expected. This work deepened the understanding of geometry-guided crystallization of DNA origami shapes and provided a new path for constructing three-dimensional functional devices with simple design.

Detection of SARS-CoV-2 RNA with a plasmonic chiral biosensor

The detection of SARS-CoV-2 infection is crucial for effective prevention and surveillance of COVID-19. In this study, we report the development of a novel detection assay named CENSOR that enables sensitive and specific detection of SARS-CoV-2 RNA using a plasmonic chiral biosensor in combination with CRISPR-Cas13a. The chiral biosensor was designed by assembling gold nanorods (AuNR) into three-dimensional plasmonic architectures of controllable chirality on a DNA origami template. This modular assembly mode enhances the flexibility and adaptability of the sensor, thereby improving its universality as a sensing platform. In the presence of SARS-CoV-2 RNA, the CRISPR-Cas13a enzyme triggers collateral cleavage of RNA molecules, resulting in a differential chiral signal readout by the biosensor compared to when there are no RNA targets present. Notably, even subtle variations in the concentration of SARS-CoV-2 RNA can provoke significant changes in chiral signals after preamplification of RNA targets (calculated LOD: 0.133 aM), which establishes the foundation for quantitative detection. Furthermore, CENSOR demonstrated high sensitivity and accuracy in detecting SARS-CoV-2 RNA from clinical samples, suggesting its potential application in clinical settings for viral detection beyond SARS-CoV-2.

Target-Induced Stepwise Disintegration of Starlike Branched and Multiplex Embedded Systems for Amplified Detection of Serum MicroRNA

DNA nanotechnology has shown great promise for biosensing and molecular recognition. However, the practical application of conventional DNA biosensors is constrained by inadequate target stimuli, intricate design schemes, multicomponent systems, and susceptibility to nuclease degradation. To overcome these limitations, we present a class of starlike branched and multiplex embedded system (SBES) with an integrated functional design and cascade exponential amplification for serum microRNA (miRNA) detection. The DNA arms can be integrated into an all-in-one system by surrounding a branch point, with each arm endowed with specific functionalities by embedding different DNA fragments. These fragments include a segment complementary to the target miRNA for the recognition element, palindromic tails for self-primed polymerization, and a region with the same sequences as the target serving as the target analogue. Upon exposure to a target miRNA, the DNA arms unwind in a stepwise manner through palindrome-mediated dimerization and polymerization. This enables target recycling for subsequent reactions while releasing the target analogue to generate a secondary response in a feedback manner. A comparative analysis illustrates that the signal-to-noise ratio (SNR) of a full SBES with a feedback strategy is approximately 250% higher than the system without a feedback design. We demonstrate that the four-arm 4pSBES has the benefits of multifunctional integration, enhanced sensitivity, and low false-positive signals, which makes this approach ideally suited for clinical diagnosis. Moreover, an upgraded SBES with additional DNA arms (e.g., 6pSBES) can be constructed to allow multifunctional extension, offering unprecedented opportunities to build versatile DNA nanostructures for biosensing.

Molecular Engineering of Colloidal Atoms

Creation of architectures with exquisite hierarchies actuates the germination of revolutionized functions and applications across a wide range of fields. Hierarchical self-assembly of colloidal particles holds the promise for materialized realization of structural programing and customizing. This review outlines the general approaches to organize atom-like micro- and nanoparticles into prescribed colloidal analogs of molecules by exploiting diverse interparticle driving motifs involving confining templates, interactive surface ligands, and flexible shape/surface anisotropy. Furthermore, the self-regulated/adaptive co-assembly of simple unvarnished building blocks is discussed to inspire new designs of colloidal assembly strategies.

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.

A covalently conjugated branched DNA aptamer cluster-based nanoplatform for efficiently targeted drug delivery

Targeted delivery of therapeutic drugs is essential for precise treatment of various diseases to reduce possible serious side-effects. A screened DNA aptamer has been widely developed for active targeting delivery. Herein, we report a facile strategy for the construction of a branched DNA aptamer cluster-based nanoplatform for efficiently targeted drug delivery. In our design, the terminal-modified DNA aptamer can be covalently conjugated to form a branched aptamer cluster by click reaction easily. The branched aptamer cluster-modified DNA tetrahedron (TET) demonstrates highly targeted cellular uptake with the modification of only one site. After loading the chemotherapeutic drug (doxorubicin, DOX), the DNA aptamer cluster-based nanoplatform elicits a remarkable and selective inhibition of tumor cell proliferation by much-enhanced targeted delivery. This covalently conjugated branched DNA aptamer cluster-based nanoplatform provides a new strategy for the development of targeted drug delivery.

Gold-Nanoparticle-Mediated Assembly of High-Order DNA Nano-Architectures

Constructing high-order DNA nano-architectures in large sizes is of critical significance for the application of DNA nanotechnology. Robust and flexible design strategies together with easy protocols to construct high-order large-size DNA nano-architectures remain highly desirable. In this work, the authors report a simple and versatile one-pot strategy to fabricate DNA architectures with the assistance of spherical gold nanoparticles modified with thiolated oligonucleotide strands (SH-DNA-AuNPs), which serve as "power strips" to connect various DNA nanostructures carrying complementary ssDNA strands as "plugs". By modulating the plug numbers and positions on each DNA nanostructure and the ratios between DNA nanostructures and AuNPs, the desired architectures are formed via the stochastic co-assembly of different modules. This SH-DNA-AuNP-mediated plug-in assembly (SAMPA) strategy offers new opportunities to drive macroscopic self-assembly to meet the demand of the fabrication of well-defined nanomaterials and nanodevices.

Modulating the Fluorescence of Silver Nanoclusters Wrapped in DNA Hairpin Loops via Confined Strand Displacement and Transient Concatenate Ligation for Amplifiable Biosensing

It is intriguing to modulate the fluorescence emission of DNA-scaffolded silver nanoclusters (AgNCs) via confined strand displacement and transient concatenate ligation for amplifiable biosensing of a DNA segment related to SARS-CoV-2 (s₂DNA). Herein, three stem-loop structural hairpins for signaling, recognizing, and assisting are designed to assemble a variant three-way DNA device (3WDD) with the aid of two linkers, in which orange-emitting AgNC (oAgNC) is stably clustered and populated in the closed loop of a hairpin reporter. The presence of s₂DNA initiates the toehold-mediated strand displacement that is confined in this 3WDD for repeatable recycling amplification, outputting numerous hybrid DNA-duplex conformers that are implemented for a transient "head-tail-head" tandem ligation one by one. As a result, the oAgNC-hosted hairpin loops are quickly opened in loose coil motifs, bringing a significant fluorescence decay of multiple clusters dependent on s₂DNA. Demonstrations and understanding of the tunable spectral performance of a hairpin loop-wrapped AgNC via switching 3WDD conformation would be highly beneficial to open a new avenue for applicable biosensing, bioanalysis, or clinical diagnostics.