Structural stability of DNA origami nanostructures under application-specific conditions

DNA as a promising biomaterial for bone regeneration and potential mechanisms of action

DNA nanotechnology has created new possibilities for the use of DNA in tissue regeneration - an important advance for DNA use beyond its paradigmatic role as the hereditary biomacromolecule. Biomaterials containing synthetic or natural DNA have been proposed for several applications including drug and gene delivery, and more recently, as osteoconductive biomaterials. This review provides an in-depth discussion of studies that have used DNA-based materials for biomineralization and/or bone repair, with expansion on the topic of DNA hydrogels specifically, and the advantages they offer for advancing the field of bone regeneration. Four mechanisms of action for the osteoconductive capabilities of DNA-based materials are discussed, and a proposed model for degradation of these materials and its link to their osteoconductive properties is later presented. Finally, the review considers current limitations of DNA-based materials and summarizes important aspects that need to be addressed for future application of DNA nanotechnology in tissue repair. STATEMENT OF SIGNIFICANCE: Herein we summarize the developing field of DNA-based materials for biomineralization and bone repair, with a focus on DNA hydrogels. We first provide a comprehensive review of different forms of DNA-based materials described thus far which have been shown to enhance bone repair and mineralization (namely DNA coatings, DNA-containing pastes, DNA nanostructures and DNA hydrogels). Next, we describe four different mechanisms by which DNA-based materials could be exerting their osteogenic effect. Then, we propose a novel model that links DNA degradation and osteoconductivity. Lastly, we suggest possible research directions to enhance DNA-based materials for future clinical application. The suggested mechanisms and the proposed model can guide future research to better understand how DNA functions as a mineral- and bone-promoting molecule.

Photo-Cross-linked DNA Structures Greatly Improves Their Serum Nuclease Resistances and Gene Knock-In Efficiencies

The stabilization and structural integrity of DNA architectures remain significant challenges in their biomedical applications, particularly when inserting functional units into the genome using long single-stranded DNA (lssDNA). To address these challenges, a site-specific photo-cross-linking method is employed. Single-stranded oligonucleotides, containing one or two photosensitive cyanovinylcarbazole nucleoside (CNVK) molecules, are precisely incorporated and cross-linked at the specific sites of ssDNA through base-pairing, followed by rapid UV irradiation at 365 nm. This interstrand photo-cross-linking improves the thermal stability of DNA duplexes and allows this study to afford a tetrahedral DNA nanostructure in a yield of >94%. Most importantly, the photo-cross-linked DNA architectures exhibit high resistances against serum degradation, especially prevent digestion of exonuclease III (exo III), which is common in conventional lambda-processing method. Meanwhile, this photo-cross-linking treatment can significantly improve the knock-in (KI) efficiencies of lssDNA in different cells including 293T, K562, and HepG2, approximately three to eightfold those of the uncross-linked lssDNA, and remain a low cytotoxicity. Given the significantly enhanced nuclease resistance in serum and improved KI efficiencies, this study anticipates that this photo-cross-linking method will become a valuable tool in technologically advanced biomedical applications, such as nanotechnology and nucleic acid therapy.

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.

Fabrication of Functional 3D Nanoarchitectures via Atomic Layer Deposition on DNA Origami Crystals

While DNA origami is a powerful bottom-up fabrication technique, the physical and chemical stability of DNA nanostructures is generally limited to aqueous buffer conditions. Wet chemical silicification can stabilize these structures but does not add further functionality. Here, we demonstrate a versatile three-dimensional (3D) nanofabrication technique to conformally coat micrometer-sized DNA origami crystals with functional metal oxides via atomic layer deposition (ALD). In addition to depositing homogeneous and conformal nanometer-thin ZnO, TiO2, and IrO2 (multi)layers inside SiO2-stabilized crystals, we establish a method to directly coat bare DNA crystals with ALD layers while maintaining the crystal integrity, enabled by critical point drying and low ALD process temperatures. As a proof-of-concept application, we demonstrate electrocatalytic water oxidation using ALD IrO2-coated DNA origami crystals, resulting in improved performance relative to that of planar films. Overall, our coating strategy establishes a tool set for designing custom-made 3D nanomaterials with precisely defined topologies and material compositions, combining the unique advantages of DNA origami and atomically controlled deposition of functional inorganic materials.

Models and simulations of structural DNA nanotechnology reveal fundamental principles of self-assembly

DNA is not only a centrally important molecule in biology: the specificity of bonding that allows it to be the primary information storage medium for life has also allowed it to become one of the most promising materials for designing intricate, self-assembling structures at the nanoscale. While the applications of these structures are both broad and highly promising, the self-assembly process itself has attracted interest not only for the practical applications of designing structures with more efficient assembly pathways, but also due to a desire to understand the principles underlying self-assembling systems more generally, of which DNA-based systems provide intriguing and unique examples. Here, we review the fundamental physical principles that underpin the self-assembly process in the field of DNA nanotechnology, with a specific focus on simulation and modelling and what we can learn from them. In particular, we compare and contrast DNA origami and bricks and briefly outline other approaches, with an overview of concepts such as cooperativity, nucleation and hysteresis; we also explain how nucleation barriers can be controlled and why they can be helpful in ensuring error-free assembly. While high-resolution models may be needed to obtain accurate system-specific properties, often very simple coarse-grained models are sufficient to extract the fundamentals of the underlying physics and can enable us to gain deep insight. By combining experimental and simulation approaches to understand the details of the self-assembly process, we can optimise its yields and fidelity, which may in turn facilitate its use in practical applications.

DNA Nanotags for Multiplexed Single-Particle Electron Microscopy and In Situ Electron Cryotomography

DNA nanostructures present new opportunities as Nanotags for electron microscopy (EM) imaging, leveraging their high programmability, unique shapes, biomolecule conjugation capability, and stability compatible with standard cryogenic sample preparation protocols. This perspective highlights the potential of DNA Nanotags to enable high-throughput multiplexed EM analysis and facilitate in situ particle identification for cryogenic electron tomography (cryo-ET). Meanwhile, applying Nanotags in live-cell environments requires the efficient cellular uptake of intact structures and successful cytosolic migration. Promising strategies such as employing direct cytosolic delivery platforms and expressing RNA-based Nanotags in situ are discussed, while more systematic studies are needed to fully understand the intracellular trafficking and achieve precise localization of DNA Nanotags.

Recent Advances in DNA Origami-Enabled Optical Biosensors for Multi-Scenario Application

Over the past few years, significant progress has been made in DNA origami technology due to the unrivaled self-assembly properties of DNA molecules. As a highly programmable, addressable, and biocompatible nanomaterial, DNA origami has found widespread applications in biomedicine, such as cell scaffold construction, antimicrobial drug delivery, and supramolecular enzyme assembly. To expand the scope of DNA origami application scenarios, researchers have developed DNA origami structures capable of actively identifying and quantitatively reporting targets. Optical DNA origami biosensors are promising due to their fast-to-use, sensitive, and easy implementation. However, the conversion of DNA origami to optical biosensors is still in its infancy stage, and related strategies have not been systematically summarized, increasing the difficulty of guiding subsequent researchers. Therefore, this review focuses on the universal strategies that endow DNA origami with dynamic responsiveness from both de novo design and current DNA origami modification. Various applications of DNA origami biosensors are also discussed. Additionally, we highlight the advantages of DNA origami biosensors, which offer a single-molecule resolution and high signal-to-noise ratio as an alternative to traditional analytical techniques. We believe that over the next decade, researchers will continue to transform DNA origami into optical biosensors and explore their infinite possible uses.

Biomimetic Origami: A Biological Influence in Design

Origami, the art of paper folding, has long fascinated researchers and designers in its potential to replicate and tap the complexity of nature. In this paper, we pursue the crossing of origami engineering structures and biology, the realm of biologically-inspired origami structures categorized by the two biggest taxonomy kingdoms and DNA origami. Given the diversity of life forms that Earth comprises, we pursue an analysis of biomimetic designs that resemble intricate patterns and functionalities occurring in nature. Our research begins by setting out a taxonomic framework for the classification of origami structures based on biologically important kingdoms. From each of these, we explore the engineering structures inspired by morphological features, behaviors, and ecological adaptations of organisms. We also discuss implications in realms such as sustainability, biomaterials development, and bioinspired robotics. Thus, by parlaying the principles found in nature's design playbook through the art of folding, biologically inspired origami becomes fertile ground for interdisciplinary collaboration and creativity. Through this approach, we aim to inspire readers, researchers, and designers to embark on a journey of discovery in which the boundaries between art, science, and nature are blurred, providing a foundation for innovation to thrive.

Design and simulation of a wireframe DNA origami nanoactuator

This paper explores the use of deoxyribonucleic acid (DNA) origami structures as nanorobot components. Investigating the functional properties of DNA origami structures can facilitate the fabrication of DNA origami-based nanorobots. The wireframe structure stands out as one of the most interesting DNA origami structures. Hence, the present study aims to employ these structures to create DNA origami nanoactuators. The research delves into the design of DNA origami structures with the aim of opening under specific temperature conditions. Short DNA strands (staples) are one of the crucial parts of DNA origami structures, and the appropriate design of these strands can lead to the creation of structures with different properties. Thus, the components of the DNA origami nanoactuator are tailored to enable intentional opening at specific temperatures while maintaining stability at lower temperatures. This structural modification showcases the functional property of the DNA origami structure. The engineered DNA origami nanoactuator holds potential applications in medicine. By carrying drugs under specific temperature conditions and releasing them under different temperature conditions, it can serve as a platform for smart drug delivery purposes.

Structural stability of DNA origami nanostructures in organic solvents

DNA origami nanostructures have attracted significant attention as an innovative tool in a variety of research areas, spanning from nanophotonics to bottom-up nanofabrication. However, the use of DNA origami is often restricted by their rather limited structural stability in application-specific conditions. The structural integrity of DNA origami is known to be superstructure-dependent, and the integrity is influenced by various external factors, for example cation concentration, temperature, and presence of nucleases. Given the necessity to functionalize DNA origami also with non-water-soluble entities, it is important to acquire knowledge of the structural stability of DNA origami in various organic solvents. Therefore, we herein systematically investigate the post-folding DNA origami stability in a variety of polar, water-miscible solvents, including acetone, ethanol, DMF, and DMSO. Our results suggest that the structural integrity of DNA origami in organic solvents is both superstructure-dependent and dependent on the properties of the organic solvent. In addition, DNA origami are generally more resistant to added organic solvents in folding buffer compared to that in deionized water. DNA origami stability can be maintained in up to 25-40% DMF or DMSO and up to 70-90% acetone or ethanol, with the highest overall stability observed in acetone. By rationally selecting both the DNA origami design and the solvent, the DNA origami stability can be maintained in high concentrations of organic solvents, which paves the way for more extensive use of non-water-soluble compounds for DNA origami functionalization and complexation.

DNA-Templated Nanofabrication of CdS-Au Nanoscale Schottky Contacts and Electrical Characterization

DNA-templated nanofabrication presents an innovative approach to creating self-assembled nanoscale metal-semiconductor-based Schottky contacts, which can advance nanoelectronics. Herein, we report the successful fabrication of metal-semiconductor Schottky contacts using a DNA origami scaffold. The scaffold, consisting of DNA strands organized into a specific linear architecture, facilitates the competitive arrangement of Au and CdS nanorods, forming heterojunctions, and addresses previous limitations in low electrical conductance making DNA-templated electronics with semiconductor nanomaterials. Electroless gold plating extends the Au nanorods and makes the necessary electrical contacts. Tungsten electrical connection lines are further created by electron beam-induced deposition. Electrical characterization reveals nonlinear Schottky barrier behavior, with electrical conductance ranging from 0.5 × 10-4 to 1.7 × 10-4 S. The conductance of these DNA-templated junctions is several million times higher than with our prior Schottky contacts. Our research establishes an innovative self-assembly approach with applicable metal and semiconductor materials for making highly conductive nanoscale Schottky contacts, paving the way for the future development of DNA-based nanoscale electronics.

Harnessing DNA origami's therapeutic potential for revolutionizing cardiovascular disease treatment: A comprehensive review

DNA origami is a cutting-edge nanotechnology approach that creates precise and detailed 2D and 3D nanostructures. The crucial feature of DNA origami is how it is created, which enables precise control over its size and shape. Biocompatibility, targetability, programmability, and stability are further advantages that make it a potentially beneficial technique for a variety of applications. The preclinical studies of sophisticated programmable nanomedicines and nanodevices that can precisely respond to particular disease-associated triggers and microenvironments have been made possible by recent developments in DNA origami. These stimuli, which are endogenous to the targeted disorders, include protein upregulation, pH, redox status, and small chemicals. Oncology has traditionally been the focus of the majority of past and current research on this subject. Therefore, in this comprehensive review, we delve into the intricate world of DNA origami, exploring its defining features and capabilities. This review covers the fundamental characteristics of DNA origami, targeting DNA origami to cells, cellular uptake, and subcellular localization. Throughout the review, we emphasised on elucidating the imperative for such a therapeutic platform, especially in addressing the complexities of cardiovascular disease (CVD). Moreover, we explore the vast potential inherent in DNA origami technology, envisioning its promising role in the realm of CVD treatment and beyond.

Folding molecular origami from ribosomal RNA

Approximately 80 percent of the total RNA in cells is ribosomal RNA (rRNA), making it an abundant and inexpensive natural source of long, single-stranded nucleic acid, which could be used as raw material for the fabrication of molecular origami. In this study, we demonstrate efficient and robust construction of 2D and 3D origami nanostructures utilizing cellular rRNA as a scaffold and DNA oligonucleotide staples. We present calibrated protocols for the robust folding of contiguous shapes from one or two rRNA subunits that are efficient to allow folding using crude extracts of total RNA. We also show that RNA maintains stability within the folded structure. Lastly, we present a novel and comprehensive analysis and insights into the stability of RNA:DNA origami nanostructures and demonstrate their enhanced stability when coated with polylysine-polyethylene glycol in different temperatures, low Mg2+ concentrations, human serum, and in the presence of nucleases (DNase I or RNase H). Thus, laying the foundation for their potential implementation in emerging biomedical applications, where folding rRNA into stable structures outside and inside cells would be desired.

The impact of nanomaterials on autophagy across health and disease conditions

Autophagy, a catabolic process integral to cellular homeostasis, is constitutively active under physiological and stress conditions. The role of autophagy as a cellular defense response becomes particularly evident upon exposure to nanomaterials (NMs), especially environmental nanoparticles (NPs) and nanoplastics (nPs). This has positioned autophagy modulation at the forefront of nanotechnology-based therapeutic interventions. While NMs can exploit autophagy to enhance therapeutic outcomes, they can also trigger it as a pro-survival response against NP-induced toxicity. Conversely, a heightened autophagy response may also lead to regulated cell death (RCD), in particular autophagic cell death, upon NP exposure. Thus, the relationship between NMs and autophagy exhibits a dual nature with therapeutic and environmental interventions. Recognizing and decoding these intricate patterns are essential for pioneering next-generation autophagy-regulating NMs. This review delves into the present-day therapeutic potential of autophagy-modulating NMs, shedding light on their status in clinical trials, intervention of autophagy in the therapeutic applications of NMs, discusses the potency of autophagy for application as early indicator of NM toxicity.

Assessing the influence of small structural modifications in simple DNA-based nanostructures on their role as drug nanocarriers

DNA nanotechnology leverages Watson-Crick-Franklin base-pairing interactions to build complex DNA-based nanostructures (DNS). Due to DNA specific self-assembly properties, DNS can be designed with a total control of their architecture, which has been demonstrated to have an impact on the overall DNS features. Indeed, structural properties such as the shape, size and flexibility of DNS can influence their biostability as well as their ability to internalise into cells. We present here two series of simple DNS with small and precise variations related to their length or flexibility and study the influence that these structural changes have on their overall properties as drug nanocarriers. Results indicate that shorter and more flexible DNS present higher stability towards nuclease degradation. These structural changes also have a certain effect on their cell internalisation ability and drug release rate. Consequently, drug-loaded DNS cytotoxicity varies according to the design, with lower cell viability values obtained in the DNS exhibiting faster drug release and larger cell interaction rates. In summary, small changes in the structure of simple DNS can have an influence on their overall capabilities as drug nanocarriers. The effects reported here could guide the design of simple DNS for future therapeutic uses.

Improving DNA nanostructure stability: A review of the biomedical applications and approaches

DNA's programmable, predictable, and precise self-assembly properties enable structural DNA nanotechnology. DNA nanostructures have a wide range of applications in drug delivery, bioimaging, biosensing, and theranostics. However, physiological conditions, including low cationic ions and the presence of nucleases in biological systems, can limit the efficacy of DNA nanostructures. Several strategies for stabilizing DNA nanostructures have been developed, including i) coating them with biomolecules or polymers, ii) chemical cross-linking of the DNA strands, and iii) modifications of the nucleotides and nucleic acids backbone. These methods significantly enhance the structural stability of DNA nanostructures and thus enable in vivo and in vitro applications. This study reviews the present perspective on the distinctive properties of the DNA molecule and explains various DNA nanostructures, their advantages, and their disadvantages. We provide a brief overview of the biomedical applications of DNA nanostructures and comprehensively discuss possible approaches to improve their biostability. Finally, the shortcomings and challenges of the current biostability approaches are examined.

Heavy Metal Stabilization of DNA Origami Nanostructures

DNA origami is a powerful tool to fold 3-dimensional DNA structures with nanometer precision. Its usage, however, is limited as high ionic strength, temperatures below ∼60 °C, and pH values between 5 and 10 are required to ensure the structural integrity of DNA origami nanostructures. Here, we demonstrate a simple and effective method to stabilize DNA origami nanostructures against harsh buffer conditions using [PdCl4]2-. It provided the stabilization of different DNA origami nanostructures against mechanical compression, temperatures up to 100 °C, double-distilled water, and pH values between 4 and 12. Additionally, DNA origami superstructures and bound cargos are stabilized with yields of up to 98%. To demonstrate the general applicability of our approach, we employed our protocol with a Pd metallization procedure at elevated temperatures. In the future, we think that our method opens up new possibilities for applications of DNA origami nanostructures beyond their usual reaction conditions.

Ion beam processing of DNA origami nanostructures

DNA origami nanostructures are emerging as a bottom-up nanopatterning approach. Direct combination of this approach with top-down nanotechnology, such as ion beams, has not been considered because of the soft nature of the DNA material. Here we demonstrate that the shape of 2D DNA origami nanostructures deposited on Si substrates is well preserved upon irradiation by ion beams, modeling ion implantation, lithography, and sputtering conditions. Structural changes in 2D DNA origami nanostructures deposited on Si are analyzed using AFM imaging. The observed effects on DNA origami include structure height decrease or increase upon fast heavy ion irradiation in vacuum and in air, respectively. Slow- and medium-energy heavy ion irradiation results in the cutting of the nanostructures or crater formation with ion-induced damage in the 10 nm range around the primary ion track. In all these cases, the designed shape of the 2D origami nanostructure remains unperturbed. Present stability and nature of damages on DNA origami nanostructures enable fusion of DNA origami advantages such as shape and positioning control into novel ion beam nanofabrication approaches.

PCNA as Protein-Based Nanoruler for Sub-10 nm Fluorescence Imaging

Super-resolution microscopy has revolutionized biological imaging enabling direct insight into cellular structures and protein arrangements with so far unmatched spatial resolution. Today, refined single-molecule localization microscopy methods achieve spatial resolutions in the one-digit nanometer range. As the race for molecular resolution fluorescence imaging with visible light continues, reliable biologically compatible reference structures will become essential to validate the resolution power. Here, PicoRulers (protein-based imaging calibration optical rulers), multilabeled oligomeric proteins designed as advanced molecular nanorulers for super-resolution fluorescence imaging are introduced. Genetic code expansion (GCE) is used to site-specifically incorporate three noncanonical amino acids (ncAAs) into the homotrimeric proliferating cell nuclear antigen (PCNA) at 6 nm distances. Bioorthogonal click labeling with tetrazine-dyes and tetrazine-functionalized oligonucleotides allows efficient labeling of the PicoRuler with minimal linkage error. Time-resolved photoswitching fingerprint analysis is used to demonstrate the successful synthesis and DNA-based points accumulation for imaging in nanoscale topography (DNA-PAINT) is used to resolve 6 nm PCNA PicoRulers. Since PicoRulers maintain their structural integrity under cellular conditions they represent ideal molecular nanorulers for benchmarking the performance of super-resolution imaging techniques, particularly in complex biological environments.

Near Quantitative Ligation Results in Resistance of DNA Origami Against Nuclease and Cell Lysate

There have been limited efforts to ligate the staple nicks in DNA origami which is crucial for their stability against thermal and mechanical treatments, and chemical and biological environments. Here, two near quantitative ligation methods are demonstrated for the native backbone linkage at the nicks in origami: i) a cosolvent dimethyl sulfoxide (DMSO)-assisted enzymatic ligation and ii) enzyme-free chemical ligation by CNBr. Both methods achieved over 90% ligation in 2D origami, only CNBr-method resulted in ≈80% ligation in 3D origami, while the enzyme-alone yielded 31-55% (2D) or 22-36% (3D) ligation. Only CNBr-method worked efficiently for 3D origami. The CNBr-mediated reaction is completed within 5 min, while DMSO-method took overnight. Ligation by these methods improved the structural stability up to 30 °C, stability during the electrophoresis and subsequent extraction, and against nuclease and cell lysate. These methods are straightforward, non-tedious, and superior in terms of cost, reaction time, and efficiency.

Platinum-DNA Origami Hybrid Structures in Concentrated Hydrogen Peroxide

The DNA origami technique allows fast and large-scale production of DNA nanostructures that stand out with an accurate addressability of their anchor points. This enables the precise organization of guest molecules on the surfaces and results in diverse functionalities. However, the compatibility of DNA origami structures with catalytically active matter, a promising pathway to realize autonomous DNA machines, has so far been tested only in the context of bio-enzymatic activity, but not in chemically harsh reaction conditions. The latter are often required for catalytic processes involving high-energy fuels. Here, we provide proof-of-concept data showing that DNA origami structures are stable in 5 % hydrogen peroxide solutions over the course of at least three days. We report a protocol to couple these to platinum nanoparticles and show catalytic activity of the hybrid structures. We suggest that the presented hybrid structures are suitable to realize catalytic nanomachines combined with precisely engineered DNA nanostructures.

Superstructure-dependent stability of DNA origami nanostructures in the presence of chaotropic denaturants

The structural stability of DNA origami nanostructures in various chemical environments is an important factor in numerous applications, ranging from biomedicine and biophysics to analytical chemistry and materials synthesis. In this work, the stability of six different 2D and 3D DNA origami nanostructures is assessed in the presence of three different chaotropic salts, i.e., guanidinium sulfate (Gdm2SO4), guanidinium chloride (GdmCl), and tetrapropylammonium chloride (TPACl), which are widely employed denaturants. Using atomic force microscopy (AFM) to quantify nanostructural integrity, Gdm2SO4 is found to be the weakest and TPACl the strongest DNA origami denaturant, respectively. Despite different mechanisms of actions of the selected salts, DNA origami stability in each environment is observed to depend on DNA origami superstructure. This is especially pronounced for 3D DNA origami nanostructures, where mechanically more flexible designs show higher stability in both GdmCl and TPACl than more rigid ones. This is particularly remarkable as this general dependence has previously been observed under Mg2+-free conditions and may provide the possibility to optimize DNA origami design toward maximum stability in diverse chemical environments. Finally, it is demonstrated that melting temperature measurements may overestimate the stability of certain DNA origami nanostructures in certain chemical environments, so that such investigations should always be complemented by microscopic assessments of nanostructure integrity.

DNA-origami-directed virus capsid polymorphism

Viral capsids can adopt various geometries, most iconically characterized by icosahedral or helical symmetries. Importantly, precise control over the size and shape of virus capsids would have advantages in the development of new vaccines and delivery systems. However, current tools to direct the assembly process in a programmable manner are exceedingly elusive. Here we introduce a modular approach by demonstrating DNA-origami-directed polymorphism of single-protein subunit capsids. We achieve control over the capsid shape, size and topology by employing user-defined DNA origami nanostructures as binding and assembly platforms, which are efficiently encapsulated within the capsid. Furthermore, the obtained viral capsid coatings can shield the encapsulated DNA origami from degradation. Our approach is, moreover, not limited to a single type of capsomers and can also be applied to RNA-DNA origami structures to pave way for next-generation cargo protection and targeting strategies.

Net-Shaped DNA Nanostructures Designed for Rapid/Sensitive Detection and Potential Inhibition of the SARS-CoV-2 Virus

We present a net-shaped DNA nanostructure (called "DNA Net" herein) design strategy for selective recognition and high-affinity capture of intact SARS-CoV-2 virions through spatial pattern-matching and multivalent interactions between the aptamers (targeting wild-type spike-RBD) positioned on the DNA Net and the trimeric spike glycoproteins displayed on the viral outer surface. Carrying a designer nanoswitch, the DNA Net-aptamers release fluorescence signals upon virus binding that are easily read with a handheld fluorimeter for a rapid (in 10 min), simple (mix-and-read), sensitive (PCR equivalent), room temperature compatible, and inexpensive (∼$1.26/test) COVID-19 test assay. The DNA Net-aptamers also impede authentic wild-type SARS-CoV-2 infection in cell culture with a near 1 × 103-fold enhancement of the monomeric aptamer. Furthermore, our DNA Net design principle and strategy can be customized to tackle other life-threatening and economically influential viruses like influenza and HIV, whose surfaces carry class-I viral envelope glycoproteins like the SARS-CoV-2 spikes in trimeric forms.

Self-Assembly of DNA Nanostructures in Different Cations

The programmable nature of DNA allows the construction of custom-designed static and dynamic nanostructures, and assembly conditions typically require high concentrations of magnesium ions that restricts their applications. In other solution conditions tested for DNA nanostructure assembly, only a limited set of divalent and monovalent ions are used so far (typically Mg2+ and Na+ ). Here, we investigate the assembly of DNA nanostructures in a wide variety of ions using nanostructures of different sizes: a double-crossover motif (76 bp), a three-point-star motif (~134 bp), a DNA tetrahedron (534 bp) and a DNA origami triangle (7221 bp). We show successful assembly of a majority of these structures in Ca2+ , Ba2+ , Na+ , K+ and Li+ and provide quantified assembly yields using gel electrophoresis and visual confirmation of a DNA origami triangle using atomic force microscopy. We further show that structures assembled in monovalent ions (Na+ , K+ and Li+ ) exhibit up to a 10-fold higher nuclease resistance compared to those assembled in divalent ions (Mg2+ , Ca2+ and Ba2+ ). Our work presents new assembly conditions for a wide range of DNA nanostructures with enhanced biostability.

Proximity-Driven DNA Nanosensors

In proximity-driven sensing, interactions between a probe and an analyte produce a detectable signal by causing a change in distance of two probe components or signaling moieties. By interfacing such systems with DNA-based nanostructures, platforms that are highly sensitive, specific, and programmable can be designed. In this Perspective, we delineate the advantages of using DNA building blocks in proximity-driven nanosensors and provide an overview of recent progress in the field, from sensors that rapidly detect pesticides in food to probes that identify rare cancer cells in blood. We also discuss current challenges and identify key areas that need further development.

In vitro transcription of self-assembling DNA nanoparticles

Nucleic acid nanoparticles are playing an increasingly important role in biomolecular diagnostics and therapeutics as well as a variety of other areas. The unique attributes of self-assembling DNA nanoparticles provide a potentially valuable addition or alternative to the lipid-based nanoparticles that are currently used to ferry nucleic acids in living systems. To explore this possibility, we have assessed the ability of self-assembling DNA nanoparticles to be constructed from complete gene cassettes that are capable of gene expression in vitro. In the current report, we describe the somewhat counter-intuitive result that despite extensive crossovers (the stereochemical analogs of Holliday junctions) and variations in architecture, these DNA nanoparticles are amenable to gene expression as evidenced by T7 RNA polymerase-driven transcription of a reporter gene in vitro. These findings, coupled with the vastly malleable architecture and chemistry of self-assembling DNA nanoparticles, warrant further investigation of their utility in biomedical genetics.

Cation-dependent assembly of hexagonal DNA origami lattices on SiO2 surfaces

DNA origami nanostructures have emerged as functional materials for applications in various areas of science and technology. In particular, the transfer of the DNA origami shape into inorganic materials using established silicon lithography methods holds great promise for the fabrication of nanostructured surfaces for nanoelectronics and nanophotonics. Using ordered DNA origami lattices directly assembled on the oxidized silicon surface instead of single nanostructures would enable the fabrication of functional nanopatterned surfaces with macroscopic dimensions. Here, we thus investigate the assembly of hexagonal DNA lattices from DNA origami triangles on RCA-cleaned silicon wafers with hydroxylated surface oxide by time-lapse atomic force microscopy (AFM). Lattice assembly on the SiO2 surface is achieved by a competition of monovalent and divalent cations at elevated temperatures. Ca2+ is found to be superior to Mg2+ in promoting the assembly of ordered lattices, while the presence of Mg2+ rather results in DNA origami aggregation and multilayer formation at the comparably high Na+ concentrations of 200 to 600 mM. Furthermore, Na+ concentration and temperature have a similar effect on lattice order, so that a reduction of temperature can be compensated to some extent by an increase in Na+ concentration. However, even under optimized conditions, the DNA origami lattices assembled on the SiO2 surface exhibit a lower degree of order than equivalent lattices assembled on mica, which is attributed to a higher desorption rate of the DNA origami nanostructures. Even though this high desorption rate also complicates any post-assembly treatment, the formed DNA origami lattices could successfully be transferred into the dry state, which is an important prerequisite for further processing steps.

Stability of DNA Origami Nanostructures in Physiological Media: The Role of Molecular Interactions

Programmable, custom-shaped, and nanometer-precise DNA origami nanostructures have rapidly emerged as prospective and versatile tools in bionanotechnology and biomedicine. Despite tremendous progress in their utilization in these fields, essential questions related to their structural stability under physiological conditions remain unanswered. Here, DNA origami stability is explored by strictly focusing on distinct molecular-level interactions. In this regard, the fundamental stabilizing and destabilizing ionic interactions as well as interactions involving various enzymes and other proteins are discussed, and their role in maintaining, modulating, or decreasing the structural integrity and colloidal stability of DNA origami nanostructures is summarized. Additionally, specific issues demanding further investigation are identified. This review - through its specific viewpoint - may serve as a primer for designing new, stable DNA objects and for adapting their use in applications dealing with physiological media.

Full Site-Specific Addressability in DNA Origami-Templated Silica Nanostructures

DNA nanotechnology allows for the fabrication of nanometer-sized objects with high precision and selective addressability as a result of the programmable hybridization of complementary DNA strands. Such structures can template the formation of other materials, including metals and complex silica nanostructures, where the silica shell simultaneously acts to protect the DNA from external detrimental factors. However, the formation of silica nanostructures with site-specific addressability has thus far not been explored. Here, it is shown that silica nanostructures templated by DNA origami remain addressable for post silicification modification with guest molecules even if the silica shell measures several nm in thickness. The conjugation of fluorescently labeled oligonucleotides is used to different silicified DNA origami structures carrying a complementary ssDNA handle as well as DNA-PAINT super-resolution imaging to show that ssDNA handles remain unsilicified and thus ensure retained addressability. It is also demonstrated that not only handles, but also ssDNA scaffold segments within a DNA origami nanostructure remain accessible, allowing for the formation of dynamic silica nanostructures. Finally, the power of this approach is demonstrated by forming 3D DNA origami crystals from silicified monomers. These results thus present a fully site-specifically addressable silica nanostructure with complete control over size and shape.

Self-assembly of DNA nanostructures in different cations

The programmable nature of DNA allows the construction of custom-designed static and dynamic nanostructures, and assembly conditions typically require high concentrations of magnesium ions which restricts their applications. In other solution conditions tested for DNA nanostructure assembly, only a limited set of divalent and monovalent ions have been used so far (typically Mg 2+ and Na + ). Here, we investigate the assembly of DNA nanostructures in a wide variety of ions using nanostructures of different sizes: a double-crossover motif (76 bp), a three-point-star motif (∼134 bp), a DNA tetrahedron (534 bp) and a DNA origami triangle (7221 bp). We show successful assembly of a majority of these structures in Ca 2+ , Ba 2+ , Na + , K + and Li + and provide quantified assembly yields using gel electrophoresis and visual confirmation of a DNA origami triangle using atomic force microscopy. We further show that structures assembled in monovalent ions (Na + , K + and Li + ) exhibit up to a 10-fold higher nuclease resistance compared to those assembled in divalent ions (Mg 2+ , Ca 2+ and Ba 2+ ). Our work presents new assembly conditions for a wide range of DNA nanostructures with enhanced biostability.

Designer DNA NanoGripper

DNA has shown great biocompatibility, programmable mechanical properties, and structural addressability at the nanometer scale, making it a versatile material for building high precision nanorobotics for biomedical applications. Herein, we present design principle, synthesis, and characterization of a DNA nanorobotic hand, called the "NanoGripper", that contains a palm and four bendable fingers as inspired by human hands, bird claws, and bacteriophages evolved in nature. Each NanoGripper finger has three phalanges connected by two flexible and rotatable joints that are bendable in response to binding to other entities. Functions of the NanoGripper have been enabled and driven by the interactions between moieties attached to the fingers and their binding partners. We showcase that the NanoGripper can be engineered to interact with and capture various objects with different dimensions, including gold nanoparticles, gold NanoUrchins, and SARS-CoV-2 virions. When carrying multiple DNA aptamer nanoswitches programmed to generate fluorescent signal enhanced on a photonic crystal platform, the NanoGripper functions as a sensitive viral biosensor that detects intact SARS-CoV-2 virions in human saliva with a limit of detection of ~ 100 copies/mL, providing RT-PCR equivalent sensitivity. Additionally, we use confocal microscopy to visualize how the NanoGripper-aptamer complex can effectively block viral entry into the host cells, indicating the viral inhibition. In summary, we report the design, synthesis, and characterization of a complex nanomachine that can be readily tailored for specific applications. The study highlights a path toward novel, feasible, and efficient solutions for the diagnosis and therapy of other diseases such as HIV and influenza.

Lab-on-a-DNA origami: nanoengineered single-molecule platforms

DNA origami nanostructures are self-assembled into almost arbitrary two- and three-dimensional shapes from a long, single-stranded viral scaffold strand and a set of short artificial oligonucleotides. Each DNA strand can be functionalized individually using well-established DNA chemistry, representing addressable sites that allow for the nanometre precise placement of various chemical entities such as proteins, molecular chromophores, nanoparticles, or simply DNA motifs. By means of microscopic and spectroscopic techniques, these entities can be visualized or detected, and either their mutual interaction or their interaction with external stimuli such as radiation can be studied. This gives rise to the Lab-on-a-DNA origami approach, which is introduced in this Feature Article, and the state-of-the-art is summarized with a focus on light-harvesting nanoantennas and DNA platforms for single-molecule analysis either by optical spectroscopy or atomic force microscopy (AFM). Light-harvesting antennas can be generated by the precise arrangement of chromophores to channel and direct excitation energy. At the same time, plasmonic nanoparticles represent a complementary approach to focus light on the nanoscale. Plasmonic nanoantennas also allow for the observation of single molecules either by Raman scattering or fluorescence spectroscopy and DNA origami platforms provide unique opportunities to arrange nanoparticles and molecules to be studied. Finally, the analysis of single DNA motifs by AFM allows for an investigation of radiation-induced processes in DNA with unprecedented detail and accuracy.

Transmembrane capability of DNA origami sheet enhanced by 3D configurational changes

DNA origami-engineered nanostructures are widely used in biomedical applications involving transmembrane delivery. Here, we propose a method to enhance the transmembrane capability of DNA origami sheets by changing their configuration from two-dimensional to three-dimensional. Three DNA nanostructures are designed and constructed, including the two-dimensional rectangular DNA origami sheet, the DNA tube, and the DNA tetrahedron. The latter two are the variants of the DNA origami sheet with three-dimensional morphologies achieved through one-step folding and multi-step parallel folding separately. The design feasibility and structural stability of three DNA nanostructures are confirmed by molecular dynamics simulations. The fluorescence signals of the brain tumor models demonstrate that the tubular and the tetrahedral configurational changes could dramatically increase the penetration efficiency of the original DNA origami sheet by about three and five times, respectively. Our findings provide constructive insights for further rational designs of DNA nanostructures for transmembrane delivery.

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.

Nucleic acid nanostructures for in vivo applications: The influence of morphology on biological fate

The development of programmable biomaterials for use in nanofabrication represents a major advance for the future of biomedicine and diagnostics. Recent advances in structural nanotechnology using nucleic acids have resulted in dramatic progress in our understanding of nucleic acid-based nanostructures (NANs) for use in biological applications. As the NANs become more architecturally and functionally diverse to accommodate introduction into living systems, there is a need to understand how critical design features can be controlled to impart desired performance in vivo. In this review, we survey the range of nucleic acid materials utilized as structural building blocks (DNA, RNA, and xenonucleic acids), the diversity of geometries for nanofabrication, and the strategies to functionalize these complexes. We include an assessment of the available and emerging characterization tools used to evaluate the physical, mechanical, physiochemical, and biological properties of NANs in vitro. Finally, the current understanding of the obstacles encountered along the in vivo journey is contextualized to demonstrate how morphological features of NANs influence their biological fates. We envision that this summary will aid researchers in the designing novel NAN morphologies, guide characterization efforts, and design of experiments and spark interdisciplinary collaborations to fuel advancements in programmable platforms for biological applications.

Self-Assembled Artificial DNA Nanocompartments and Their Bioapplications

Compartmentalization is the strategy evolved by nature to control reactions in space and time. The ability to emulate this strategy through synthetic compartmentalization systems has rapidly evolved in the past years, accompanied by an increasing understanding of the effects of spatial confinement on the thermodynamic and kinetic properties of the guest molecules. DNA nanotechnology has played a pivotal role in this scientific endeavor and is still one of the most promising approaches for the construction of nanocompartments with programmable structural features and nanometer-scaled addressability. In this review, the design approaches, bioapplications, and theoretical frameworks of self-assembled DNA nanocompartments are surveyed. From DNA polyhedral cages to virus-like capsules, the construction principles of such intriguing architectures are illustrated. Various applications of DNA nanocompartments, including their use for programmable enzyme scaffolding, single-molecule studies, biosensing, and as artificial nanofactories, ending with an ample description of DNA nanocages for biomedical purposes, are then reported. Finally, the theoretical hypotheses that make DNA nanocompartments, and nanosystems in general, a topic of great interest in modern science, are described and the progresses that have been done until now in the comprehension of the peculiar phenomena that occur within nanosized environments are summarized.

DNA-nanostructure-templated assembly of planar and curved lipid-bilayer membranes

Lipid-bilayer nanodiscs and liposomes have been developed to stabilize membrane proteins in order to study their structures and functions. Nanodiscs are detergent-free, water-soluble, and size-controlled planar phospholipid-bilayer platforms. On the other hand, liposomes are curved phospholipid-bilayer spheres with an aqueous core used as drug delivery systems and model membrane platforms for studying cellular activities. A long-standing challenge is the generation of a homogenous and monodispersed lipid-bilayer system with a very wide range of dimensions and curvatures (elongation, bending, and twisting). A DNA-origami template provides a way to control the shapes, sizes, and arrangements of lipid bilayers via enforcing the assembly of lipid bilayers within the cavities created by DNA nanostructures. Here, we provide a concise overview and discuss how to design planar and curved lipid-bilayer membranes by using DNA-origami nanostructures as templates. Finally, we will discuss the potential applications of DNA-origami nanostructures in the structural and functional studies of large membrane proteins and their complexes.

Stabilization of Functional DNA Structures with Mild Photochemical Methods

A significant barrier to biological applications of DNA structures is their instability to nucleases. UV-mediated thymine dimerization can crosslink and stabilize DNA nanostructures, but its effect on DNA strand hybridization fidelity and function is unclear. In this work, we first compare a number of methods for DNA irradiation with different wavelengths of light and different photosensitizers. We demonstrate that all approaches can achieve nuclease protection; however, the levels of DNA off-target crosslinking and damage vary. We then describe mild irradiation conditions intended to safeguard DNA against nuclease degradation. We demonstrate up to 25× increase in serum stability while minimizing off-target damage and maintaining functions such as hybridization efficiency, gene silencing, aptamer binding, and DNA nanostructure formation. Our methodology requires no complex instruments beyond a UV light source and no synthetic modification of the DNA itself, allowing for applications in numerous areas of nucleic acid therapy and nanotechnology.

Advancing the Utility of DNA Origami Technique through Enhanced Stability of DNA-Origami-Based Assemblies

Since its discovery in 2006, the DNA origami technique has revolutionized bottom-up nanofabrication. This technique is simple yet versatile and enables the fabrication of nanostructures of almost arbitrary shapes. Furthermore, due to their intrinsic addressability, DNA origami structures can serve as templates for the arrangement of various nanoscale components (small molecules, proteins, nanoparticles, etc.) with controlled stoichiometry and nanometer-scale precision, which is often beyond the reach of other nanofabrication techniques. Despite the multiple benefits of the DNA origami technique, its applicability is often restricted by the limited stability in application-specific conditions. This Review provides an overview of the strategies that have been developed to improve the stability of DNA-origami-based assemblies for potential biomedical, nanofabrication, and other applications.

Structure-Dependent Electrical Conductance of DNA Origami Nanowires

Exploring the structural and electrical properties of DNA origami nanowires is an important endeavor for the advancement of DNA nanotechnology and DNA nanoelectronics. Highly conductive DNA origami nanowires are a desirable target for creating low-cost self-assembled nanoelectronic devices and circuits. In this work, the structure-dependent electrical conductance of DNA origami nanowires is investigated. A silicon nitride (Si₃ N₄ ) on silicon semiconductor chip with gold electrodes was used for collecting electrical conductance measurements of DNA origami nanowires, which are found to be an order of magnitude less electrically resistive on Si₃ N₄ substrates treated with a monolayer of hexamethyldisilazane (HMDS) (∼10¹³ ohms) than on native Si₃ N₄ substrates without HMDS (∼10¹⁴ ohms). Atomic force microscopy (AFM) measurements of the height of DNA origami nanowires on mica and Si₃ N₄ substrates reveal that DNA origami nanowires are ∼1.6 nm taller on HMDS-treated substrates than on the untreated ones indicating that the DNA origami nanowires undergo increased structural deformation when deposited onto untreated substrates, causing a decrease in electrical conductivity. This study highlights the importance of understanding and controlling the interface conditions that affect the structure of DNA and thereby affect the electrical conductance of DNA origami nanowires.

Protein Coating of DNA Origami

DNA origami has emerged as a common technique to create custom two- (2D) and three-dimensional (3D) structures at the nanoscale. These DNA nanostructures have already proven useful in development of many biotechnological tools; however, there are still challenges that cast a shadow over the otherwise bright future of biomedical uses of these DNA objects. The rather obvious obstacles in harnessing DNA origami as drug-delivery vehicles and/or smart biodevices are related to their debatable stability in biologically relevant media, especially in physiological low-cation and endonuclease-rich conditions, relatively poor transfection rates, and, although biocompatible by nature, their unpredictable compatibility with the immune system. Here we demonstrate a technique for coating DNA origami with albumin proteins for enhancing their pharmacokinetic properties. To facilitate protective coating, a synthesized positively charged dendron was linked to bovine serum albumin (BSA) through a covalent maleimide-cysteine bonding, and then the purified dendron-protein conjugates were let to assemble on the negatively charged surface of DNA origami via electrostatic interaction. The resulted BSA-dendron conjugate-coated DNA origami showed improved transfection, high resistance against endonuclease digestion, and significantly enhanced immunocompatibility compared to bare DNA origami. Furthermore, our proposed coating strategy can be considered highly versatile as a maleimide-modified dendron serving as a synthetic DNA-binding domain can be linked to any protein with an available cysteine site.

Recent advances of metal-based nanoparticles in nucleic acid delivery for therapeutic applications

Recent efforts in designing nanomaterials to deliver potential therapeutics to the targeted site are overwhelming and palpable. Engineering nanomaterials to deliver biological molecules to exert desirable physiological changes, with minimized side effects and optimal dose, has revolutionized the next-generation therapy for several diseases. The rapid progress of nucleic acids as biopharmaceutics is going to alter the traditional pharmaceutics practices in modern medicine. However, enzymatic instability, large size, dense negative charge (hydrophilic for cell uptake), and unintentional adverse biological responses-such as prolongation of the blood coagulation and immune system activation-hamper the potential use of nucleic acids for therapeutic purposes. Moreover, the safe delivery of nucleic acids into the clinical setting is an uphill task, and several efforts are being put forward to deliver them to targeted cells. Advances in Metal-based NanoParticles (MNPs) are drawing attention due to the unique properties offered by them for drug delivery, such as large surface-area-to-volume ratio for surface modification, increased therapeutic index of drugs through site-specific delivery, increased stability, enhanced half-life of the drug in circulation, and efficient biodistribution to the desired targeted site. Here, the potential of nanoparticles delivery systems for the delivery of nucleic acids, specially MNPs, and their ability and advantages over other nano delivery systems are reviewed.

DNA Nanotechnology-Empowered Live Cell Measurements

The systematic analysis and precise manipulation of a variety of biomolecules should lead to unprecedented findings in fundamental biology. However, conventional technology cannot meet the current requirements. Despite this, there has been progress as DNA nanotechnology has evolved to generate DNA nanostructures and circuits over the past four decades. Many potential applications of DNA nanotechnology for live cell measurements have begun to emerge owing to the biocompatibility, nanometer addressability, and stimulus responsiveness of DNA. In this review, the DNA nanotechnology-empowered live cell measurements which are currently available are summarized. The stability of the DNA nanostructures, in a cellular microenvironment, which is crucial for accomplishing precise live cell measurements, is first summarized. Thereafter, measurements in the extracellular and intracellular microenvironment, in live cells, are introduced. Finally, the challenges that are innate to, and the further developments that are possible in this nascent field are discussed.

DNA Origami Disguises Herpes Simplex Virus 1 Particles and Controls Their Virulence

DNA nanostructures are well-established vectors for packaging diversified payloads for targeted cellular delivery. Here, DNA origami rectangular sheets were combined with Herpes Simplex Virus 1 (HSV1) capsids to demonstrate surface coverage of the particle via electrostatic interactions. The optimized origami:HSV1 molar ratios led to characteristic packaging geometries ranging from dispersed "HSV1 pockets" to agglomerated "HSV1 sleeves". "Pockets" were disguised from cells in HeLa and B16F10 cells and were 44.2% less infective than naked HSV1 particles. However, the pockets were 117% more infective than naked HSV1 particles when the origami sheets were coated with folic acid. We observed infectivity from naked origami, but they are 99.1% less infective with respect to HSV1 and 99.6% less infective with respect to the pocket complexes. This work suggests that DNA origami can selectively modulate virus infectivity.

Functionalized-DNA nanostructures as potential targeted drug delivery systems for cancer therapy

Seeman's pioneer idea has led to the foundation of DNA nanostructures, resulting in a remarkable advancement in DNA nanotechnology. Over the last few decades, remarkable advances in drug delivery techniques have resulted in the self-assembly of DNA for encapsulating candidate drug molecules. The nuclear targeting capability of DNA nanostructures is lies within their high spatial addressability and tremendous potential for active targeting. However, effective programming and assembling those DNA molecules remains a challenge, making the path to DNA nanostructures for real-world applications difficult. Because of their small size, most nanostructures are self-capable of infiltrating into the tumor cellular environment. Furthermore, to enable controlled and site-specific delivery of encapsulated drug molecules, DNA nanostructures are functionalized with special moieties that allow them to bind specific targets and release cargo only at targeted sites rather than non-specific sites, resulting in the prevention/limitation of cellular toxicity. In light of this, the current review seeks to shed light on the versatility of the DNA molecule as a targeting and encapsulating moiety for active drugs in order to achieve controlled and specific drug release with spatial and temporal precision. Furthermore, this review focused on the challenges associated with the construction of DNA nanostructures as well as the most recent advances in the functionalization of DNA nanostructures using various materials for controlled and targeted delivery of medications for cancer therapy.

A Tetrahedral Framework DNA-Based Bioswitchable miRNA Inhibitor Delivery System: Application to Skin Anti-Aging

MicroRNA (miR)-based therapy shows strong potential; however, structural limitations pose a challenge in fully exploiting its biomedical functionality. Tetrahedral framework DNA (tFNA) has proven to be an ideal vehicle for miR therapy. Inspired by the ancient Chinese myth "Sun and Immortal Birds," a novel bioswitchable miR inhibitor delivery system (BiRDS) is designed with three miR inhibitors (the three immortal birds) and a nucleic acid core (the central sun). The BiRDS fuses miR inhibitors within the framework, maximizing their loading capacity, while allowing the system to retain the characteristics of small-sized tFNA and avoiding uncertainty associated with RNA exposure in traditional loading protocols. The RNase H-responsive sequence at the tail of each "immortal bird" enables the BiRDS to transform from a 3D to a 2D structure upon entering cells, promoting the delivery of miR inhibitors. To confirm the application potential, the BiRDS is used to deliver the miR-31 inhibitor, with antiaging effects on hair follicle stem cells, into a skin aging model. Superior skin penetration ability and RNA delivery are observed with significant anti-aging effects. These findings demonstrate the capability and editability of the BiRDS to improve the stability and delivery efficacy of miRs for future innovations.

Reconfiguration of DNA nanostructures induced by enzymatic ligation treatment

Enzymatic ligation is a popular method in DNA nanotechnology for structural enforcement. When employed as stability switch for chosen components, ligation can be applied to induce DNA nanostructure reconfiguration. In this study, we investigate the reinforcement effect of ligation on addressable DNA nanostructures assembled entirely from short synthetic strands as the basis of structural reconfiguration. A careful calibration of ligation efficiency is performed on structures with programmable nicks. Systematic investigation using comparative agarose gel electrophoresis enables quantitative assessment of enhanced survivability with ligation treatment on a number of unique structures. The solid ligation performance sets up the foundation for the ligation-based structural reconfiguration. With the capability of switching base pairing status between permanent and transient (ON and OFF) by a simple round of enzymatic treatment, ligation induced reconfiguration can be engineered for DNA nanostructures accordingly.