Designer, Programmable 3D DNA Nanodevices to Probe Biological Systems

Superlarge, Rigidified DNA Tetrahedron with a Y-Shaped Backbone for Organizing Biomolecules Spatially and Maintaining Their Full Bioactivity

A major impediment to the clinical translation of DNA tiling nanostructures is a technical bottleneck for the programmable assembly of DNA architectures with well-defined local geometry due to the inability to achieve both sufficient structural rigidity and a large framework. In this work, a Y-backbone was inserted into each face to construct a superlarge, sufficiently rigidified tetrahedral DNA nanostructure (called RDT) with extremely high efficiency. In RDT, the spatial size increased by 6.86-fold, and the structural rigidity was enhanced at least 4-fold, contributing to an ∼350-fold improvement in the resistance to nucleolytic degradation even without a protective coating. RDT can be mounted onto an artificial lipid-bilayer membrane with molecular-level precision and well-defined spatial orientation that can be validated using the fluorescence resonance energy transfer (FRET) assay. The spatial orientation of Y-shaped backbone-rigidified RDT is unachievable for conventional DNA polyhedrons and ensures a high level of precision in the geometric positioning of diverse biomolecules with an approximately homogeneous environment. In tests of RDT, surface-confined horseradish peroxidase (HRP) exhibited nearly 100% catalytic activity and targeting aptamer-immobilized gold nanoparticles showed 5.3-fold enhanced cellular internalization. Significantly, RDT exhibited a 27.5-fold enhanced structural stability in a bodily environment and did not induce detectable systemic toxicity.

Triple multivalent aptamers within DNA tetrahedron on reduced graphene oxide electrode: Unlocking enhanced sensitivity and accelerated reactions in electrochemical sensing

DNA nanostructures are emerging as promising biosensing platforms due to their programmability, predictable assembly, and compatibility with aptamers for enhanced selectivity. This study focuses on a triple-multivalent aptamer (tApt) complex immobilized on a tetrahedral DNA nanostructure (TDN) and integrated with an electrochemically reduced graphene oxide (ERGO) electrode for highly sensitive mercury ion (Hg2+) detection. Compared to a linear multivalent aptamer-modified electrode (S2/ERGO-GCE), the 3D tApt/ERGO-GCE aptasensor exhibits superior sensitivity, signal amplification, and reaction kinetics. The tApt/ERGO-GCE sensor achieves an exceptional limit of detection (LOD) of 4.1 zM, surpassing the LOD of 0.71 fM for S2/ERGO-GCE. Additionally, the tApt/ERGO-GCE sensor demonstrates faster response times, with a half-saturation time (T1/2) of 6 minutes compared to 17 minutes for S2/ERGO/GCE. The 3D tApt aptamer's superior performance is attributed to its tetrahedral DNA structure integrated on ERGO, providing multiple aptamer binding sites, facilitating oriented immobilization on the electrode surface, and enhancing analyte capture and concentration. In contrast, the linear S2 aptamers lack rigidity, resulting in a disordered orientation on the electrode surface, hindering efficient Hg2+ binding and reducing target molecule binding efficiency. This study underscores the potential of triple-multivalent aptamer-based nanostructures for ultrasensitive and rapid biosensing applications. The tApt/ERGO-GCE aptasensor's exceptional sensitivity, signal amplification, and reaction kinetics make it a promising tool for Hg2+ detection and other biosensing applications.

Structural DNA nanotechnology at the nexus of next-generation bio-applications: challenges and perspectives

DNA nanotechnology has significantly progressed in the last four decades, creating nucleic acid structures widely used in various biological applications. The structural flexibility, programmability, and multiform customization of DNA-based nanostructures make them ideal for creating structures of all sizes and shapes and multivalent drug delivery systems. Since then, DNA nanotechnology has advanced significantly, and numerous DNA nanostructures have been used in biology and other scientific disciplines. Despite the progress made in DNA nanotechnology, challenges still need to be addressed before DNA nanostructures can be widely used in biological interfaces. We can open the door for upcoming uses of DNA nanoparticles by tackling these issues and looking into new avenues. The historical development of various DNA nanomaterials has been thoroughly examined in this review, along with the underlying theoretical underpinnings, a summary of their applications in various fields, and an examination of the current roadblocks and potential future directions.

Progress in Programmable DNA-Aided Self-Assembly of the Master Frame of a Drug Delivery System

Every year cancer causes approximately 10 million deaths globally. Researchers have developed numerous targeted drug delivery systems (DDSs) with nanoparticles, polymers, and liposomes, but these synthetic materials have poor degradability and low biocompatibility. Because DNA nanostructures have good degradability and high biocompatibility, extensive studies have been performed to construct DDSs with DNA nanostructures as the molecular-layer master frame (MF) assembled via programmable DNA-aided self-assembly for targeted drug release. To learn the progressing trend of self-assembly techniques and keep pace with their recent rapid advancements, it is crucial to provide an overview of their past and recent progress. In this review article, we first present the techniques to assemble the MF of a DDS with solely DNA strands; to assemble MFs with one or more additional type of construction materials, e.g., polymers (including RNA and protein), inorganic nanoparticle, or metal ions, in addition to DNA strands; and to assemble the more complex DNA nanocomplexes. It is observed that both the techniques used and the MFs constructed have become increasingly complex and that the DDS constructed has an increasing number of advanced functions. From our focused review, we anticipate that DDSs with the MF of multiple building materials and DNA nanocomplexes will attract an increasing number of researchers' interests. On the basis of knowledge about materials and functional components (e.g., targeting aptamers/peptides/antibodies and stimuli for drug release) obtained from previously performed studies, researchers can combine more materials with DNA strands to assemble more powerful MFs and incorporate more components to endow DDSs with improved or additional properties/functions, thereby subsequently contributing to cancer prevention.

Template-Assisted Assembly of Hybrid DNA/RNA Nanostructures Using Branched Oligodeoxy- and Oligoribonucleotides

A template-assisted assembly approach to a C24 fullerene-like double-stranded DNA polyhedral shell is proposed. The assembly employed a supramolecular oligonucleotide dendrimer as a 3D template that was obtained via the hybridization of siRNA strands and a single-stranded DNA oligonucleotide joined to three- or four-way branched junctions. A four-way branched oligonucleotide building block (a starlet) was designed for the assembly of the shell composed of three identical self-complementary DNA single strands and a single RNA strand for hybridization to the DNA oligonucleotides of the template. To prevent premature auto-hybridization of the self-complementary oligonucleotides in the starlet, a photolabile protecting group was introduced via the N3-substituted thymidine phosphoramidite. Cleavable linkers such as a disulfide linkage, RNase A sensitive triribonucleotides, and di- and trideoxynucleotides were incorporated into the starlet and template at specific points to guide the post-assembly disconnection of the shell from the template, and enzymatic disassembly of the template and the shell in biological media. At the same time, siRNA strands were modified with 2'-OMe ribonucleotides and phosphorothioate groups in certain positions to stabilize toward enzymatic digestion. We report herein a solid-phase synthesis of branched oligodeoxy and oligoribonucleotide building blocks for the DNA/RNA dendritic template and the branched DNA starlet for a template-assisted construction of a C24 fullerene-like DNA shell after initial molecular modeling, followed by the assembly of the shell around the DNA-coated RNA dendritic template, and visualization of the resulting nanostructure by transmission electron microscopy.

Spatiotemporal dynamics of DNA nanocage uptake in zebrafish embryos for targeted tissue bioimaging applications

Three-dimensional DNA nanocages have attracted significant attention for various biomedical applications including targeted bioimaging in vivo. Despite the numerous advantages, the use and in vivo exploration of DNA nanocages are limited as the cellular targeting and intracellular fate of these DNA nanocages within various model systems have not been explored well. Herein, using a zebrafish model system, we provide a detailed understanding of time-, tissue- and geometry-dependent DNA nanocage uptake in developing embryos and larvae. Of all the geometries tested, tetrahedrons showed significant internalization in 72 hours post-fertilized larvae upon exposure, without disturbing the expression of genes involved in embryo development. Our study provides a detailed understanding of the time and tissue-specific uptake of DNA nanocages in the zebrafish embryos and larvae. These findings will provide valuable insights into the internalization and biocompatible potential of DNA nanocages and will help to predict their candidature for biomedical applications.

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.

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.

Designer, Programmable DNA-peptide hybrid materials with emergent properties to probe and modulate biological systems

The chemistry of DNA endows it with certain functional properties that facilitate the generation of self-assembled nanostructures, offering precise control over their geometry and morphology, that can be exploited for advanced biological applications. Despite the structural promise of these materials, their applications are limited owing to lack of functional capability to interact favourably with biological systems, which has been achieved by functional proteins or peptides. Herein, we outline a strategy for functionalizing DNA structures with short-peptides, leading to the formation of DNA-peptide hybrid materials. This proposition offers the opportunity to leverage the unique advantages of each of these bio-molecules, that have far reaching emergent properties in terms of better cellular interactions and uptake, better stability in biological media, an acceptable and programmable immune response and high bioactive molecule loading capacities. We discuss the synthetic strategies for the formation of these materials, namely, solid-phase functionalization and solution-coupling functionalization. We then proceed to highlight selected biological applications of these materials in the domains of cell instruction & molecular recognition, gene delivery, drug delivery and bone & tissue regeneration. We conclude with discussions shedding light on the challenges that these materials pose and offer our insights on future directions of peptide-DNA research for targeted biomedical applications.

Cationic lipid modification of DNA tetrahedral nanocages enhances their cellular uptake

Self-assembled DNA nanocages are among the most promising candidates for bioimaging and payload delivery into cells. DNA nanocages have great potential to efficiently address drug resistance and nucleic acid delivery problems due to precise control of their shape and size, and excellent biocompatibility. Although DNA nanostructures demonstrate some cellular uptake, because they bear a highly negative charge, the uptake of tetrahedral nanostructures is hindered by electrostatic repulsion. In this study, we describe a method to enhance the cellular uptake of DNA nanostructures using a binary system containing DNA and a positively charged head group with a hydrophobic lipid chain containing lipids for cellular internalization. Here we represent the functionalization of a model cage, DNA tetrahedron (TD) with a cationic lipid, N-[1-(2,3-dioleyloxy)propyl]-N,N,N-trimethylammonium chloride (DOTMA). Atomic force microscopy (AFM) and other standard characterization techniques were used to explore the co-assembly of the DNA tetrahedron and DOTMA. We revealed a simple confocal microscopy-based approach to show the enhancement in the cellular uptake of DNA nanocages. This new method will find multiple applications in delivery applications such as gene transfection, drug delivery and targeted bioimaging.

Preparation, applications, and challenges of functional DNA nanomaterials

As a carrier of genetic information, DNA is a versatile module for fabricating nanostructures and nanodevices. Functional molecules could be integrated into DNA by precise base complementary pairing, greatly expanding the functions of DNA nanomaterials. These functions endow DNA nanomaterials with great potential in the application of biomedical field. In recent years, functional DNA nanomaterials have been rapidly investigated and perfected. There have been reviews that classified DNA nanomaterials from the perspective of functions, while this review primarily focuses on the preparation methods of functional DNA nanomaterials. This review comprehensively introduces the preparation methods of DNA nanomaterials with functions such as molecular recognition, nanozyme catalysis, drug delivery, and biomedical material templates. Then, the latest application progress of functional DNA nanomaterials is systematically reviewed. Finally, current challenges and future prospects for functional DNA nanomaterials are discussed.

Geometry of a DNA Nanostructure Influences Its Endocytosis: Cellular Study on 2D, 3D, and in Vivo Systems

Fabrication of nanoscale DNA devices to generate 3D nano-objects with precise control of shape, size, and presentation of ligands has shown tremendous potential for therapeutic applications. The interactions between the cell membrane and different topologies of 3D DNA nanostructures are crucial for designing efficient tools for interfacing DNA devices with biological systems. The practical applications of these DNA nanocages are still limited in cellular and biological systems owing to the limited understanding of their interaction with the cell membrane and endocytic pathway. The correlation between the geometry of DNA nanostructures and their internalization efficiency remains elusive. We investigated the influence of the shape and size of 3D DNA nanostructures on their cellular internalization efficiency. We found that one particular geometry, i.e., the tetrahedral shape, is more favored over other designed geometries for their cellular uptake in 2D and 3D cell models. This is also replicable for cellular processes like cell invasion assays in a 3D spheroid model, and passing the epithelial barriers in in vivo zebrafish model systems. Our work provides detailed information for the rational design of DNA nanodevices for their upcoming biological and biomedical applications.

Integrated DNA triangular prism nanomachines for two-stage dynamic recognizing and bio-imaging from surface to the inside of living cells

The identification and detection of biomarkers in cancer cells play an essential role in the early detection of diseases, especially the detection of dual-biomarker. However, one of the most important limiting factors is how to realize the identification and labeling of biomarkers dynamically from the plasma membrane to the cytoplasm in living cells. In this study, integrated DNA triangular prism nanomachines (IDTPNs), a two-stage identification and dynamic bio-imaging strategy, recognize biomarkers from the plasma membrane to the cytoplasm have been designed. DNA triangular prism (DTP) was selected to act as a delivery platform with the aptamer Sgc8c and P53 modified on the side as the recognition molecules. Through the specific recognition of aptamers and the superior internalization of DTP, the IDTPNs realize the dynamic responses to PTK7 and p53 from the membrane to the cytoplasm in living cells. It is proved that the IDTPNs can be used for dynamic dual-biomarker recognition and bio-image from the surface to the inside of tumor cells automatically. Therefore, the strategy we developed provides a reliable platform for tumor diagnosis and biomarker research.

An ultrasensitive carcinoembryonic antigen electrochemical aptasensor based on 3D DNA nanoprobe and Exo III

In this study, a highly ordered three dimensional (3D) DNA nanostructure was self-assembled by label-free DNA nanotweezers, which was used as recognized probe to interact with target. Once the target was recognized by the 3D DNA nanoprobe (3D DNT), DNA nanotweezers opened to release target analog (T1). This recognition process was proceeded in homogeneous solution, which can avoid complex electrode modification and improve reaction efficiency. Then these target analogs were captured by the signal DNA probes (E1) modified on the electrode. In the assistance of Exo III, E1 was digested and the T1 was released to participate in the next cycle to realize signal amplification. Finally, an ultrasensitive carcinoembryonic antigen (CEA) electrochemical biosensing with a detection limit of 4.88 fg mL^-1 was developed.

T Lymphocyte-Captured DNA Network for Localized Immunotherapy

The efficient isolation of immune cells with high purity and low cell damage is important for immunotherapy and remains highly challenging. We herein report a cell capture DNA network containing polyvalent multimodules for the specific isolation and in situ incubation of T lymphocytes (T-cells). Two ultralong DNA chains synthesized by an enzymatic amplification process were rationally designed to include functional multimodules as cell anchors and immune adjuvants. Mutually complementary sequences facilitated the formation of a DNA network and encapsulation of T-cells, as well as offering cutting sites of a restriction enzyme for the responsive release of T-cells and immune adjuvants. The purity of captured tumor-infiltrating T-cells reached 98%, and the viability of T-cells maintained ∼90%. The T-cells-containing DNA network was further administrated to a tumor lesion for localized immunotherapy. Our work provides a robust nanobiotechnology for efficient isolation of immune cells and other biological particles.

Nitrogen-Incorporated Boron-Doped Nanocrystalline Diamond Nanowires for Microplasma Illumination

The origin of nitrogen-incorporated boron-doped nanocrystalline diamond (NB-NCD) nanowires as a function of substrate temperature (T_s) in H₂/CH₄/B₂H₆/N₂ reactant gases is systematically addressed. Because of T_s, there is a drastic modification in the dimensional structure and microstructure and hence in the several properties of the NB-NCD films. The NB-NCD films grown at low T_s (400 °C) contain faceted diamond grains. The morphology changes to nanosized diamond grains for NB-NCD films grown at 550 °C (or 700 °C). Interestingly, the NB-NCD films grown at 850 °C possess one-dimensional nanowire-like morphological grains. These nanowire-like NB-NCD films possess the co-existence of the sp³-diamond phase and the sp²-graphitic phase, where diamond nanowires are surrounded by sp²-graphitic phases at grain boundaries. The optical emission spectroscopy studies stated that the CN, BH, and C₂ species in the plasma are the main factors for the origin of nanowire-like conducting diamond grains and the materialization of graphitic phases at the grain boundaries. Moreover, conductive atomic force microscopy studies reveal that the NB-NCD films grown at 850 °C show a large number of emission sites from the grains and the grain boundaries. While boron doping improved the electrical conductivity of the NCD grains, the nitrogen incorporation eased the generation of graphitic phases at the grain boundaries that afford conducting channels for the electrons, thus achieving a high electrical conductivity for the NB-NCD films grown at 850 °C. The microplasma devices using these nanowire-like NB-NCD films as cathodes display superior plasma illumination properties with a threshold field of 3300 V/μm and plasma current density of 1.04 mA/cm² with a supplied voltage of 520 V and a lifetime stability of 520 min. The outstanding plasma illumination characteristics of these conducting nanowire-like NB-NCD films make them appropriate as cathodes and pave the way for the utilization of these materials in various microplasma device applications.

Aptamer-Programmed DNA Nanodevices for Advanced, Targeted Cancer Theranostics

DNA has been demonstrated to be a versatile material for construction at the nanoscale. DNA nanodevices are highly programmable and allow functionalization with multiple entities such as imaging modalities (fluorophores), targeting entities (aptamers), drug conjugation (chemical linkers), and triggered release (photoresponsive molecules). These features enhance the use of DNA nanodevices in biological applications, catalyzing the rapid growth of this domain of research. In this review, we focus on recent progress in the development and use of aptamer-functionalized DNA nanodevices as theranostic agents, their characterization, applications as delivery platforms, and advantages. We provide a brief background on the development of aptamers and DNA nanodevices in biomedical applications, and we present specific applications of these entities in cancer diagnosis and therapeutics. We conclude with a perspective on the challenges and possible solutions for the clinical translation of aptamer-functionalized DNA nanodevices in the domain of cancer therapeutics.

Nuclease resistance of DNA nanostructures

DNA nanotechnology has progressed from proof-of-concept demonstrations of structural design towards application-oriented research. As a natural material with excellent self-assembling properties, DNA is an indomitable choice for various biological applications, including biosensing, cell modulation, bioimaging and drug delivery. However, a major impediment to the use of DNA nanostructures in biological applications is their susceptibility to attack by nucleases present in the physiological environment. Although several DNA nanostructures show enhanced resistance to nuclease attack compared with duplexes and plasmid DNA, this may be inadequate for practical application. Recently, several strategies have been developed to increase the nuclease resistance of DNA nanostructures while retaining their functions, and the stability of various DNA nanostructures has been studied in biological fluids, such as serum, urine and cell lysates. This Review discusses the approaches used to modulate nuclease resistance in DNA nanostructures and provides an overview of the techniques employed to evaluate resistance to degradation and quantify stability.