Self-assembled DNA Nanostructures Research Articles

Shape-controllable Synthesis of Functional Nanomaterials on DNA Templates

DNA nanotechnology enables precise organization of nanoscale objects with extraordinarily structural programmability. Self-assembled DNA nanostructures possess a lot of interesting features, such as designable size and shape, and structural addressability at nanometer scale. Taking advantage of these properties, DNA nanostructures could work as templates or molds for the controllable synthesis of functional nanomaterials, such as organic macromolecules, metallic or inorganic nonmetallic nanomaterials. In this review, we summarize the recent progress in the shape-controllable synthesis of functional nanomaterials on DNA templates. The potential application fields of these nanomaterials are also discussed.

Sensitive and specific detection of tumour cells based on a multivalent DNA nanocreeper and a multiplexed fluorescence supersandwich.

A self-assembled DNA nanostructure based on a DNA nanocreeper and multiplexed fluorescence supersandwich was designed for the sensitive and specific detection of tumour cells. This nanostructure could improve the binding affinity of current aptamers and trigger signal amplification, which provide potential for the discrimination of low abundant target cells in liquid biopsy.

Multiform DNA origami arrays using minimal logic control.

Self-assembled DNA nanostructures significantly contribute to DNA nanotechnology. Algorithmic guiding of the assembly of DNA arrays remains a challenge in nanoarchitecture. Usually, the more sophisticated a DNA nanoarchitecture, the more DNA connections with specific sequences are required. This study aimed to investigate the feasibility of using the minimum pairs of DNA connection strands to implement algorithm-based self-assembly with finite DNA origamis. We found that the DNA origami linking complexity was markedly reduced. By rotating and turning the origami tile in different linking directions, we obtained 2 × 2 arrays of DNA origamis using a pair of DNA connections, 2 × 4 arrays using two pairs of DNA connections, and 4 × 4 arrays using three pairs of connection strands. We further analysed the effects of distortion on array formation. Overall, this study presents a hierarchical assembly strategy with minimal connections to generate multi-scale DNA arrays.

Self-assembly of DNA Nanostructures via Bioinspired Metal Ion Coordination

Despite a growing interest in DNA nanomaterials, their simple synthesis remains a challenge. A simple and general strategy for constructing DNA-based nanomaterials by metal ion coordination is reported. The metal-DNA nanoparticles(NPs) could be synthesized with DNA molecules of diverse sequence and various metal ions of intrinsic property, resulting in multifunctional NPs with the combined advantages of both inorganic and DNA building blocks. It is demonstrated that the hybrid metal-DNA NPs could be engineered for magnetic resonance and luminescence imaging, encapsulation of multifarious nucleic acids with controlled ratio, and co-assembly with small drug molecules. Furthermore, because these metal-DNA NPs exhibited enhanced cellular uptake compared to free synthetic DNA, they hold potential for applications in diagnostics and therapeutics.

DNA Nanostructures that Self-Heal in Serum.

Self-assembled DNA nanostructures have potential applications in therapeutics, diagnostics, and synthetic biology. A challenge in using DNA nanostructures in biological environments or cell culture, however, is that they may be degraded by enzymes found in these environments, such as nucleases. Such degradation can be slowed by introducing alternative substrates for nucleases, or by coating nanostructures with membranes or peptides. Here we demonstrate a means by which degradation can be reversed in situ through the repair of nanostructure defects. To demonstrate this effect, we show that degradation rates of DNA nanotubes, micron-scale self-assembled structures, are at least 4-fold lower in the presence of tiles that can repair nanotube defects during the degradation process. Micrographs of nanotubes show that tiles from solution incorporate into nanotubes and that this incorporation increases nanotube lifetime to several days in serum. We use experimental data to formulate a simple model of nanostructure self-healing. This model suggests how introducing even a relatively low rate of repair could allow a nanostructure to survive almost indefinitely because of a dynamic equilibrium between microscale repair and degradation processes. The ability to repair nanostructures could thus allow particular structures or devices to operate for long periods of time and might offer a single means to resist different types of chemical degradation.

Self-assembled DNA structures for nanotheranostic applications

DNA molecule is regarded as the basic material to construct novel nanomaterials due to its good biocompatibility and programmability. Self-assembled DNA structures with controllable size, shape, symmetry, as well as environment-responsive properties were designed and fabricated, which has great potential for application in nanotheranostic fields such as imaging, detection, and drug delivery. However, there are some problems on in vivo application of these DNA-based materials, such as poor stability in living systems, low cell uptake efficiency and drug delivery and controllable release. This review briefly summarized the design methods of self-assembled DNA structures, and their applications in imaging, bioassay, and drug delivery, and provided the strategies to improve the stability and cell penetration ability of these nanostructures. We finally discussed the opportunities and challenges for using self-assembled DNA nanostructures for nanotheranostic applications.

Targeted Delivery of Rab26 siRNA with Precisely Tailored DNA Prism for Lung Cancer Therapy.

Programmable DNA nanostructures are a new class of biocompatible, nontoxic nanomaterials. Nevertheless, their application in the field of biomedical research is still in its infancy, especially as drug delivery vehicles for gene therapy. In this study, a GTPase Rab26 was investigated as a new potential therapeutic target using a precisely tailored DNA nanoprism for targeted lung cancer therapy. Specifically, a DNA nanoprism platform with tunable targeting and siRNA loading capability is designed and synthesized. The as-prepared DNA prisms were decorated with two functional units: a Rab26 siRNA as the drug and MUC-1 aptamers as a targeting moiety for non-small cell lung cancer. The number and position of both siRNA and MUC-1 aptamers can be readily tuned by switching two short, single-stranded DNA. Native polyacrylamide gel electrophoresis (PAGE) and dynamic light scattering technique (DLS) demonstrate that all nanoprisms with different functionalities are self-assembled with high yield. It is also found that the cellular uptake of DNA prisms is proportional to the aptamer number on each nanoprism, and the as-prepared DNA nanoprism show excellent anti-cancer activities and targeting capability. This study suggests that by careful design, self-assembled DNA nanostructures are highly promising, customizable, multifunctional nanoplatforms for potential biomedical applications, such as personalized precision therapy.

Patterning Nanoparticles with DNA Molds.

We report a nanopatterning strategy in which self-assembled DNA nanostructures serve as structural templates. In previous work, ordering of NPs primarily relied on specific recognition, e.g., DNA-DNA hybridization. Only a few cases have been reported on nonspecific adsorption. Unfortunately, these studies were limited by the integrity and homogeneity of templates and the variety of patterned nanoparticles (NPs). Herein, we have developed a general method to pattern various NPs. The NPs adsorb onto substrate via NP-substrate direct interactions and the substrates are patterned into large arrays (>4 × 4 μm) of tiny, accessible cavities by self-assembled DNA arrays. As a demonstration, DNA templates include tetragonal and hexagonal arrays and the NPs include individual DNA nanomotifs, gold nanoparticles (AuNPs), and proteins. All nanostructures have been confirmed by atomic force microscopy and corresponding fast Fourier transform (FFT) analysis.

DNA nanostructure-based siRNA delivery systems

With the approval of multiple nucleic acid drugs for clinic use by FDA, we witness a revival of gene therapy in recent years. As one of the most important drug candidates, small interfering ribonucleic acid (siRNA) plays an essential role in gene silencing. Although a large variety of siRNA delivery systems have been developed, lack of efficient way to deliver siRNA to target tissue remains as a hurdle that retards the translation of siRNA for clinic use. Different from traditional cationic liposome and polymer based nano-delivery systems that load and compress the siRNA by electrostatic interaction, self-assembled DNA nanostructures can be equipped with functional nucleic acids by DNA hybridization, which further serve as vehicles for siRNA delivery. In this mini-review, first we introduce the concept of RNA interference (RNAi) based gene silencing and emphasize the importance. It is well known that siRNA can disturb the process of translating, silence genes, and further inhibit the expression of corresponding proteins via RNAi. However, naked siRNA is not stable during the circulation. Besides that, it is difficult for siRNA itself to enter the cells, demanding proper gene vehicles to assist its cellular and systemic delivery. Unlike traditional cationic carriers that are usually toxic to cells, DNA nanostructures have been verified with excellent biocompatibility and biodegradability. Along with the rapid development of DNA nanotechnology and tremendous DNA-based nanostructures that have been assembled, more attentions have been paid on using DNA nanostructures as new carriers for siRNA delivery. Subsequently, we systematically summarize the recent progress of DNA-based siRNA delivery systems, including their designs, structures, functions, and various applications. For instance, DNA nanocage is one representative carrier used for siRNA delivery. Lee once assembled DNA tetrahedron with 6 siRNAs on each strut and folate ligands on its surface, achieving enhanced efficiency of siRNA delivery for both in vitro and in vivo. Sleiman group also reported a DNA nanosuitcase to encapsulate siRNA and release it upon specific trigger. By virtue of DNA origami, Ke et al. designed DNA nanoparticles to transport siRNA and further investigated the morphology influence on cellular uptake efficiency. Moreover, taking advantage of rolling-circle amplification (RCA) method, new DNA-based delivery systems with different shapes, including Y-DNA structure and periodic DNA nanoribbons, were developed for siRNA delivery. Except barely loading functional siRNA on DNA nanostructures, protecting siRNA from degradation in the new delivery systems is also important. Recently, we also reported a crosslinked DNA hydrogel platform for siRNA delivery, in which siRNA can embedded inside the nanogel to avoid the enzymatic degradation. Both in vivo and in vitro results revealed that the crosslinked nanogel had excellent delivery efficiency and antitumor effect in an siRNA-based therapy. Despite great advances have been achieved, several problems remain to be solved in using DNA nanostructure for siRNA delivery. Lastly, we discuss the main challenges in this field, including the stability, immunogenicity, targeting capability, cost of the delivery vehicles and make a brief prospect. Once these problems are nicely addressed, we believe that DNA-based gene vectors will take a huge step toward practical use in clinic.

Gene-therapy Inspired Polycation Coating for Protection of DNA Origami Nanostructures.

DNA origami nanostructures hold an immense potential to be used for biological and medical applications. However, low-salt conditions and nucleases in physiological fluids induce denaturation and degradation of self-assembled DNA nanostructures. In non-viral gene delivery, enzymatic degradation of DNA is overcome by the encapsulation of the negatively charged DNA in a cationic shell. Herein, inspired by gene delivery advancements, a simple, one-step and robust methodology is presented for the stabilization of DNA origami nanostructures by coating them with chitosan and linear polyethyleneimine. The polycation coating efficiently protects DNA origami nanostructures in Mg-depleted and nuclease-rich media. This method also preserves the full addressability of enzyme- and aptamer-based functionalization of DNA nanostructures.

Engineering electrochemical interface for biomolecular sensing

Abstract Sensing interfaces where molecular recognition processes occur plays a central role in biosensors, which directly affect the biosensing sensitivity, specificity, stability, and response dynamics. However, the target accessibility of conventional sensing interfaces is limited, resulting in low molecular recognition efficiency. Engineering the sensing interfaces of biosensors provides an effective strategy to improve the performance of the biosensors. In this review, we summarize recent advances during the past two years in the development of biosensing interface engineering for enhanced electrochemical sensing. Three types of emerging engineering approaches, including constructing nanostructured sensing interfaces, molecule-mediated interfacial regulation, and functionalizing the interfaces with self-assembled DNA nanostructures, especially framework nucleic acid, are discussed. Also, the remaining challenges and opportunities are outlined for the important research area.

Single-Step Organization of Plasmonic Gold Metamaterials with Self-Assembled DNA Nanostructures

Self-assembled DNA nanostructures hold great promise as nanoscale templates for organizing nanoparticles (NPs) with near-atomistic resolution. However, large-scale organization of NPs with high yield is highly desirable for nanoelectronics and nanophotonic applications. Here, we design five-strand DNA tiles that can readily self-assemble into well-organized micrometer-scale DNA nanostructures. By organizing gold nanoparticles (AuNPs) on these self-assembled DNA nanostructures, we realize the fabrication of one- and two-dimensional Au nanostructures in single steps. We further demonstrate the one-pot synthesis of Au metamaterials for highly amplified surface-enhanced Raman Scattering (SERS). This single-step and high-yield strategy thus holds great potential for fabricating plasmonic metamaterials.

Self-assembly of DNA Nanostructures on Phase-separated Lipid Bilayer Membranes Depending on Lipid Phases and Salt Condition

Self-assembly of DNA Nanostructures on Phase-separated Lipid Bilayer Membranes Depending on Lipid Phases and Salt Condition

Praseodymium promotes B-Z transition in self-assembled DNA nanostructures.

Millimolar concentrations of PrCl3 can induce sequence-specific B–Z transition in various-self-assembled branched DNA (bDNA) nanostructures. Competitive dye binding and thermal kinetics suggest that the phosphate backbone and grooves of bDNA are wrapped with Pr3+ for stabilizing the Z-bDNA. Application of EDTA can convert Z-DNA back to the B-form.

Directional Preference of DNA-Mediated Electron Transfer in Gold-Tethered DNA Duplexes: Is DNA a Molecular Rectifier?

Electrical properties of self-assembling DNA nanostructures underlie the paradigm of nanoscale bioelectronics, and as such require clear understanding. DNA-mediated electron transfer (ET) from a gold electrode to DNA-bound Methylene Blue (MB) shows directional preference, and it is sequence-specific. During the electrocatalytic reduction of [Fe(CN)6 ]3- catalyzed by DNA-bound MB, the ET rate constant for DNA-mediated reduction of MB reaches (1.32±0.2)103 and (7.09±0.4)103 s-1 for (dGdC)20 and (dAdT)25 duplexes. The backward oxidation process is less efficient, making the DNA duplex a molecular rectifier. Lower rates of ET via (dGdC)20 agree well with its disturbed π-stacked sub-molecular structure. Such direction- and sequence-specific ET may be implicated in DNA oxidative damage and repair, and be relevant to other polarized surfaces, such as cell membranes and biomolecular interfaces.

DNA Nanostructure-Programmed Like-Charge Attraction at the Cell-Membrane Interface.

Cell entry of anionic nano-objects has been observed in various types of viruses and self-assembled DNA nanostructures. Nevertheless, the physical mechanism underlying the internalization of these anionic particles across the negatively charged cell membrane remains poorly understood. Here, we report the use of virus-mimicking designer DNA nanostructures with near-atomic resolution to program “like-charge attraction” at the interface of cytoplasmic membranes. Single-particle tracking shows that cellular internalization of tetrahedral DNA nanostructures (TDNs) depends primarily on the lipid-raft-mediated pathway, where caveolin plays a key role in providing the short-range attraction at the membrane interface. Both simulation and experimental data establish that TDNs approach the membrane primarily with their corners to minimize electrostatic repulsion, and that they induce uneven charge redistribution in the membrane under the short-distance confinement by caveolin. We expect that the nanoscale like-charge attraction mechanism provides new clues for viral entry and general rules for rational design of anionic carriers for therapeutics.

Spatial Regulation of Biomolecular Interactions with a Switchable Trident-Shaped DNA Nanoactuator.

DNA nanostructures with controllable motions and functions have been used as flexible scaffolds to precisely and spatially organize molecular reactions at the nanoscale. The construction of dynamic DNA nanostructures with site-specifically incorporated functional elements is a critical step toward building nanomachines. Artificial self-assembled DNA nanostructures have also been developed to mimic key biological processes like various small biomolecule- and protein-based functional biochemistry pathways. Here, we report a self-assembled dynamic trident-shaped DNA (TS DNA) nanoactuator, in which biomolecules can be tethered to the three "arms" of the TS DNA nanoactuator. The TS DNA nanoactuator is implemented as the mechanical scaffold for the reconfiguration of fluorescent/quenching molecules and the assembly of gold nanoparticles, which exhibit controlled spatial separation. Furthermore, two enzymes (glucose oxidase and horseradish peroxidase) are attached to the two outer arms of the TS DNA nanoactuator, which show an enhanced cascade reaction efficiency compared to free enzymes. The efficiency of the two-enzyme cascade reaction can be spatially regulated by switching the TS DNA nanoactuator between opened, semiopened, and closed states through adding the "thermodynamic drivers" (fuels or antifuels). This is the first report to precisely modulate the relative position of coupled enzyme with multiple states and only based on one dynamic DNA scaffold. The present TS DNA nanoactuator with multistage conformational transition functionality could be applied as a potential platform to precisely and dynamically control the multienzyme pathways and would broaden the scope of DNA nanostructures in single-molecule biology applications.

Surface-Guided Chemical Processes on Self-Assembled DNA Nanostructures.

Solid-liquid interfaces have been of great significance in the activation of chemical reactions via restricting the conformation or orientation of the reactants. Self-assembled DNA nanostructures encoded with tremendous chemical and physical information provide an efficient platform to unravel and regulate mechanisms of surface chemical processes. In this review, we discuss the surface addressability, morphological features, and charged properties of DNA nanostructures as well as the recognition, catalytic, and dynamic properties of DNA molecules. We highlight the synergies between the surface properties of DNA nanostructures and the molecular features of DNA strands, which is a key to the synthesis of conductive polymer nanomaterials with well-defined shapes or electronic/optical properties. We also focus on the control over the substrate channeling pathways of enzyme networks or metal nucleation on DNA nanostructures toward the production of specifically emissive metal nanoclusters. In the end, we provide an outlook of future possible directions based on the rational design of DNA-based self-assembly, including dynamic energy transfer, stimuli-responsive synthesis, and programmable activation of the mechanophores on the surfaces of DNA nanostructures.

Quantifying absolute addressability in DNA origami with molecular resolution

Self-assembled DNA nanostructures feature an unprecedented addressability with sub-nanometer precision and accuracy. This addressability relies on the ability to attach functional entities to single DNA strands in these structures. The efficiency of this attachment depends on two factors: incorporation of the strand of interest and accessibility of this strand for downstream modification. Here we use DNA-PAINT super-resolution microscopy to quantify both incorporation and accessibility of all individual strands in DNA origami with molecular resolution. We find that strand incorporation strongly correlates with the position in the structure, ranging from a minimum of 48% on the edges to a maximum of 95% in the center. Our method offers a direct feedback for the rational refinement of the design and assembly process of DNA nanostructures and provides a long sought-after quantitative explanation for efficiencies of DNA-based nanomachines.

DNA Directed Self-Assembly of Single Walled Carbon Nanotubes into Three-Way Junction Nanostructures.

Utilization of a self-assembled two-dimensional DNA nanostructure to arrange single-walled carbon nanotubes (SWNTs) into predetermined structures at controllable angles is presented. A specially designed DNA three-way junction (3WJ) composed of three double-stranded DNA arms containing single-stranded overhang sequences was prepared by annealing of partially complementary ssDNA sequences and ultrasonicated with SWNTs, resulting in DNA-3WJ/SWNT hybrid nanostructures. Utilization of DNA-3WJ not only allowed the precise dispersion of SWNTs but also acted as a rigid template for the self-assembly of SWNTs into three-armed junctions at an angle of approximately 120° to each other as visualized by scanning electron microscopy and atomic force microscopy. Prepared DNA-3WJ/SWNT nanostructures were also demonstrated to have the appropriate binding sites for fluorophores, providing a simple method for the fluorescent labeling of SWNTs. When ssDNA sequences forming the DNA-3WJ are ultrasonicated with SWNTs, followed by annealing of resulting ssDNA wrapped SWNTs, instead of hybrid junctions composed of three SWNT molecules, a web-like structure composed of interconnected SWNT junctions was obtained. The design approaches demonstrated here provide simple methods for the arrangement of SWNTs into desired nanostructures utilizing pre-assembled DNA nanostructures as linkers in aqueous solution through noncovalent interactions which can greatly contribute to efforts along the controlled assembly of SWNTs.