Self‐Assembly of Complex DNA Tessellations by Using Low‐Symmetry Multi‐arm DNA Tiles

Modular DNA tile‐based self‐assembly is a versatile way to engineer basic tessellation patterns on the nanometer scale, but it remains challenging to achieve high levels of structural complexity. We introduce a set of general design principles to create intricate DNA tessellations by employing multi‐arm DNA motifs with low symmetry. We achieved two novel Archimedean tiling patterns, (4.8.8) and (3.6.3.6), and one pattern with higher‐order structures beyond the complexity observed in Archimedean tiling. Our success in assembling complicated DNA tessellations demonstrates the broad design space of DNA structural motifs, enriching the toolbox of DNA tile‐based self‐assembly and expanding the complexity boundaries of DNA tile‐based tessellation.     

Synchronization of Two Assembly Processes To Build Responsive DNA Nanostructures

Herein, we report a strategy for the synchronization of two self‐assembly processes to assemble stimulus‐responsive DNA nanostructures under isothermal conditions. We hypothesized that two independent assembly processes, when brought into proximity in space, could be synchronized and would exhibit positive synergy. To demonstrate this strategy, we assembled a ladderlike DNA nanostructure and a ringlike DNA nanostructure through two hybridization chain reactions (HCRs) and an HCR in combination with T‐junction cohesion, respectively. Such proximity‐induced synchronization adds a new element to the tool box of DNA nanotechnology. We believe that it will be a useful approach for the assembly of complex and responsive nanostructures.     

Programming the Nucleation of DNA Brick Self‐Assembly with a Seeding Strand

Recently, the DNA brick strategy has provided a highly modular and scalable approach for the construction of complex structures, which can be used as nanoscale pegboards for the precise organization of molecules and nanoparticles for many applications. Despite the dramatic increase of structural complexity provided by the DNA brick method, the assembly pathways are still poorly understood. Herein, we introduce a “seed” strand to control the crucial nucleation and assembly pathway in DNA brick assembly. Through experimental studies and computer simulations, we successfully demonstrate that the regulation of the assembly pathways through seeded growth can accelerate the assembly kinetics and increase the optimal temperature by circa 4–7 °C for isothermal assembly. By improving our understanding of the assembly pathways, we provide new guidelines for the design of programmable pathways to improve the self‐assembly of DNA nanostructures.     

Enhancing Biocompatible Stability of DNA Nanostructures Using Dendritic Oligonucleotides and Brick Motifs

The use of DNA‐based nanomaterials in biomedical applications is continuing to grow, yet more emphasis is being put on the need for guaranteed structural stability of DNA nanostructures in physiological conditions. Various methods have been developed to stabilize DNA origami against low concentrations of divalent cations and the presence of nucleases. However, existing strategies typically require the complete encapsulation of nanostructures, which makes accessing the encased DNA strands difficult, or chemical modification, such as covalent crosslinking of DNA strands. We present a stabilization method involving the synthesis of DNA brick nanostructures with dendritic oligonucleotides attached to the outer surface. We find that nanostructures assembled from DNA brick motifs remain stable against denaturation without any chemical modifications. Furthermore, densely coating the outer surface of DNA brick nanostructures with dendritic oligonucleotides prevents nuclease digestion.     

A Signal‐Passing DNA‐Strand‐Exchange Mechanism for Active Self‐Assembly of DNA Nanostructures

DNA nanostructured tiles play an active role in their own self‐assembly in the system described herein whereby they initiate a binding event that produces a cascading assembly process. We present DNA tiles that have a simple but powerful property: they respond to a binding event at one end of the tile by passing a signal across the tile to activate a binding site at the other end. This action allows sequential, virtually irreversible self‐assembly of tiles and enables local communication during the self‐assembly process. This localized signal‐passing mechanism provides a new element of control for autonomous self‐assembly of DNA nanostructures.     

Assembly of DNA Nanostructures with Branched Tris‐DNA

Branched tris‐DNA, in which two oligonucleotides of the same sequence and one other oligonucleotide of a different sequence are connected with a rigid central linker, was prepared chemically by using a DNA synthesizer. Two branched tris‐DNA molecules with complementary DNA sequences form dimer and tetramer as well as linear and spherical oligomer complexes. The complex formation was studied by UV/thermal denaturation, enzyme digestion, gel electrophoresis, and AFM imaging.     

In Vitro Selection of pH‐Activated DNA Nanostructures

We report the first in vitro selection of DNA nanostructures that switch their conformation when triggered by change in pH. Previously, most pH‐active nanostructures were designed using known pH‐active motifs, such as the i‐motif or the triplex structure. In contrast, we performed de novo selections starting from a random library and generated nanostructures that can sequester and release Mipomersen, a clinically approved antisense DNA drug, in response to pH change. We demonstrate extraordinary pH‐selectivity, releasing up to 714‐fold more Mipomersen at pH 5.2 compared to pH 7.5. Interestingly, none of our nanostructures showed significant sequence similarity to known pH‐sensitive motifs, suggesting that they may operate via novel structure‐switching mechanisms. We believe our selection scheme is general and could be adopted for generating DNA nanostructures for many applications including drug delivery, sensors and pH‐active surfaces.     

A Case Study of the Likes and Dislikes of DNA and RNA in Self‐Assembly

Programmed self‐assembly of nucleic acids (DNA and RNA) is an active research area as it promises a general approach for nanoconstruction. Whereas DNA self‐assembly has been extensively studied, RNA self‐assembly lags much behind. One strategy to boost RNA self‐assembly is to adapt the methods of DNA self‐assembly for RNA self‐assembly because of the chemical and structural similarities of DNA and RNA. However, these two types of molecules are still significantly different. To enable the rational design of RNA self‐assembly, a thorough examination of their likes and dislikes in programmed self‐assembly is needed. The current work begins to address this task. It was found that similar, two‐stranded motifs of RNA and DNA lead to similar, but clearly different nanostructures.     

pH‐Responsive Self‐Assembly by Molecular Recognition on a Macroscopic Scale

Macroscopic pH‐responsive self‐assembly is successfully constructed by polyacrylamide(pAAm)‐based gels carrying dansyl (Dns) and β‐cyclodextrin (βCD) residues, which are represented as Dns‐gel and βCD‐gel, respectively. Dns‐gel and βCD‐gel assemble together at pH ≥ 4.0, but disassemble at pH ≤ 3.0. The adhesion strengths for pairs of Dns‐gel/βCD‐gel increase with increasing pH. The fluorescence study on the model system of pAAm modified with 1 mol% Dns moieties (pAAm/Dns) reveals that Dns residues are protonated at a lower pH, which results in the reduction in binding constant (K) for Dns residues and βCD.

     

Vesicle Tubulation with Self‐Assembling DNA Nanosprings

A major goal of nanotechnology and bioengineering is to build artificial nanomachines capable of generating specific membrane curvatures on demand. Inspired by natural membrane‐deforming proteins, we designed DNA‐origami curls that polymerize into nanosprings and show their efficacy in vesicle deformation. DNA‐coated membrane tubules emerge from spherical vesicles when DNA‐origami polymerization or high membrane‐surface coverage occurs. Unlike many previous methods, the DNA self‐assembly‐mediated membrane tubulation eliminates the need for detergents or top‐down manipulation. The DNA‐origami design and deformation conditions have substantial influence on the tubulation efficiency and tube morphology, underscoring the intricate interplay between lipid bilayers and vesicle‐deforming DNA structures.     

pH‐Responsive Drug‐Delivery Systems

In many biomedical applications, drugs need to be delivered in response to the pH value in the body. In fact, it is desirable if the drugs can be administered in a controlled manner that precisely matches physiological needs at targeted sites and at predetermined release rates for predefined periods of time. Different organs, tissues, and cellular compartments have different pH values, which makes the pH value a suitable stimulus for controlled drug release. pH‐Responsive drug‐delivery systems have attracted more and more interest as “smart” drug‐delivery systems for overcoming the shortcomings of conventional drug formulations because they are able to deliver drugs in a controlled manner at a specific site and time, which results in high therapeutic efficacy. This focus review is not intended to offer a comprehensive review on the research devoted to pH‐responsive drug‐delivery systems; instead, it presents some recent progress obtained for pH‐responsive drug‐delivery systems and future perspectives. There are a large number of publications available on this topic, but only a selection of examples will be discussed.     

DNA–Polymer Nanostructures by RAFT Polymerization and Polymerization‐Induced Self‐Assembly

Nanostructures derived from amphiphilic DNA–polymer conjugates have emerged prominently due to their rich self‐assembly behavior; however, their synthesis is traditionally challenging. Here, we report a novel platform technology towards DNA–polymer nanostructures of various shapes by leveraging polymerization‐induced self‐assembly (PISA) for polymerization from single‐stranded DNA (ssDNA). A “grafting from” protocol for thermal RAFT polymerization from ssDNA under ambient conditions was developed and utilized for the synthesis of functional DNA–polymer conjugates and DNA–diblock conjugates derived from acrylates and acrylamides. Using this method, PISA was applied to manufacture isotropic and anisotropic DNA–polymer nanostructures by varying the chain length of the polymer block. The resulting nanostructures were further functionalized by hybridization with a dye‐labelled complementary ssDNA, thus establishing PISA as a powerful route towards intrinsically functional DNA–polymer nanostructures.     

Site‐Directed,On‐Surface Assembly of DNA Nanostructures

Two‐dimensional DNA lattices have been assembled from DNA double‐crossover (DX) motifs on DNA‐encoded surfaces in a site‐specific manner. The lattices contained two types of single‐stranded protruding arms pointing into opposite directions of the plane. One type of these protruding arms served to anchor the DNA lattice on the solid support through specific hybridization with surface‐bound, complementary capture oligomers. The other type of arms allowed for further attachment of DNA‐tethered probe molecules on the opposite side of the lattices exposed to the solution. Site‐specific lattice assembly and attachment of fluorophore‐labeled oligonucleotides and DNA–protein conjugates was demonstrated using DNA microarrays on flat, transparent mica substrates. Owing to their programmable orientation and addressability over a broad dynamic range from the nanometer to the millimeter length scale, such supramolecular architecture might be used for presenting biomolecules on surfaces, for instance, in biosensor applications.     

DNA Nanoribbon‐Templated Self‐Assembly of Ultrasmall Fluorescent Copper Nanoclusters with Enhanced Luminescence

Fluorescent copper nanoclusters (CuNCs) have been widely used in chemical sensors, biological imaging, and light‐emitting devices. However, individual fluorescent CuNCs have limitations in their capabilities arising from poor photostability and weak emission intensities. As one kind of aggregation‐induced emission luminogen (AIEgen), the formation of aggregates with high compactness and good order can efficiently improve the emission intensity, stability, and tunability of CuNCs. Here, DNA nanoribbons, containing multiple specific binding sites, serve as a template for in situ synthesis and assembly of ultrasmall CuNCs (0.6 nm). These CuNC self‐assemblies exhibit enhanced luminescence and excellent fluorescence stability because of tight and ordered arrangement through DNA nanoribbons templating. Furthermore, the stable and bright CuNC assemblies are demonstrated in the high‐sensitivity detection and intracellular fluorescence imaging of biothiols.     

Continuous and Segmented Semiconducting Fiber‐like Nanostructures with Spatially Selective Functionalization by Living Crystallization‐Driven Self‐Assembly

Fiber‐like π‐conjugated nanostructures are important components of flexible organic electronic and optoelectronic devices. To broaden the range of potential applications, one needs to control not only the length of these nanostructures, but the introduction of diverse functionality with spatially selective control. Here we report the synthesis of a crystalline‐coil block copolymer of oligo(p‐phenylenevinylene)‐b‐poly(2‐vinylpyridine) (OPV₅‐b‐P2VP₄₄), in which the basicity and coordinating/chelating ability of the P2VP segment provide a landscape for the incorporation of a variety of functional inorganic NPs. Through a self‐seeding strategy, we were able to prepare monodisperse fiber‐like micelles of OPV₅‐b‐P2VP₄₄ with lengths ranging from 50 to 800 nm. Significantly, the exposed two ends of OPV core of these fiber‐like micelles remained active toward further epitaxial deposition of OPV₅‐b‐PNIPAM₄₉ and OPV₅‐b‐P2VP₄₄ to generate uniform A‐B‐A and B‐A‐B‐A‐B segmented block comicelles with tunable lengths for each block. The P2VP domains in these (co‐)micelles can be selectively decorated with inorganic and polymeric nanoparticles as well as metal oxide coatings, to afford hybrid fiber‐like nanostructures. This work provides a versatile strategy toward the fabrication of narrow length dispersity continuous and segmented π‐conjugated OPV‐containing fiber‐like micelles with the capacity to be decorated in a spatially selective way with varying functionalities.     

Single‐Molecule Mechanochemical Sensing Using DNA Origami Nanostructures

While single‐molecule sensing offers the ultimate detection limit, its throughput is often restricted as sensing events are carried out one at a time in most cases. 2D and 3D DNA origami nanostructures are used as expanded single‐molecule platforms in a new mechanochemical sensing strategy. As a proof of concept, six sensing probes are incorporated in a 7‐tile DNA origami nanoassembly, wherein binding of a target molecule to any of these probes leads to mechanochemical rearrangement of the origami nanostructure, which is monitored in real time by optical tweezers. Using these platforms, 10 pM platelet‐derived growth factor (PDGF) are detected within 10 minutes, while demonstrating multiplex sensing of the PDGF and a target DNA in the same solution. By tapping into the rapid development of versatile DNA origami nanostructures, this mechanochemical platform is anticipated to offer a long sought solution for single‐molecule sensing with improved throughput.