Transient DNA‐Based Nanostructures Controlled by Redox Inputs

Synthetic DNA has emerged as a powerful self‐assembled material for the engineering of nanoscale supramolecular devices and materials. Recently dissipative self‐assembly of DNA‐based supramolecular structures has emerged as a novel approach providing access to a new class of kinetically controlled DNA materials with unprecedented life‐like properties. So far, dissipative control has been achieved using DNA‐recognizing enzymes as energy dissipating units. Although highly efficient, enzymes pose limits in terms of long‐term stability and inhibition of enzyme activity by waste products. Herein, we provide the first example of kinetically controlled DNA nanostructures in which energy dissipation is achieved through a non‐enzymatic chemical reaction. More specifically, inspired by redox signalling, we employ redox cycles of disulfide‐bond formation/breakage to kinetically control the assembly and disassembly of tubular DNA nanostructures in a highly controllable and reversible fashion.     

Fabrication of Defined Polydopamine Nanostructures by DNA Origami‐Templated Polymerization

A versatile, bottom‐up approach allows the controlled fabrication of polydopamine (PD) nanostructures on DNA origami. PD is a biosynthetic polymer that has been investigated as an adhesive and promising surface coating material. However, the control of dopamine polymerization is challenged by the multistage‐mediated reaction mechanism and diverse chemical structures in PD. DNA origami decorated with multiple horseradish peroxidase‐mimicking DNAzyme motifs was used to control the shape and size of PD formation with nanometer resolution. These fabricated PD nanostructures can serve as “supramolecular glue” for controlling DNA origami conformations. Facile liberation of the PD nanostructures from the DNA origami templates has been achieved in acidic medium. This presented DNA origami‐controlled polymerization of a highly crosslinked polymer provides a unique access towards anisotropic PD architectures with distinct shapes that were retained even in the absence of the DNA origami template.     

Spatiotemporal Control over Polynucleotide Brush Growth on DNA Origami Nanostructures

DNA nanotechnology provides an approach to create precise, tunable, and biocompatible nanostructures for biomedical applications. However, the stability of these structures is severely compromised in biological milieu due to their fast degradation by nucleases. Recently, we showed how enzymatic polymerization could be harnessed to grow polynucleotide brushes of tunable length and location on the surface of DNA origami nanostructures, which greatly enhances their nuclease stability. Here, we report on strategies that allow for both spatial and temporal control over polymerization through activatable initiation, cleavage, and regeneration of polynucleotide brushes using restriction enzymes. The ability to site-specifically decorate DNA origami nanostructures with polynucleotide brushes in a spatiotemporally controlled way provides access to “smart” functionalized DNA architectures with potential applications in drug delivery and supramolecular assembly.     

Control over the Aspect Ratio of Supramolecular Nanosheets by Molecular Design

Recent developments in kinetically controlled supramolecular polymerization permit control of the size (i.e., length and area) of self-assembled nanostructures. However, control of molecular self-assembly at a level comparable with organic synthetic chemistry and the achievement of structural complexity at a hierarchy larger than the molecular level remain challenging. This study focuses on controlling the aspect ratio of supramolecular nanosheets. A systematic understanding of the relationship between the monomer structure and the self-assembly energy landscape has derived a new monomer capable of forming supramolecular nanosheets. With this monomer in hand, the aspect ratio of a supramolecular nanosheet is demonstrated that it can be controlled by modulating intermolecular interactions in two dimensions.     

Disulfide-Linked Allosteric Modulators for Multi-cycle Kinetic Control of DNA-Based Nanodevices

Nature employs sulfur switches, that is, redox-active disulfides, to kinetically control biological pathways in a highly efficient and reversible way. Inspired by this mechanism, we describe herein a DNA-based synthetic nanodevice that acts as a sulfur switch and can be temporally controlled though redox regulation. To do this, we rationally designed disulfide DNA strands (modulators) that hybridize to a ligand-binding DNA nanodevice and act as redox-active allosteric regulators inducing the nanodevice to release or load its ligand. Upon reduction, the allosteric modulator spontaneously de-hybridizes from the nanodevice and, as a result, its effect is transient. The system is reversible and has an unprecedented high tolerance to waste products and displays transient behavior for over 40 cycles without significant loss of efficiency. Kinetic control of DNA-based ligand-binding nanodevices through purely chemical reactions paves the way for temporal regulation of more complex chemical pathways.     

Controlled synthesis of organic two-dimensional nanostructures via reaction-driven,cooperative supramolecular polymerization

The bottom-up approach of supramolecular polymerization is an effective synthetic method for functional organic nanostructures. However, the uncontrolled growth and polydisperse structural outcome often lead to low functional efficiency. Thus, precise control over the structural characteristics of supramolecular polymers is the current scientific hurdle. Research so far has tended to focus on systems with inherent kinetic control by the presence of metastable state monomers either through conformational molecular design or by exploring pathway complexity. The need of the hour is to create generic strategies for dormant states of monomers that can be extended to different molecules and various structural organizations and dimensions. Here we venture to demonstrate chemical reaction-driven cooperative supramolecular polymerization as an alternative strategy for the controlled synthesis of organic two-dimensional nanostructures. In our approach, the dynamic imine bond is exploited to convert a non-assembling dormant monomer to an activated amphiphilic structure in a kinetically controlled manner. The chemical reaction governed retarded nucleation–elongation growth provides control over dispersity and size.

We report the kinetically controlled supramolecular polymerization of organic two-dimensional charge-transfer nanostructures via a chemical reaction (imine)-driven approach.     

Four‐Dimensional Deoxyribonucleic Acid–Gold Nanoparticle Assemblies

Organization of gold nanoobjects by oligonucleotides has resulted in many three‐dimensional colloidal assemblies with diverse size, shape, and complexity; nonetheless, autonomous and temporal control during formation remains challenging. In contrast, living systems temporally and spatially self‐regulate formation of functional structures by internally orchestrating assembly and disassembly kinetics of dissipative biomacromolecular networks. We present a novel approach for fabricating four‐dimensional gold nanostructures by adding an additional dimension: time. The dissipative character of our system is achieved using exonuclease III digestion of deoxyribonucleic acid (DNA) fuel as an energy‐dissipating pathway. Temporal control over amorphous clusters composed of spherical gold nanoparticles (AuNPs) and well‐defined core–satellite structures from gold nanorods (AuNRs) and AuNPs is demonstrated. Furthermore, the high specificity of DNA hybridization allowed us to demonstrate selective activation of the evolution of multiple architectures of higher complexity in a single mixture containing small and larger spherical AuNPs and AuNRs.     

Light-Activated Assembly of DNA Origami into Dissipative Fibrils

Hierarchical DNA nanostructures offer programmable functions at scale, but making these structures dynamic, while keeping individual components intact, is challenging. Here we show that the DNA A-motif—protonated, self-complementary poly(adenine) sequences—can propagate DNA origami into one-dimensional, micron-length fibrils. When coupled to a small molecule pH regulator, visible light can activate the hierarchical assembly of our DNA origami into dissipative fibrils. This system is recyclable and does not require DNA modification. By employing a modular and waste-free strategy to assemble and disassemble hierarchical structures built from DNA origami, we offer a facile and accessible route to developing well-defined, dynamic, and large DNA assemblies with temporal control. As a general tool, we envision that coupling the A-motif to cycles of dissipative protonation will allow the transient construction of diverse DNA nanostructures, finding broad applications in dynamic and non-equilibrium nanotechnology.     

Four-Dimensional Deoxyribonucleic Acid–Gold Nanoparticle Assemblies

Organization of gold nanoobjects by oligonucleotides has resulted in many three-dimensional colloidal assemblies with diverse size, shape, and complexity; nonetheless, autonomous and temporal control during formation remains challenging. In contrast, living systems temporally and spatially self-regulate formation of functional structures by internally orchestrating assembly and disassembly kinetics of dissipative biomacromolecular networks. We present a novel approach for fabricating four-dimensional gold nanostructures by adding an additional dimension: time. The dissipative character of our system is achieved using exonuclease III digestion of deoxyribonucleic acid (DNA) fuel as an energy-dissipating pathway. Temporal control over amorphous clusters composed of spherical gold nanoparticles (AuNPs) and well-defined core–satellite structures from gold nanorods (AuNRs) and AuNPs is demonstrated. Furthermore, the high specificity of DNA hybridization allowed us to demonstrate selective activation of the evolution of multiple architectures of higher complexity in a single mixture containing small and larger spherical AuNPs and AuNRs.     

Hybrid Soft Nanomaterials Composed of DNA Microspheres and Supramolecular Nanostructures of Semi-artificial Glycopeptides

Aqueous hybrid soft nanomaterials consisting of plural supramolecular architectures with a high degree of segregation (orthogonal coexistence) and precise hierarchy at the nano- and microscales, which are reminiscent of complex biomolecular systems, have attracted increasing attention. Remarkable progress has been witnessed in the construction of DNA nanostructures obtained by rational sequence design and supramolecular nanostructures of peptide derivatives through self-assembly under aqueous conditions. However, orthogonal self-assembly of DNA nanostructures and supramolecular nanostructures of peptide derivatives in a single medium has not yet been explored in detail. In this study, DNA microspheres, which can be obtained from three single-stranded DNAs, and three different supramolecular nanostructures (helical nanofibers, straight nanoribbons, and flowerlike microaggregates) of semi-artificial glycopeptides were simultaneously constructed in a single medium by a simple thermal annealing process, which gives rise to hybrid soft nanomaterials. Fluorescence imaging with selective staining of each supramolecular nanostructure uncovered the orthogonal coexistence of these structures with only marginal impact on their morphology. Additionally, the biostimuli-responsive degradation propensity of each supramolecular architecture is retained, and this may allow the construction of active soft nanomaterials exhibiting intelligent biofunctions.     

Biocatalytic Self-Assembly Cascades

The properties of supramolecular materials are dictated by both kinetic and thermodynamic aspects, providing opportunities to dynamically regulate morphology and function. Herein, we demonstrate time-dependent regulation of supramolecular self-assembly by connected, kinetically competing enzymatic reactions. Starting from Fmoc-tyrosine phosphate and phenylalanine amide in the presence of an amidase and phosphatase, four distinct self-assembling molecules may be formed which each give rise to distinct morphologies (spheres, fibers, tubes/tapes and sheets). By varying the sequence or ratio in which the enzymes are added to mixtures of precursors, these structures can be (transiently) accessed and interconverted. The approach provides insights into dynamic self-assembly using competing pathways that may aid the design of soft nanostructures with tunable dynamic properties and life times.     

Self‐Assembly of DNA–Oligo(p‐phenylene‐ethynylene) Hybrid Amphiphiles into Surface‐Engineered Vesicles with Enhanced Emission

Surface‐addressable nanostructures of linearly π‐conjugated molecules play a crucial role in the emerging field of nanoelectronics. Herein, by using DNA as the hydrophilic segment, we demonstrate a solid‐phase “click” chemistry approach for the synthesis of a series of DNA–chromophore hybrid amphiphiles and report their reversible self‐assembly into surface‐engineered vesicles with enhanced emission. DNA‐directed surface addressability of the vesicles was demonstrated through the integration of gold nanoparticles onto the surface of the vesicles by sequence‐specific DNA hybridization. This system could be converted to a supramolecular light‐harvesting antenna by integrating suitable FRET acceptors onto the surface of the nanostructures. The general nature of the synthesis, surface addressability, and biocompatibility of the resulting nanostructures offer great promises for nanoelectronics, energy, and biomedical applications.     

Biocatalytic Self‐Assembly Cascades

The properties of supramolecular materials are dictated by both kinetic and thermodynamic aspects, providing opportunities to dynamically regulate morphology and function. Herein, we demonstrate time‐dependent regulation of supramolecular self‐assembly by connected, kinetically competing enzymatic reactions. Starting from Fmoc‐tyrosine phosphate and phenylalanine amide in the presence of an amidase and phosphatase, four distinct self‐assembling molecules may be formed which each give rise to distinct morphologies (spheres, fibers, tubes/tapes and sheets). By varying the sequence or ratio in which the enzymes are added to mixtures of precursors, these structures can be (transiently) accessed and interconverted. The approach provides insights into dynamic self‐assembly using competing pathways that may aid the design of soft nanostructures with tunable dynamic properties and life times.     

Dynamic Reconfigurable DNA Nanostructures,Networks and Materials

DNA nanotechnology relies on the structural and functional information encoded in nucleic acids. Specifically, the sequence-guided reconfiguration of nucleic acids by auxiliary triggers provides a means to develop DNA switches, machines and stimuli-responsive materials. The present Review addresses recent advances in the construction and applications of dynamic reconfigurable DNA nanostructures, networks and materials. Dynamic transformations proceeding within engineered origami frames or between origami tiles, and the triggered dynamic reconfiguration of scaled supramolecular origami structures are addressed. The use of origami frameworks to assemble dynamic chiroplasmonic optical devices and to operate switchable chemical processes are discussed. Also, the dynamic operation of DNA networks is addressed, and the design of “smart” stimuli-responsive all-DNA materials and their applications are introduced. Future perspectives and applications of dynamic reconfigurable DNA nanostructures are presented.     

Electrochemical charge transfer mediated by metal nanoparticles and quantum dots

Electron transfer processes mediated by nanostructured materials assembled at electrode surfaces underpin fundamental processes in novel electrochemical sensors, light energy conversion systems and molecular electronics. Functionalisation of electrode surfaces with hierarchical architectures incorporating self-assembling molecular systems and materials, such as metal nanostructures, quantum dots, carbon nanotubes, graphene or biomolecules have been intensively studied over the last 20 years. Important steps have been made towards the rationalisation of the charge transfer dynamics from redox species in solution across molecular self-assembling systems to electrode surfaces. For instance, a unified picture has emerged describing the factors which determine the rate constant for electron transfer processes across rigid self-assembling molecular barriers. An increasing bulk of evidence has recently shown that the incorporation of nanomaterials into self-assembling monolayers leads to an entirely different electrochemical behaviour. This perspective rationalises some of the key observations associated with nanoparticle mediated charge transfer, such as the apparent distance independent charge transfer resistance observed for redox species in solution. This behaviour only manifests itself clearly in the case where the probability of direct charge transfer from the redox probe to the electrode is strongly attenuated by self-assembling molecular barriers. Here we will highlight specific issues concerning self-assembled monolayers as blocking barriers prior to discussing the effect of nanoparticles on the electrochemical response of the system. Selected examples will provide conclusive evidence that the extent of charge transfer mediation is determined by the overlap between the density of states of the nanostructures and the energy levels of redox species in solution. Only in the case where a strong overlap exists between the energy levels of the two components, the nanostructures behave as "electron launchers", allowing efficient charge transfer across insulating molecular layers.     

Precisely Tailored DNA Nanostructures and their Theranostic Applications

A critical challenge in nanotechnology is the limited precision and controllability of the structural parameters, which brings about concerns in uniformity, reproducibility and performance. Self‐assembled DNA nanostructures, as a newly emerged type of nano‐biomaterials, possess low‐nanometer precision, excellent programmability and addressability. They can precisely arrange various molecules and materials to form spatially ordered complex, resulting in unambiguous physical or chemical properties. Because of these, DNA nanostructures have shown great promise in numerous biomedical theranostic applications. In this account, we briefly review the history and advances on construction of DNA nanoarchitectures and superstructures with accurate structural parameters. We focus on recent progress in exploiting these DNA nanostructures as platforms for quantitative biosensing, intracellular diagnosis, imaging, and smart drug delivery. We also discuss key challenges in practical applications.     

Gold‐Nanoparticle‐Mediated Jigsaw‐Puzzle‐like Assembly of Supersized Plasmonic DNA Origami

DNA origami has rapidly emerged as a powerful and programmable method to construct functional nanostructures. However, the size limitation of approximately 100 nm in classic DNA origami hampers its plasmonic applications. Herein, we report a jigsaw‐puzzle‐like assembly strategy mediated by gold nanoparticles (AuNPs) to break the size limitation of DNA origami. We demonstrated that oligonucleotide‐functionalized AuNPs function as universal joint units for the one‐pot assembly of parent DNA origami of triangular shape to form sub‐microscale super‐origami nanostructures. AuNPs anchored at predefined positions of the super‐origami exhibited strong interparticle plasmonic coupling. This AuNP‐mediated strategy offers new opportunities to drive macroscopic self‐assembly and to fabricate well‐defined nanophotonic materials and devices.     

Click Modification of Diazido Acridine Intercalators: A Versatile Route towards Decorated DNA Nanostructures

Diazido derivatives of 3,6‐diamino acridine (proflavine) intercalate into DNA and undergo functionalization through click chemistry to form 1D nanostructures with redox active, conductive nanowire, and fluorescent properties. This two‐step approach, intercalation followed by click modification allows for the controlled decoration of DNA nanostructures.     

Visualization of Stereoselective Supramolecular Polymers by Chirality‐Controlled Energy Transfer

Chirality‐driven self‐sorting is envisaged to efficiently control functional properties in supramolecular materials. However, the challenge arises because of a lack of analytical methods to directly monitor the enantioselectivity of the resulting supramolecular assemblies. Presented herein are two fluorescent core‐substituted naphthalene‐diimide‐based donor and acceptor molecules with minimal structural mismatch and they comprise strong self‐recognizing chiral motifs to determine the self‐sorting process. As a consequence, stereoselective supramolecular polymerization with an unprecedented chirality control over energy transfer has been achieved. This chirality‐controlled energy transfer has been further exploited as an efficient probe to visualize microscopically the chirality driven self‐sorting.     

Stereoselective Seed-Induced Living Supramolecular Polymerization

Stereoselective and temporally controlled supramolecular polymerizations are ubiquitous in nature and are desirable attributes for the design of chiral, well-defined functional materials. Kinetically controlled, living supramolecular polymerization (LSP) has emerged recently for the synthesis of supramolecular polymers with controlled length and narrow dispersity. On the other hand, stringent design requirements for chiral-discriminating monomers precludes the stereoselective control of the supramolecular polymer structure. Herein, a synergetic stereo- and structural control of supramolecular polymerization by the realization of an unprecedented stereoselective seed-induced LSP is reported. Homochiral and seeded growth is demonstrated with bischromophoric naphthalene diimide (NDI) enantiomers with a chiral binaphthyl amine core, exhibiting strong self-recognition abilities and pathway complexity.