A plasmonic nanorod that walks on DNA origami

Bioinspired Toolkit Based on Intermolecular Encoder toward Evolutionary 4D Chiral Plasmonic Materials

Over the last two decades, nanophotonics, including plasmonics and metamaterials, have promised compelling opportunities for exotic control over light-matter interactions. The strong chiral light-matter interaction is a representative example. Three-dimensional (3D) chirality has existed naturally only in organic molecules and bio-organisms, but a negligible chiroptic effect was attained with these naturally occurring materials because of their small absorption cross sections. However, inspired by biological chirality, nanophotonic chiral materials have greatly expanded the design space of accessible chiroptic effects (e.g., pushing the chiral light-matter interaction to an exceptional regime, such as a broad-band circular polarizer, negative refractive index, and sensitive chiral sensing). Nevertheless, it is still a challenge to achieve precisely defined and dynamically reconfigurable chiral morphologies that further increase the chiroptic effect. Biological systems continue to inspire approaches to the design and synthesis of precisely defined 3D nanostructures. In particular, a living organism can program the evolutionary pathway of highly complexed 3D chiral morphology precisely from the molecular scale to the macroscopic scale while simultaneously enabling dynamic reconfiguration of their chirality. What if we could harness the power of biological selectivity and evolutionary capability in synthesizing chiral plasmonic materials? We envisioned that platform technology mimicking biological principles would enable control of 3D chiral structures for effective plasmonic interactions with polarized light and further impart the concept of time-dependent evolution (3D + 1D = 4D) to bring about responsive and dynamic changes in chiral plasmonics. In this Account, we review our efforts to develop the biomolecule-based synthesis of 3D chiral plasmonic materials and share the vision that as in biological systems, chirality can be programmed at the molecular level and hierarchically transferred at multiple scales to develop macroscopic chirality. Accompanied by a biomimetic time-dependent chirality of singular plasmonic nanometals, we also summarize recent achievements in the chemistry and nanophotonics communities pursuing 4D plasmonics that are closely related to our research. The biomimetic and bioinspired approaches discussed in this Account will provide new synthetic insights into implementing chiral nanomaterials and extend the range of accessible nanophotonic design. We hope that the molecular encoding approach will be useful to achieve dynamic light-matter interactions at unprecedented dimensions, time scales, and chirality.

Highly Polyvalent DNA Motors Generate 100+ pN of Force via Autochemophoresis

Motor proteins such as myosin, kinesin, and dynein are essential to eukaryotic life and power countless processes including muscle contraction, wound closure, cargo transport, and cell division. The design of synthetic nanomachines that can reproduce the functions of these motors is a longstanding goal in the field of nanotechnology. DNA walkers, which are programmed to "walk" along defined tracks via the burnt bridge Brownian ratchet mechanism, are among the most promising synthetic mimics of these motor proteins. While these DNA-based motors can perform useful tasks such as cargo transport, they have not been shown to be capable of cooperating to generate large collective forces for tasks akin to muscle contraction. In this work, we demonstrate that highly polyvalent DNA motors (HPDMs), which can be viewed as cooperative teams of thousands of DNA walkers attached to a microsphere, can generate and sustain substantial forces in the 100+ pN regime. Specifically, we show that HPDMs can generate forces that can unzip and shear DNA duplexes (∼12 and ∼50 pN, respectively) and rupture biotin-streptavidin bonds (∼100-150 pN). To help explain these results, we present a variant of the burnt-bridge Brownian ratchet mechanism that we term autochemophoresis, wherein many individual force generating units generate a self-propagating chemomechanical gradient that produces large collective forces. In addition, we demonstrate the potential of this work to impact future engineering applications by harnessing HPDM autochemophoresis to deposit "molecular ink" via mechanical bond rupture. This work expands the capabilities of synthetic DNA motors to mimic the force-generating functions of biological motors. Our work also builds upon previous observations of autochemophoresis in bacterial transport processes, indicating that autochemophoresis may be a fundamental mechanism of pN-scale force generation in living systems.

DNA-Assembled Multilayer Sliding Nanosystems

DNA nanotechnology allows for the realization of complex nanoarchitectures in which the spatial arrangements of different constituents and most functions can be enabled by DNA. When optically active components are integrated in such systems, the resulting nanoarchitectures not only provide great insights into the self-assembly of nanoscale elements in a systematic way but also impart tailored optical functionality to DNA origami. In this Letter, we demonstrate DNA-assembled multilayer nanosystems, which can carry out coordinated and reversible sliding motion powered by DNA fuels. Gold nanoparticles cross-link DNA origami filaments to define the configurations of the multilayer nanoarchitectures as well as to mediate relative sliding between the neighboring origami filaments. Meanwhile, the gold nanoparticles serve as optical probes to dynamically interact with the fluorophores tethered on the filaments, rendering in situ detection of the stepwise sliding processes possible. This work seeds the basis to implement DNA-assembled complex optical nanoarchitectures with programmability and addressability, advancing the field with new momentum.

Plasmonics in Atomically Thin Crystalline Silver Films

Light-matter interaction at the atomic scale rules fundamental phenomena such as photoemission and lasing while enabling basic everyday technologies, including photovoltaics and optical communications. In this context, plasmons, the collective electron oscillations in conducting materials, are important because they allow the manipulation of optical fields at the nanoscale. The advent of graphene and other two-dimensional crystals has pushed plasmons down to genuinely atomic dimensions, displaying appealing properties such as a large electrical tunability. However, plasmons in these materials are either too broad or lying at low frequencies, well below the technologically relevant near-infrared regime. Here, we demonstrate sharp near-infrared plasmons in lithographically patterned wafer-scale atomically thin silver crystalline films. Our measured optical spectra reveal narrow plasmons (quality factor of ∼4), further supported by a low sheet resistance comparable to bulk metal in few-atomic-layer silver films down to seven Ag(111) monolayers. Good crystal quality and plasmon narrowness are obtained despite the addition of a thin passivating dielectric, which renders our samples resilient to ambient conditions. The observation of spectrally sharp and strongly confined plasmons in atomically thin silver holds great potential for electro-optical modulation and optical sensing applications.

DNA bipedal motor walking dynamics: an experimental and theoretical study of the dependency on step size

We present a detailed coarse-grained computer simulation and single molecule fluorescence study of the walking dynamics and mechanism of a DNA bipedal motor striding on a DNA origami. In particular, we study the dependency of the walking efficiency and stepping kinetics on step size. The simulations accurately capture and explain three different experimental observations. These include a description of the maximum possible step size, a decrease in the walking efficiency over short distances and a dependency of the efficiency on the walking direction with respect to the origami track. The former two observations were not expected and are non-trivial. Based on this study, we suggest three design modifications to improve future DNA walkers. Our study demonstrates the ability of the oxDNA model to resolve the dynamics of complex DNA machines, and its usefulness as an engineering tool for the design of DNA machines that operate in the three spatial dimensions.

Chiral Plasmonic Nanostructures Enabled by Bottom-Up Approaches

We present a comprehensive review of recent developments in the field of chiral plasmonics. Significant advances have been made recently in understanding the working principles of chiral plasmonic structures. With advances in micro- and nanofabrication techniques, a variety of chiral plasmonic nanostructures have been experimentally realized; these tailored chiroptical properties vastly outperform those of their molecular counterparts. We focus on chiral plasmonic nanostructures created using bottom-up approaches, which not only allow for rational design and fabrication but most intriguingly in many cases also enable dynamic manipulation and tuning of chiroptical responses. We first discuss plasmon-induced chirality, resulting from the interaction of chiral molecules with plasmonic excitations. Subsequently, we discuss intrinsically chiral colloids, which give rise to optical chirality owing to their chiral shapes. Finally, we discuss plasmonic chirality, achieved by arranging achiral plasmonic particles into handed configurations on static or active templates. Chiral plasmonic nanostructures are very promising candidates for real-life applications owing to their significantly larger optical chirality than natural molecules. In addition, chiral plasmonic nanostructures offer engineerable and dynamic chiroptical responses, which are formidable to achieve in molecular systems. We thus anticipate that the field of chiral plasmonics will attract further widespread attention in applications ranging from enantioselective analysis to chiral sensing, structural determination, and in situ ultrasensitive detection of multiple disease biomarkers, as well as optical monitoring of transmembrane transport and intracellular metabolism.

Controlling Chirality across Length Scales using DNA

Nano-objects with chiral properties attract growing interest due to their relevance for a wide variety of technological applications. For example, chiral nano-objects may be used in characterization platforms that involve chiral molecular recognition of proteins or in the fabrication of nanomechanical devices such as screw-gears or nanoswimmers. Spatial ordering of emitters of circularly polarized light might greatly benefit from the utilization of chiral shapes. Tools developed in DNA nanotechnology now allow precise tailoring of the chiral properties of molecules and materials at various length scales. Among others, they have already been applied to control the handedness of helical shapes (configurational chirality) or the chiral positioning of different-sized nanoparticles at the vertices of tetrahedra (compositional chirality). This work covers some of the key advances and recent developments in the field of chiral DNA nanoarchitectures and discusses their future perspectives and potential applications.

Create Nanoscale Patterns with DNA Origami

Structural deoxyribonucleic acid (DNA) nanotechnology offers a robust platform for diverse nanoscale shapes that can be used in various applications. Among a wide variety of DNA assembly strategies, DNA origami is the most robust one in constructing custom nanoshapes and exquisite patterns. In this account, the static structural and functional patterns assembled on DNA origami are reviewed, as well as the reconfigurable assembled architectures regulated through dynamic DNA nanotechnology. The fast progress of dynamic DNA origami nanotechnology facilitates the construction of reconfigurable patterns, which can further be used in many applications such as optical/plasmonic sensors, nanophotonic devices, and nanorobotics for numerous different tasks.

Programming Motions of DNA Origami Nanomachines

DNA nanotechnology enables the precise fabrication of DNA-based machines with nanoscale dimensions. A wide range of DNA nanomachines are designed, which can be activated by specific inputs to perform various movement and functions. The excellent rigidity and unprecedented addressability of DNA origami have made it an excellent platform for manipulating and investigating the motion behaviors of DNA machines at single-molecule level. In this Concept, power supply, machine actuation, and motion behavior of DNA machines on origami platforms are summarized and classified. The strategies utilized for programming motion behavior of DNA machines on DNA origami are also discussed with representative examples. The challenges and outlook for future development of manipulating DNA nanomachines at the single molecule level are presented and discussed.

Growing prospects of DNA nanomaterials in novel biomedical applications

As an important genetic material for life, DNA has been investigated widely in recent years, especially in interdisciplinary fields crossing nanomaterials and biomedical applications. It plays an important role because of its extraordinary molecular recognition capability and novel conformational polymorphism. DNA is also a powerful and versatile building block for the fabrication of nanostructures and nanodevices. Such DNA-based nanomaterials have also been successfully applied in various aspects ranging from biosensors to biomedicine and special logic gates, as well as in emerging molecular nanomachines. In this present mini-review, we briefly overview the recent progress in these fields. Furthermore, some challenges are also discussed in the conclusions and perspectives section, which aims to stimulate broader scientific interest in DNA nanotechnology and its biomedical applications.

Chiral Plasmons: Au Nanoparticle Assemblies on Thermoresponsive Organic Templates

Template-assisted strategies are widely used to fabricate nanostructured materials. By taking these strategies a step forward, herein we report the design of two chiral plasmonic nanostructures based on Au nanoparticle (NP) assemblies organized in clockwise and anticlockwise directions, having opposite response to circularly polarized light. The chiral plasmonic nanostructures are obtained by growing Au NPs on chiral templates based on d- and l-forms of alanine functionalized phenyleneethynylenes. Interestingly, Au NP assemblies show mirror symmetrical electronic circular dichroism (ECD) bands at their surface plasmon frequency originating through their asymmetric organization. Upon increasing the temperature, the chiral templates dissociate as evident from the disappearance of their ECD signal. The profound advantage of the thermoresponsive nature of the templates is employed to obtain free-standing chiral plasmonic nanostructures. The tilt angle high-resolution transmission electron microscopic measurements indicate that the NP assemblies, grown on a template based on the d-isomer, organize in clockwise direction ( P-form) and on l-isomer in anticlockwise direction ( M-form). The inherent chirality prevailing on the surface of the template drives the helical growth of the Au NPs in opposite directions. Experimental results are rationalized by a model which accounts for the large polarizability of Au NPs. The large polarizability leads to large oscillating dipole moments whose effects become prominent when interparticle distances are comparable to the particle size.

Chiral Metamolecules with Active Plasmonic Transition

Energy-dissipating self-assembly is at the basis of many important cellular processes, such as cell organization, proliferation, and morphogenesis. Beyond equilibrium self-assembled molecular systems and materials, it is increasingly recognized that the control of assembly kinetics provides great opportunity for the next generation of molecular materials with intelligent behavior including programmed spatiotemporal organization. Here we show the transient self-assembly of active chiral plasmonic metamolecules (CPMs), which is controlled by the proton flux generated from a positive-feedback chemical reaction network. The fuel-conversion kinetics allows for temporal control and adaptive tuning of multiple structures of plasmonic metamolecules (PMs). This approach enables autonomous tuning of chiroptical properties of metamolecules with dynamic behavior. Moreover, we show that 11 types of spatial configurations of PMs are assembled, and 9 types of temporal configurations of CPMs are differentiated.

Fabrication of Metal Nanostructures on DNA Templates

Metal nanoarchitectures fabrication based on DNA assembly has attracted a good deal of attention. DNA nanotechnology enables precise organization of nanoscale objects with extraordinary structural programmability. The spatial addressability of DNA nanostructures and sequence-dependent recognition allow functional elements to be precisely positioned; thus, novel functional materials that are difficult to produce using conventional methods could be fabricated. This review focuses on the recent development of the fabrication strategies toward manipulating the shape and morphology of metal nanoparticles and nanoassemblies based on the rational design of DNA structures. DNA-mediated metallization, including DNA-templated conductive nanowire fabrication and sequence-selective metal deposition, etc., is briefly introduced. The modifications of metal nanoparticles (NPs) with DNA and subsequent construction of heterogeneous metal nanoarchitectures are highlighted. Importantly, DNA-assembled dynamic metal nanostructures that are responsive to different stimuli are also discussed as they allow the design of smart and dynamic materials. Meanwhile, the prospects and challenges of these shape-and morphology-controlled strategies are summarized.

Two-layer three-dimensional DNA walker with highly integrated entropy-driven and enzyme-powered reactions for HIV detection

Here, we propose a new two-layer three-dimensional (3-D) DNA walker sensor with highly integrated entropy-driven and enzyme-powered reactions for the first time. The 3-D DNA walker sensor is constructed by assembling densely carboxyfluorescein-labeled single strand oligonucleotides (inner-layer tracks) and nucleic acid complex S (outer-layer tracks) on a microparticle. In the presence of the target, outer and inner tracks are activated in turn, thereby releasing a great deal of the signal reporters for signal reading. As a result, our 3-D DNA walker sensor can realize the target detection in the range from 2 pM to 5 nM within one hour. Besides, the specific walker sensor can clearly distinguish even one-base mismatched target analogue. More importantly, our walker sensor can also test the target in human serum samples in the concentrations as low as 0.1 nM, which provides a bridge between real sample detection and clinical application. Certainly, this smart strategy could also be generalized to any target of interest by proper design.

Solving mazes with single-molecule DNA navigators

Molecular devices with information-processing capabilities hold great promise for developing intelligent nanorobotics. Here we demonstrate a DNA navigator system that can perform single-molecule parallel depth-first search on a ten-vertex rooted tree defined on a two-dimensional DNA origami platform. Pathfinding by the DNA navigators exploits a localized strand exchange cascade, which is initiated at a unique trigger site on the origami with subsequent automatic progression along paths defined by DNA hairpins containing a universal traversal sequence. Each single-molecule navigator autonomously explores one of the possible paths through the tree. A specific solution path connecting a given pair of start and end vertices can then be easily extracted from the set of all paths taken by the navigators collectively. The solution path laid out on origami is illustrated with single-molecule imaging. Our approach points towards the realization of molecular materials with embedded computational functions operating at the single-molecule level.

DNA-Decorated, Helically Twisted Nanoribbons: A Scaffold for the Fabrication of One-Dimensional, Chiral, Plasmonic Nanostructures

Crafting of chiral plasmonic nanostructures is extremely important and challenging. DNA-directed organization of nanoparticle on a chiral template is the most appealing strategy for this purpose. Herein, we report a supramolecular approach for the design of DNA-decorated, helically twisted nanoribbons through the amphiphilicity-driven self-assembly of a new class of amphiphiles derived from DNA and hexaphenylbenzene (HPB). The ribbons are self-assembled in a lamellar fashion through the hydrophobic interactions of HPB. The transfer of molecular chirality of ssDNA into the HPB core results in the bias of one of the chiral propeller conformations for HPB and induces a helical twist into the lamellar packing, and leads to the formation of DNA-wrapped nanoribbons with M-helicity. The potential of the ribbon to act as a reversible template for the 1D chiral organization of plasmonic nanomaterials through DNA hybridization is demonstrated.

Principles and Applications of Nucleic Acid Strand Displacement Reactions

Dynamic DNA nanotechnology, a subfield of DNA nanotechnology, is concerned with the study and application of nucleic acid strand-displacement reactions. Strand-displacement reactions generally proceed by three-way or four-way branch migration and initially were investigated for their relevance to genetic recombination. Through the use of toeholds, which are single-stranded segments of DNA to which an invader strand can bind to initiate branch migration, the rate with which strand displacement reactions proceed can be varied by more than 6 orders of magnitude. In addition, the use of toeholds enables the construction of enzyme-free DNA reaction networks exhibiting complex dynamical behavior. A demonstration of this was provided in the year 2000, in which strand displacement reactions were employed to drive a DNA-based nanomachine (Yurke, B.; et al. Nature 2000, 406, 605-608). Since then, toehold-mediated strand displacement reactions have been used with ever increasing sophistication and the field of dynamic DNA nanotechnology has grown exponentially. Besides molecular machines, the field has produced enzyme-free catalytic systems, all DNA chemical oscillators and the most complex molecular computers yet devised. Enzyme-free catalytic systems can function as chemical amplifiers and as such have received considerable attention for sensing and detection applications in chemistry and medical diagnostics. Strand-displacement reactions have been combined with other enzymatically driven processes and have also been employed within living cells (Groves, B.; et al. Nat. Nanotechnol. 2015, 11, 287-294). Strand-displacement principles have also been applied in synthetic biology to enable artificial gene regulation and computation in bacteria. Given the enormous progress of dynamic DNA nanotechnology over the past years, the field now seems poised for practical application.

Chemistries for DNA Nanotechnology

The predictable nature of DNA interactions enables the programmable assembly of highly advanced 2D and 3D DNA structures of nanoscale dimensions. The access to ever larger and more complex structures has been achieved through decades of work on developing structural design principles. Concurrently, an increased focus has emerged on the applications of DNA nanostructures. In its nature, DNA is chemically inert and nanostructures based on unmodified DNA mostly lack function. However, functionality can be obtained through chemical modification of DNA nanostructures and the opportunities are endless. In this review, we discuss methodology for chemical functionalization of DNA nanostructures and provide examples of how this is being used to create functional nanodevices and make DNA nanostructures more applicable. We aim to encourage researchers to adopt chemical modifications as part of their work in DNA nanotechnology and inspire chemists to address current challenges and opportunities within the field.

An ultrasensitive aptasensor based on self-enhanced Au nanoclusters as highly efficient electrochemiluminescence indicator and multi-site landing DNA walker as signal amplification

Gold nanoclusters (Au NCs) have been shown to be prospective nanoscale electrochemiluminescence (ECL) materials that are being extensively explored in bioanalysis. However, the low ECL efficiency of Au NCs has been a bottleneck barrier for their better bioapplications. To overcome this disadvantage, a low oxidation potential co-reactant N,N-diisopropylethylenediamine (DPEA) was first used to prepare self-enhanced Au NCs (Au-DPEA NCs) for drastically enhancing the ECL efficiency of Au NCs in this study. In addition, an efficient multi-site landing DNA walker with multidirectional motion track and rapid payloads release compared to directional DNA walker was constructed for converting target mucin 1 (MUC1) to intermediate DNA and achieving significant signal amplification. On the basis of the Au-DPEA NCs as efficient ECL signal labels and multi-site landing DNA walker as signal amplification strategy, an ECL aptasensor was established for the ultrasensitive detection of MUC1 in the range from 1 fg mL^-1 to 1 ng mL^-1 with a limit of detection down to 0.54 fg mL^-1. The results demonstrated that the present study opened a new research direction for the development of high-efficiency Au NCs indicator as well as ultrasensitive ECL sensing platform for applications in clinical and bioanalysis.

A quantum mechanical study of optical excitations in nanodisk plasmonic oligomers

Using state-of-the-art quantum-mechanical calculations, we investigate the optical excitations in plasmonic nanodisk oligomers.

Programmable Target-Initiated DNAzyme Walker Walking along a Spatially Isolated and Highly Hybridizable Substrate Track on a Nanoparticle Surface

Synthetic DNA machines that operate on the nanoscale three-dimensional (3D) track have attracted rapidly increasing interest because of their potential in biocomputing, drug delivery, and biosensing applications. Current nanoscale 3D DNA tracks are typically created by self-assembling thiolated oligonucleotides at gold nanoparticle (AuNP) surfaces via the strong Au-S chemistry. However, it remains challenging to accurately control the conformation and orientation of the 3D DNA track on AuNP surfaces and finely adjust the hybridization ability of the 3D track. Herein, we describe for the first time a polyadenine (polyA)-based, spatially isolated 3D DNA track, on which a target-initiated DNAzyme walker moves by a burnt-bridge mechanism with improved efficiency and processivity. PolyA serves as an anchoring block for preferential binding with the AuNP surface, and the appended substrate block adopts an upright conformation that favors the hybridization and subsequent DNAzyme-mediated cleavage. The operation of this target-initiated DNAzyme walker was monitored in real time and at a single-particle level. We tested the cleavage efficiency of 3D substrates with various polyA block lengths, which displayed that the DNAzyme activity was remarkably improved as compared with a thiol-based 3D track. We also explored bioanalytical applications of this DNAzyme nanomachine by movement-triggered cascade signal amplification.

Overview of DNA Self-Assembling: Progresses in Biomedical Applications

Molecular self-assembling is ubiquitous in nature providing structural and functional machinery for the cells. In recent decades, material science has been inspired by the nature's assembly principles to create artificially higher-order structures customized with therapeutic and targeting molecules, organic and inorganic fluorescent probes that have opened new perspectives for biomedical applications. Among these novel man-made materials, DNA nanostructures hold great promise for the modular assembly of biocompatible molecules at the nanoscale of multiple shapes and sizes, designed via molecular programming languages. Herein, we summarize the recent advances made in the designing of DNA nanostructures with special emphasis on their application in biomedical research as imaging and diagnostic platforms, drug, gene, and protein vehicles, as well as theranostic agents that are meant to operate in-cell and in-vivo.

DNA Origami Nanophotonics and Plasmonics at Interfaces

DNA nanotechnology provides a versatile toolbox for creating custom and accurate shapes that can serve as versatile templates for nanopatterning. These DNA templates can be used as molecular-scale precision tools in, for example, biosensing, nanometrology, and super-resolution imaging, and biocompatible scaffolds for arranging other nano-objects, for example, for drug delivery applications and molecular electronics. Recently, increasing attention has been paid to their potent use in nanophotonics since these modular templates allow a wide range of plasmonic and photonic ensembles ranging from DNA-directed nanoparticle and fluorophore arrays to entirely metallic nanostructures. This Feature Article focuses on the DNA-origami-based nanophotonics and plasmonics-especially on the methods that take advantage of various substrates and interfaces for the foreseen applications.

Modular Assembly of Plasmonic Nanoparticles Assisted by DNA Origami

Arraying noble metal nanoparticles with nanoscale features is an important way to develop plasmonic devices with novel optical properties such as plasmonic chiral metamolecules, optical waveguides, and so forth. Along with top-down methods of fabricating plasmonic nanostructures, solution-based self-assembly provides an alternative approach. There are mainly two routes to organizing metal nanoparticles via self-assembly. One is directly linking nanoparticles through linker molecules, and the other is using nanoparticles to decorate a preformed template. We combine these two routes and herein report a strategy for the DNA origami-assisted modular assembly of gold nanoparticles into homogeneous and heterogeneous plasmonic nanostructures. For each module, we designed W-shaped DNA origami with two troughs as two domains. One domain is used to host a gold nanoparticle, and the other domain is designed to capture another gold nanoparticle hosted on a different module. By simply tuning the sequences of capture DNA strands on each module, gold nanoparticles including spherical and rod-shaped gold nanoparticles (denoted as AuNPs and AuNRs) could be well organized in a predefined manner to form versatile plasmonic nanostructures. Since the interparticle distances could be precisely controlled at the nanoscale, we also studied the plasma coupling among the assembled plasmonic nanostructures. This modular assembly strategy represents a simple yet general and effective design principle for DNA-assembled plasmonic nanostructures.

Simultaneous Surface Plasmon Resonance/Fluorescence Spectroelectrochemical in Situ Monitoring of Dynamic Changes on Functional Interfaces: A Study of the Electrochemical Proximity Assay Model System

Understanding the chemical composition and morphology of interfaces plays a vital role in the development of sensors, drug delivery systems, coatings for biomedical implants, and so forth. In many cases, the interface characterization can be performed by a combination of electrochemical and one of the optical techniques. In this study, we further enhanced capabilities in probing interfaces by combining electrochemical characterization with multiple optical techniques, that is, surface plasmon resonance (SPR) and fluorescence spectroscopy. This new combination was utilized to study the electrochemical proximity assay (ECPA)-a recently developed protein recognition strategy for the point-of-care test. The SPR/fluorescence spectroelectrochemical technique has achieved not only recognition of binding components involved in the ECPA model system, estimation of their thicknesses and surface coverages, but more importantly, highly reliable in situ monitoring of dynamic changes of components involved in interfacial binding via cross-validation and confirmation from three simultaneously generated signals-SPR, fluorescence, and electrochemistry. In addition, the obtained corresponding proportions among magnitudes of three signals provide crucial information for future studies on simultaneous characterization of multiple components in one step and differentiation of nonspecific binding events. Another advantage using this technique is that the excitation of fluorescence is not only confined by surface plasmons, but by photons, so the fluorescence information can be also gained as the distance of fluorophores from the surface exceeds the decay length of surface plasmons.

Dynamic Plasmonic System That Responds to Thermal and Aptamer-Target Regulations

The DNA origami technique has empowered a new paradigm in plasmonics for manipulating light and matter at the nanoscale. This interdisciplinary field has witnessed vigorous growth, outlining a viable route to construct advanced plasmonic architectures with tailored optical properties. However, so far plasmonic systems templated by DNA origami have been restricted to respond to only single stimuli. Despite broad interest and scientific importance, thermal and aptamer-target regulations have not yet been widely utilized to reconfigure three-dimensional plasmonic architectures. In this Letter, we demonstrate a chiral plasmonic nanosystem integrated with split aptamers, which can respond to both thermal and aptamer-target regulations. We show that our dual-responsive system can be noninvasively tuned in a wide range of temperatures, readily correlating thermal control with optical signal changes. Meanwhile, our system can detect specific targets including adenosine triphosphate and cocaine molecules, which further enhance the optical response modulations and in turn influence the thermal tunability.

Quantitative Nanoplasmonics

Plasmonics, the study of the interactions between photons and collective oscillations of electrons, has seen tremendous advances during the past decade. Controllable nanometer- and sub-nanometer-scale engineering in plasmonic resonance and electromagnetic field localization at the subwavelength scale have propelled diverse studies in optics, materials science, chemistry, biotechnology, energy science, and various applications in spectroscopy. However, for translation of these accomplishments from research into practice, major hurdles including low reproducibility and poor controllability in target structures must be overcome, particularly for reliable quantification of plasmonic signals and functionalities. This Outlook introduces and summarizes the recent attempts and findings of many groups toward more quantitative and reliable nanoplasmonics, and discusses the challenges and possible future directions.

Improving the fluorometric determination of the cancer biomarker 8-hydroxy-2'-deoxyguanosine by using a 3D DNA nanomachine

The authors describe a fluorometric method for improving the determination of the cancer biomarker 8-hydroxy-2'-deoxyguanosine (8-OHdG). A nicking endonuclease (NEase)-powered 3-D DNA nanomachine was constructed by assembling hundreds of carboxyfluorescein-labeled single strand oligonucleotides (acting as signal reporter) and tens of swing arms (acting as single-foot DNA walkers) on a gold nanoparticle (AuNP). The activity of this DNA nanomachine was controlled by introducing the protecting oligonucleotides. In the presence of aptamer against 8-OHdG, the protecting oligonucleotides are removed from the swing arms by toehold-mediated strand displacement reaction. In the next step, detached DNA walker hybridizes to the labelled DNA so that the DNA nanomachine becomes activated. Special sequences of signal reporter in the formed duplex can be recognized and cleaved by NEase. As a result, the DNA walker autonomously and progressively moves along the surface of the AuNP, thereby releasing hundreds of signal reporters and causing a rapid increase in green fluorescence. This 3-D nanomachine is highly efficient because one aptamer can release hundreds of signal reporters. These unique properties allowed for the construction of a DNA nanomachine-based method for sensitively detecting 8-OHdG in concentrations as low as 4 pM. This is three orders of magnitude lower compared to previously reported methods. Graphical abstract Schematic of a fluorometric method for determination of the cancer biomarker 8-hydroxy-2'-deoxyguanosine. A nicking endonuclease powered 3D-DNA nanomachine was used to improve the sensitivity. Limit of detection is three orders of magnitude lower than reported methods.

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.

Design and Synthesis of a Reconfigurable DNA Accordion Rack

DNA nanostructure-based mechanical systems or DNA nanomachines, which produce complex nanoscale motion in 2D and 3D in the nanometer to ångström resolution, show great potential in various fields of nanotechnology such as the molecular reactors, drug delivery, and nanoplasmonic systems. The reconfigurable DNA accordion rack, which can collectively manipulate a 2D or 3D nanoscale network of elements, in multiple stages in response to the DNA inputs, is described. The platform has potential to increase the number of elements that DNA nanomachines can control from a few elements to a network scale with multiple stages of reconfiguration. In this protocol, we describe the entire experimental process of the reconfigurable DNA accordion rack of 6 by 6 meshes. The protocol includes a design rule and simulation procedure of the structures and a wet-lab experiment for synthesis and reconfiguration. In addition, analysis of the structure using TEM (transmission electron microscopy) and FRET (fluorescence resonance energy transfer) is included in the protocol. The novel design and simulation methods covered in this protocol will assist researchers to use the DNA accordion rack for further applications.

Simulation-guided engineering of an enzyme-powered three dimensional DNA nanomachine for discriminating single nucleotide variants

Single nucleotide variants (SNVs) are important both clinically and biologically because of their profound biological consequences. Herein, we engineered a nicking endonuclease-powered three dimensional (3D) DNA nanomachine for discriminating SNVs with high sensitivity and specificity. Particularly, we performed a simulation-guided tuning of sequence designs to achieve the optimal trade-off between device efficiency and specificity. We also introduced an auxiliary probe, a molecular fuel capable of tuning the device in solution via noncovalent catalysis. Collectively, our device produced discrimination factors comparable with commonly used molecular probes but improved the assay sensitivity by ∼100 times. Our results also demonstrate that rationally designed DNA probes through computer simulation can be used to quantitatively improve the design and operation of complexed molecular devices and sensors.

Multipedal DNA Walker Biosensors Based on Catalyzed Hairpin Assembly and Isothermal Strand-Displacement Polymerase Reaction for the Chemiluminescent Detection of Proteins

In this study, two kinds of sensitive biosensors based on a multipedal DNA walker along a three-dimensional DNA functional magnet particles track for the chemiluminescent detection of streptavidin (SA) are constructed and compared. In the presence of SA, a multipedal DNA walker was constructed by a biotin-modified catalyst as a result of the terminal protection to avoid being digested by exonuclease I. Then, through a toehold-mediated strand exchange, a "leg" of a multipedal DNA walker interacted with a toehold of a catalyzed hairpin assembly (CHA)-H1 coupled with magnetic microparticles (MMPs) and opened its hairpin structure. The newly open stem in CHA-H1 was hybridized with a toehold of biotin-labeled H2. Via the strand displacement process, H2 displaced one "leg" of a multipedal DNA walker, and the other "leg" continued to interact with the neighboring H1 to initiate the next cycle. In order to solve the high background caused by the hybridization between CHA-H1 and H2 without a CHA-catalyst, the other model was designed. The principle of the other model (isothermal strand-displacement polymerase reaction (ISDPR)-DNA walker) was similar to that of the above one. After the terminal protection of SA, a "leg" of a multipedal DNA walker was triggered to open the hairpin of the ISDPR-H1 conjugated with MMPs. Then, the biotin-modified primer hybridized with the newly exposed DNA segment, triggering the polymerization reaction with the assistance of dNTPs/polymerase. As for the extension of the primer, the "leg" of a multipedal DNA walker was displaced so that the other "leg" could trigger the proximal H1 to go onto the next cycle. Due to its lower background and stronger signal, a multipedal DNA walker based on an ISDPR had a lower limit of detection for SA. The limit of detection for SA was 6.5 pM, and for expanding the application of the method, the detections of the folate receptor and thrombin were explored. In addition, these DNA walker methods were applied in complex samples successfully.

Dynamic DNA Origami Devices: from Strand-Displacement Reactions to External-Stimuli Responsive Systems

DNA nanotechnology provides an excellent foundation for diverse nanoscale structures that can be used in various bioapplications and materials research. Among all existing DNA assembly techniques, DNA origami proves to be the most robust one for creating custom nanoshapes. Since its invention in 2006, building from the bottom up using DNA advanced drastically, and therefore, more and more complex DNA-based systems became accessible. So far, the vast majority of the demonstrated DNA origami frameworks are static by nature; however, there also exist dynamic DNA origami devices that are increasingly coming into view. In this review, we discuss DNA origami nanostructures that exhibit controlled translational or rotational movement when triggered by predefined DNA sequences, various molecular interactions, and/or external stimuli such as light, pH, temperature, and electromagnetic fields. The rapid evolution of such dynamic DNA origami tools will undoubtedly have a significant impact on molecular-scale precision measurements, targeted drug delivery and diagnostics; however, they can also play a role in the development of optical/plasmonic sensors, nanophotonic devices, and nanorobotics for numerous different tasks.

3D Hybrid Small Scale Devices

Interfacing nano/microscale elements with biological components in 3D contexts opens new possibilities for mimicry, bionics, and augmentation of organismically and anatomically inspired materials. Abiotic nanoscale elements such as plasmonic nanostructures, piezoelectric ribbons, and thin film semiconductor devices interact with electromagnetic fields to facilitate advanced capabilities such as communication at a distance, digital feedback loops, logic, and memory. Biological components such as proteins, polynucleotides, cells, and organs feature complex chemical synthetic networks that can regulate growth, change shape, adapt, and regenerate. Abiotic and biotic components can be integrated in all three dimensions in a well-ordered and programmed manner with high tunability, versatility, and resolution to produce radically new materials and hybrid devices such as sensor fabrics, anatomically mimetic microfluidic modules, artificial tissues, smart prostheses, and bionic devices. In this critical Review, applications of small scale devices in 3D hybrid integration, biomicrofluidics, advanced prostheses, and bionic organs are discussed.

DNA Origami Route for Nanophotonics

The specificity and simplicity of the Watson-Crick base pair interactions make DNA one of the most versatile construction materials for creating nanoscale structures and devices. Among several DNA-based approaches, the DNA origami technique excels in programmable self-assembly of complex, arbitrary shaped structures with dimensions of hundreds of nanometers. Importantly, DNA origami can be used as templates for assembly of functional nanoscale components into three-dimensional structures with high precision and controlled stoichiometry. This is often beyond the reach of other nanofabrication techniques. In this Perspective, we highlight the capability of the DNA origami technique for realization of novel nanophotonic systems. First, we introduce the basic principles of designing and fabrication of DNA origami structures. Subsequently, we review recent advances of the DNA origami applications in nanoplasmonics, single-molecule and super-resolution fluorescent imaging, as well as hybrid photonic systems. We conclude by outlining the future prospects of the DNA origami technique for advanced nanophotonic systems with tailored functionalities.

Three dimensional chiral plasmon rulers based on silver nanorod trimers

The symmetry dependences of plasmon excitation modes are studied in 3D silver nanorod trimers. The degenerate plasmon modes split into chiral modes by breaking the inversion and mirror symmetry of the nanorod trimer through translation and/or rotation of the middle rod. With a translation operation, successive evolution of the circular dichroism (CD) spectrum can be achieved through gradual breaking of the inversion symmetry. An additional rotation operation produces even dramatic spectral changes due to breaking a quasi-mirror symmetry resulted from the same angular distance of the middle rod to the top and bottom rods. Especially, pairs of new chiral modes can be excited due to the contact of the middle rod with the top-bottom rod pair. The spectral changes in the simulations, which are also demonstrated experimentally, envision the 3D chiral nanorod trimer system as plasmon ruler for spatial configuration retrieval and dynamic bio-process analysis at the single molecule level.

Gold nanocrystal-mediated sliding of doublet DNA origami filaments

Sliding is one of the fundamental mechanical movements in machinery. In macroscopic systems, double-rack pinion machines employ gears to slide two linear tracks along opposite directions. In microscopic systems, kinesin-5 proteins crosslink and slide apart antiparallel microtubules, promoting spindle bipolarity and elongation during mitosis. Here we demonstrate an artificial nanoscopic analog, in which gold nanocrystals can mediate coordinated sliding of two antiparallel DNA origami filaments powered by DNA fuels. Stepwise and reversible sliding along opposite directions is in situ monitored and confirmed using fluorescence spectroscopy. A theoretical model including different energy transfer mechanisms is developed to understand the observed fluorescence dynamics. We further show that such sliding can also take place in the presence of multiple DNA sidelocks that are introduced to inhibit the relative movements. Our work enriches the toolbox of DNA-based nanomachinery, taking one step further toward the vision of molecular nanofactories.

Kinesin, a motor protein, moves along filaments in a walk-like fashion to transport cargo to specific places in the cell. Here, the authors developed an analogous, artificial system consisting of nanoparticles moving along DNA filaments.

Mix-and-match nanobiosensor design: Logical and spatial programming of biosensors using self-assembled DNA nanostructures

The evergrowing need to understand and engineer biological and biochemical mechanisms has led to the emergence of the field of nanobiosensing. Structural DNA nanotechnology, encompassing methods such as DNA origami and single-stranded tiles, involves the base pairing-driven knitting of DNA into discrete one-, two-, and three-dimensional shapes at nanoscale. Such nanostructures enable a versatile design and fabrication of nanobiosensors. These systems benefit from DNA's programmability, inherent biocompatibility, and the ability to incorporate and organize functional materials such as proteins and metallic nanoparticles. In this review, we present a mix-and-match taxonomy and approach to designing nanobiosensors in which the choices of bioanalyte and transduction mechanism are fully independent of each other. We also highlight opportunities for greater complexity and programmability of these systems that are built using structural DNA nanotechnology. This article is categorized under: Implantable Materials and Surgical Technologies > Nanomaterials and Implants Diagnostic Tools > Biosensing Biology-Inspired Nanomaterials > Nucleic Acid-Based Structures Nanotechnology Approaches to Biology > Nanoscale Systems in Biology.

Structural DNA Nanotechnology: Artificial Nanostructures for Biomedical Research

Structural DNA nanotechnology utilizes synthetic or biologic DNA as designer molecules for the self-assembly of artificial nanostructures. The field is founded upon the specific interactions between DNA molecules, known as Watson-Crick base pairing. After decades of active pursuit, DNA has demonstrated unprecedented versatility in constructing artificial nanostructures with significant complexity and programmability. The nanostructures could be either static, with well-controlled physicochemical properties, or dynamic, with the ability to reconfigure upon external stimuli. Researchers have devoted considerable effort to exploring the usability of DNA nanostructures in biomedical research. We review the basic design methods for fabricating both static and dynamic DNA nanostructures, along with their biomedical applications in fields such as biosensing, bioimaging, and drug delivery.

DNA-Assembled Advanced Plasmonic Architectures

The interaction between light and matter can be controlled efficiently by structuring materials at a length scale shorter than the wavelength of interest. With the goal to build optical devices that operate at the nanoscale, plasmonics has established itself as a discipline, where near-field effects of electromagnetic waves created in the vicinity of metallic surfaces can give rise to a variety of novel phenomena and fascinating applications. As research on plasmonics has emerged from the optics and solid-state communities, most laboratories employ top-down lithography to implement their nanophotonic designs. In this review, we discuss the recent, successful efforts of employing self-assembled DNA nanostructures as scaffolds for creating advanced plasmonic architectures. DNA self-assembly exploits the base-pairing specificity of nucleic acid sequences and allows for the nanometer-precise organization of organic molecules but also for the arrangement of inorganic particles in space. Bottom-up self-assembly thus bypasses many of the limitations of conventional fabrication methods. As a consequence, powerful tools such as DNA origami have pushed the boundaries of nanophotonics and new ways of thinking about plasmonic designs are on the rise.

Construction of a DNA Origami Based Molecular Electro-optical Modulator

An electro-optical modulator was constructed using a DNA nanostructure scaffold with oligomers of poly(phenylenevinylene) and polyaniline. A molecular device containing one each of the functional molecules was assembled in a DNA origami. The constructs formed an "X" shape and were visualized by atomic force microscopy. In response to redox reconfiguration, the device reversibly altered fluorescence signal output. This molecular self-assembly strategy provides opportunities to make unique material composites that are difficult to achieve by blending. The strategy offers a "plug and play" format that may lead to many new functions.

Metal-ion responsive reversible assembly of DNA origami dimers: G-quadruplex induced intermolecular interaction

We present a novel metal-ion stimulated organization of DNA origami nanostructures by employing G-quadruplexes as stimuli-responsive bridges. The reversible assembly process of DNA origami was the result of conformational changes between the G-quadruplex and its single-strand state induced by monovalent cations. This study might stimulate a new design of responsive DNA-based intelligent nanomaterials.