A light-driven three-dimensional plasmonic nanosystem that translates molecular motion into reversible chiroptical function

DNA Nanodevices: from Mechanical Motions to Biomedical Applications

Inspired by molecular machines in nature, artificial nanodevices have been designed to realize various biomedical functions. Self-assembled deoxyribonucleic acid (DNA) nanostructures that feature designed geometries, excellent spatial accuracy, nanoscale addressability and marked biocompatibility provide an attractive candidate for constructing dynamic nanodevices with biomarker-targeting and stimuli-responsiveness for biomedical applications. Here, a summary of typical construction strategies of DNA nanodevices and their operating mechanisms are presented. We also introduced recent advances in employing DNA nanodevices as platforms for biosensing and intelligent drug delivery. Finally, the broad prospects and main challenges of the DNA nanodevices in biomedical applications are discussed.

Stimuli-Responsive DNA Origami Nanodevices and Their Biological Applications

DNA origami nanotechnology has provided predictable static nanoarchitectures and dynamic nanodevices with rationally designed geometries, precise spatial addressability, and marked biocompatibility. Multiple functional elements, such as peptides, aptamers, nanoparticles, fluorescence probes, and proteins, etc. can be easily integrated into DNA origami templates with nanoscale precision, leading to a variety of promising applications. Triggered by chemical/physical stimuli, dynamic DNA origami nanodevices can switch between defined conformations or translocate autonomously, providing powerful tools for intelligent biosensing and drug delivery. In this minireview, we summarize the recent progress of dynamic DNA origami nanodevices with desired reconfigurability and feasibility to perform multiple biological tasks. We introduce varieties of DNA nanodevices that can be controlled by different molecular triggers and external stimuli. Subsequently, we highlight the recent advances in employing DNA nanodevices as biosensors and drug delivery vehicles. At last, future possibilities and perspectives are also discussed.

Synthesis, Assembly, Optical Properties, and Sensing Applications of Plasmonic Gap Nanostructures

Plasmonic gap nanostructures (PGNs) have been extensively investigated mainly because of their strongly enhanced optical responses, which stem from the high intensity of the localized field in the nanogap. The recently developed methods for the preparation of versatile nanogap structures open new avenues for the exploration of unprecedented optical properties and development of sensing applications relying on the amplification of various optical signals. However, the reproducible and controlled preparation of highly uniform plasmonic nanogaps and the prediction, understanding, and control of their optical properties, especially for nanogaps in the nanometer or sub-nanometer range, remain challenging. This is because subtle changes in the nanogap significantly affect the plasmonic response and are of paramount importance to the desired optical performance and further applications. Here, recent advances in the synthesis, assembly, and fabrication strategies, prediction and control of optical properties, and sensing applications of PGNs are discussed, and perspectives toward addressing these challenging issues and the future research directions are presented.

Chiral Photomelting of DNA-Nanocrystal Assemblies Utilizing Plasmonic Photoheating

Chiral plasmonic nanostructures exhibit anomalously strong chiroptical signals and offer the possibility to realize asymmetric photophysical and photochemical processes controlled by circularly polarized light. Here, we use a chiral DNA-assembled nanorod pair as a model system for chiral plasmonic photomelting. We show that both the enantiomeric excess and consequent circular dichroism can be controlled with chiral light. The nonlinear chiroptical response of our plasmonic system results from the chiral photothermal effect leading to selective melting of the DNA linker strands. Our study describes both the single-complex and collective heating regimes, which should be treated with different models. The chiral asymmetry factors of the calculated photothermal and photomelting effects exceed the values typical for the chiral molecular photochemistry at least 10-fold. Our proposed mechanism can be used to develop chiral photoresponsive systems controllable with circularly polarized light.

Obtaining Precise Molecular Information via DNA Nanotechnology

Precise characterization of biomolecular information such as molecular structures or intermolecular interactions provides essential mechanistic insights into the understanding of biochemical processes. As the resolution of imaging-based measurement techniques improves, so does the quantity of molecular information obtained using these methodologies. DNA (deoxyribonucleic acid) molecule have been used to build a variety of structures and dynamic devices on the nanoscale over the past 20 years, which has provided an accessible platform to manipulate molecules and resolve molecular information with unprecedented precision. In this review, we summarize recent progress related to obtaining precise molecular information using DNA nanotechnology. After a brief introduction to the development and features of structural and dynamic DNA nanotechnology, we outline some of the promising applications of DNA nanotechnology in structural biochemistry and in molecular biophysics. In particular, we highlight the use of DNA nanotechnology in determination of protein structures, protein-protein interactions, and molecular force.

Double- to Single-Strand Transition Induces Forces and Motion in DNA Origami Nanostructures

The design of dynamic, reconfigurable devices is crucial for the bottom-up construction of artificial biological systems. DNA can be used as an engineering material for the de-novo design of such dynamic devices. A self-assembled DNA origami switch is presented that uses the transition from double- to single-stranded DNA and vice versa to create and annihilate an entropic force that drives a reversible conformational change inside the switch. It is distinctively demonstrated that a DNA single-strand that is extended with 0.34 nm per nucleotide - the extension this very strand has in the double-stranded configuration - exerts a contractive force on its ends leading to large-scale motion. The operation of this type of switch is demonstrated via transmission electron microscopy, DNA-PAINT super-resolution microscopy and darkfield microscopy. The work illustrates the intricate and sometimes counter-intuitive forces that act in nanoscale physical systems that operate in fluids.

DNA Balance for Native Characterization of Chemically Modified DNA

Chemical modification is a powerful approach to expand the chemical diversity and functionality of natural DNA. However, when chemically modified oligonucleotides are employed in DNA-based reactions or structures, it becomes quite difficult to predict, understand, and control their kinetics and thermodynamics. To address this challenge, we introduce a rationally designed DNA balance capable of measuring critical thermodynamic and kinetic properties of chemically modified DNA in their native environment. Our DNA balance is operated using the principle of toehold-exchange, where a panel of weight probes were designed by tuning the lengths of forward and reverse toeholds. Once placed on the DNA balance, the chemical modification will be interrogated using the weight probes to determine changes in both Gibbs free energy and hybridization rate constant. Using cyclic-azobenzene (cAB)-modified DNA as a model system, we demonstrated that our DNA balance could not only measure stable chemical modifications, but also solve more challenging issues where unstable chemical modifications and transient isomerization reactions were involved. We anticipate that our DNA balance will find wide uses for measuring important thermodynamic and kinetic parameters for DNA carrying various chemical modifications, as well as for probing transient chemical changes in DNA.

A synthetic tubular molecular transport system

Creating artificial macromolecular transport systems that can support the movement of molecules along defined routes is a key goal of nanotechnology. Here, we report the bottom-up construction of a macromolecular transport system in which molecular pistons diffusively move through micrometer-long, hollow filaments. The pistons can cover micrometer distances in fractions of seconds. We build the system using multi-layer DNA origami and analyze the structures of the components using transmission electron microscopy. We study the motion of the pistons along the tubes using single-molecule fluorescence microscopy and perform Langevin simulations to reveal details of the free energy surface that directs the motions of the pistons. The tubular transport system achieves diffusivities and displacement ranges known from natural molecular motors and realizes mobility improvements over five orders of magnitude compared to previous artificial random walker designs. Electric fields can also be employed to actively pull the pistons along the filaments, thereby realizing a nanoscale electric rail system. Our system presents a platform for artificial motors that move autonomously driven by chemical fuels and for performing nanotribology studies, and it could form a basis for future molecular transportation networks.

DNA origami can be used to control the movement of nanoscale assemblies. Here the authors construct multiple-micrometer-long hollow DNA filaments through which DNA pistons move with micrometer-per-second speeds.

DNA-based plasmonic nanostructures and their optical and biomedical applications

In the past few decades, DNA nanotechnology has been developed a lot due to their appealing features such as structural programmability and easy functionalization. In the emerging field of DNA nanotechnology, DNA molecules are regarded not only as biological information carriers but also as building blocks in the assembly of various two-dimensional and three-dimensional nanostructures, serving as outstanding templates for the bottom-up fabrication of plasmonic nanostructures. By arranging nanoparticles with different components and morphologies on the predesigned DNA templates, various static and dynamic plasmonic nanostructures with tailored optical properties have been obtained. In this review, we summarized recent advances in the design and construction of static and dynamic DNA-based plasmonic nanostructures. In addition, we addressed their emerging applications in the fields of optics and biosensors. At the end of this review, the open questions and future directions of DNA-based plasmonic nanostructure are also discussed.

Photocontrolled Nanopipette Biosensor for ATP Gradient Electroanalysis of Single Living Cells

Emerging nanopipette tools have demonstrated substantial potential for advanced single-cell analysis, which plays vital roles from fundamental cellular biology to biomedical diagnostics. Highly recyclable nanopipettes with easy and quick regeneration are of special interest for precise and multiple measurements. However, existing recycle strategies are generally plagued by operational complexity and limited efficiency. Light, acting in a noncontact way, should be the ideal external stimulus to address this issue. Herein, we present the photocontrolled nanopipette capable of probing cellular adenosine triphosphate (ATP) gradient at single-cell level with good sensitivity, selectivity, and reversibility, which stems from the use of ATP-specific azobenzene (Azo)-incorporated DNA aptamer strands (AIDAS) and thereby the sensible transduction of variable nanopore size by the ionic currents passing through the aperture. Photoisomerized conformational change of the AIDAS by alternative UV/vis light stimulation ensures its noninvasive regeneration and repeated detection. Inducement and inhibition of the cellular ATP could also be probed by this nanosensor.

Review of optical sensing and manipulation of chiral molecules and nanostructures with the focus on plasmonic enhancements [Invited]

Chiral molecules are ubiquitous in nature; many important synthetic chemicals and drugs are chiral. Detecting chiral molecules and separating the enantiomers is difficult because their physiochemical properties can be very similar. Here we review the optical approaches that are emerging for detecting and manipulating chiral molecules and chiral nanostructures. Our review focuses on the methods that have used plasmonics to enhance the chiroptical response. We also review the fabrication and assembly of (dynamic) chiral plasmonic nanosystems in this context.

Assembly of Dynamic Supramolecular Polymers on a DNA Origami Platform

Biological processes rely on transient interactions that govern assembly of biomolecules into higher order, multi-component systems. A synthetic platform for the dynamic assembly of multicomponent complexes would provide novel entries to study and modulate the assembly of artificial systems into higher order topologies. Here, we establish a hybrid DNA origami-based approach as an assembly platform that enables dynamic templating of supramolecular architectures. It entails the site-selective recruitment of supramolecular polymers to the platform with preservation of the intrinsic dynamics and reversibility of the assembly process. The composition of the supramolecular assembly on the platform can be tuned dynamically, allowing for monomer rearrangement and inclusion of molecular cargo. This work should aid the study of supramolecular structures in their native environment in real-time and incites new strategies for controlled multicomponent self-assembly of synthetic building blocks.

DNA Origami-Enabled Plasmonic Sensing

The reliable programmability of DNA origami makes it an extremely attractive tool for bottom-up self-assembly of complex nanostructures. Utilizing this property for the tuned arrangement of plasmonic nanoparticles holds great promise particularly in the field of biosensing. Plasmonic particles are beneficial for sensing in multiple ways, from enhancing fluorescence to enabling a visualization of the nanoscale dynamic actuation via chiral rearrangements. In this Perspective, we discuss the recent developments and possible future directions of DNA origami-enabled plasmonic sensing systems. We start by discussing recent advancements in the area of fluorescence-based plasmonic sensing using DNA origami. We then move on to surface-enhanced Raman spectroscopy sensors followed by chiral sensing, both utilizing DNA origami nanostructures. We conclude by providing our own views on the future prospects for plasmonic biosensors enabled using DNA origami.

DNA origami: an outstanding platform for functions in nanophotonics and cancer therapy

Due to the proposal and evolution of the DNA origami technique over the past decade, DNA molecules have been utilized as building blocks for the precise construction of nanoscale architectures. Benefiting from the superior programmability of DNA molecules, the sequence-dependent recognition mechanism and robust complementation among DNA strands make it possible to customize almost arbitrary structures. Such an assembly strategy bypasses some of the limits of conventional fabrication methods; the fabrication accuracy and complexity of the target product are unprecedentedly promoted as well. Furthermore, due to the spatial addressability of the final products, nanostructures assembled through the DNA origami technique can also serve as a versatile platform for the spatial positioning of functional elements, represented by colloidal nanoparticles (NPs). The subsequent fabrication of heterogeneous functional nanoarchitectures is realized via modifying colloidal NPs with DNA strands and manipulating them to anchor into DNA origami templates. This has given rise to investigations of their novel properties in nanophotonics and therapeutic effects towards some diseases. In this review, we survey the crucial progress in the development of DNA origami design, assembly and structural analysis and summarize available applications in nanophotonics and cancer therapy based on the object-dressed DNA origami complex. Moreover, we elucidate the development of this field and discuss the potential directions of this kind of application-oriented nanomanufacturing.

3D DNA Nanostructures: The Nanoscale Architect

Structural DNA nanotechnology is a pioneering biotechnology that presents the opportunity to engineer DNA-based hardware that will mediate a profound interface to the nanoscale. To date, an enormous library of shaped 3D DNA nanostructures have been designed and assembled. Moreover, recent research has demonstrated DNA nanostructures that are not only static but can exhibit specific dynamic motion. DNA nanostructures have thus garnered significant research interest as a template for pursuing shape and motion-dependent nanoscale phenomena. Potential applications have been explored in many interdisciplinary areas spanning medicine, biosensing, nanofabrication, plasmonics, single-molecule chemistry, and facilitating biophysical studies. In this review, we begin with a brief overview of general and versatile design techniques for 3D DNA nanostructures as well as some techniques and studies that have focused on improving the stability of DNA nanostructures in diverse environments, which is pivotal for its reliable utilization in downstream applications. Our main focus will be to compile a wide body of existing research on applications of 3D DNA nanostructures that demonstrably rely on the versatility of their mechanical design. Furthermore, we frame reviewed applications into three primary categories, namely encapsulation, surface templating, and nanomechanics, that we propose to be archetypal shape- or motion-related functions of DNA nanostructures found in nanoscience applications. Our intent is to identify core concepts that may define and motivate specific directions of progress in this field as we conclude the review with some perspectives on the future.

Construction of Smart Stimuli-Responsive DNA Nanostructures for Biomedical Applications

DNA nanostructures have recently attracted increasing interest in biological and biomedical applications by virtue of their unique properties, such as structural programmability, multi-functionality, stimuli-responsive behaviors, and excellent biocompatibility. In particular, the intelligent responsiveness of smart DNA nanostructures to specific stimuli has facilitated their extensive development in the field of high-performance biosensing and controllable drug delivery. This minireview begins with different self-assembly strategies for the construction of various DNA nanostructures, followed by the introduction of a variety of stimuli-responsive functional DNA nanostructures for assembling metastable soft materials and for facilitating amplified biosensing. The recent achievements of smart DNA nanostructures for controllable drug delivery are highlighted. Finally, the current challenges and possible developments of this promising research are discussed in the fields of intelligent nanomedicine.

DNA-Guided Programmable Protein Assemblies for Biomedical Applications

While the protein assemblies have been found widely existing and playing significant roles in biological systems, their imitation and re-construction is further boosting more applications in biomedical research, such as enzymatic reaction regulation, sensing, and biomedicine. DNA nanotechnology provides a programmable strategy for the fabrication of nanostructures with unprecedented accuracy on the nanoscale. By linking the DNA nanotechnology with proteins of different functions, the precise construction of DNA-guided protein assemblies can be achieved for various biomedical applications. This minireview summarizes the recent advances in the programmable protein assemblies on DNA nanoplatforms and discusses the outlook of DNA-guided protein assemblies in the biomedical research.

Light-Responsive Dynamic DNA-Origami-Based Plasmonic Assemblies

DNA nanotechnology offers a versatile toolbox for precise spatial and temporal manipulation of matter on the nanoscale. However, rendering DNA‐based systems responsive to light has remained challenging. Herein, we describe the remote manipulation of native (non‐photoresponsive) chiral plasmonic molecules (CPMs) using light. Our strategy is based on the use of a photoresponsive medium comprising a merocyanine‐based photoacid. Upon exposure to visible light, the medium decreases its pH, inducing the formation of DNA triplex links, leading to a spatial reconfiguration of the CPMs. The process can be reversed simply by turning the light off and it can be repeated for multiple cycles. The degree of the overall chirality change in an ensemble of CPMs depends on the CPM fraction undergoing reconfiguration, which, remarkably, depends on and can be tuned by the intensity of incident light. Such a dynamic, remotely controlled system could aid in further advancing DNA‐based devices and nanomaterials.

Tunable Chiral Optics in All-Solid-Phase Reconfigurable Dielectric Nanostructures

Subwavelength nanostructures with tunable compositions and geometries show favorable optical functionalities for the implementation of nanophotonic systems. Precise and versatile control of structural configurations on solid substrates is essential for their applications in on-chip devices. Here, we report all-solid-phase reconfigurable chiral nanostructures with silicon nanoparticles and nanowires as the building blocks in which the configuration and chiroptical response can be tailored on-demand by dynamic manipulation of the silicon nanoparticle. We reveal that the optical chirality originates from the handedness-dependent coupling between optical resonances of the silicon nanoparticle and the silicon nanowire via numerical simulations and coupled-mode theory analysis. Furthermore, the coexisting electric and magnetic resonances support strong enhancement of optical near-field chirality, which enables label-free enantiodiscrimination of biomolecules in single nanostructures. Our results not only provide insight into the design of functional high-index materials but also bring new strategies to develop adaptive devices for photonic and electronic applications.

Photocontrolled DNA Origami Assembly by Using Two Photoswitches

Stimuli-responsive switching molecules have been widely investigated for the purpose of the mechanical control of biomolecules. Recently developed arylazopyrazole (AAP) shows photoisomerization activity, displaying a faster response to light-induced conformational changes and unique absorption spectral properties compared with those of conventionally used azobenzene. Herein, it is demonstrated that AAP can be used as a photoswitching molecule to control photoinduced assembly and disassembly of DNA origami nanostructures. An AAP-modified DNA origami has been designed and constructed. It is observed that the repeated assembly and disassembly of AAP-modified X-shaped DNA origami and hexagonal origami with complementary strands can be achieved by alternating UV and visible-light irradiation. Closed and linear assemblies of AAP-modified X-shaped origami were successfully formed by photoirradiation, and more than 1 μm linear assemblies were formed. Finally, it is shown that the two photoswitches, AAP and azobenzene, can be used in tandem to independently control different assembly configurations by using different irradiation wavelengths. AAP can extend the variety of available wavelengths of photoswitches and stably result in the assembly and disassembly of various DNA origami nanostructures.

Chiral Plasmonic Metamaterials with Tunable Chirality

Chiral hollow nanovolcano array (HNVA) film and chiral hollow nanoshells (HNSs) are simultaneously fabricated via a new strategy of colloidal lithography technique. The chirality of both chiral plasmonic nanostructures, which arises from the asymmetric charge oscillation and electric field distributions, can be well controlled by regulating the opening-angle of the nanounits during the metal depositions. The large-area HNVA films exhibit strong chiroptical responses in the ultraviolet-visible region with g-factor of 0.15 and possess remarkable transferability for better adaptability of different application situations. The chiral HNSs, which are simultaneously obtained during the deposition, is equipped with adjustable chirality and integrability. The obtained HNVA films were transferred to specific substrates, e.g., polydimethylsiloxane (PDMS), hydrogels, and high-curvature surfaces, maintaining the original chiroptical properties and excellent mechanical strength. Deformable chiral flexible metamaterial is obtained by incorporating the chiral HNSs in the hydrogel, enabling the ultrasensitive detection of water content in the hydrogel. Overall, this work will contribute to the study of chiral metamaterials by providing two kinds of newly developed chiral plasmonic metamaterials with tunable chirality and inspiring progressing ways for the flexible devices of artificial chirality.

Programmed catalysis within stimuli-responsive mechanically unlocked nanocavities in DNA origami tiles

The assembly of reversible stimuli-responsive locked DNA origami tiles being unlocked, in the presence of appropriate triggers, to form nanocavities in the origami rafts, is introduced. In the presence of ATP, K⁺-ion-stabilized G-quadruplexes or pH-responsive T-A·T triggers and appropriately engineered "helper units", the origami rafts are unlocked to form nanocavities. By the application of appropriate counter-triggers, the nanocavities are relocked, thus establishing the switchable and reversible "mechanical" opening and closure mechanism of the nanocavities. The interconnection of the stimuli-responsive origami tiles into dimer structures enables the programmed triggered unlocking of each of the origami tiles, or both of the origami tiles, to yield dictated nanocavity-containing tiles. In addition, the functionalization of the opposite faces of the origami tiles with Mg²⁺-ion-dependent DNAzyme subunits leads, upon the triggered unlocking of the nanocavities, to the self-assembly of the active DNAzymes in the confined cavities. By the cyclic opening and closure of the cavities the reversible "ON"/"OFF" activation of the Mg²⁺-ion-dependent DNAzyme is demonstrated. Furthermore, upon the tethering of different Mg²⁺-ion-dependent subunits to the opposite faces of stimuli-responsive dimer origami tiles, the triggered programmed catalytic operation of different Mg²⁺-ion-dependent DNAzymes in the confined nanocavities, associated with the origami tiles, is demonstrated.

Reconfigurable Plasmonic Chirality: Fundamentals and Applications

Molecular chirality is a geometric property that is of great importance in chemistry, biology, and medicine. Recently, plasmonic nanostructures that exhibit distinct chiroptical responses have attracted tremendous interest, given their ability to emulate the properties of chiral molecules with tailored and pronounced optical characteristics. However, the optical chirality of such human-made structures is in general static and cannot be manipulated postfabrication. Herein, different concepts to reconfigure the chiroptical responses of plasmonic nano- and micro-objects are outlined. Depending on the utilized strategies and stimuli, the chiroptical signature, the 3D structural conformation, or both can be reconfigured. Optical devices based on plasmonic nanostructures with reconfigurable chirality possess great potential in practical applications, ranging from polarization conversion elements to enantioselective analysis, chiral sensing, and catalysis.

Reversible Ion-Conducting Switch by Azobenzene Molecule with Light-Controlled Sol-Gel Transitions of the PNIPAm Ion Gel

Exploring a simple, on-demanding method of manipulating ionic conduction of ionic liquids with large amplitudes is a challenging task. Here, a reversible ion-conducting switch was obtained based on photoswitchable sol-gel transitions. The device was successfully applied in an electronic circuit to switch it on/off. The ion gel was prepared by directly mixing following individual components: azobenzene (Azo), poly(N-isopropylacrylamide) (PNIPAm), and 1-ethyl-3-methylimidazolium bis(trifluoromethylsulfonyl)imide ([C₂mim][NTf₂]). The mixture is denoted as Azo/PNIPAm/[C₂mim][NTf₂]. The framework of this gel structure was particularly designed as an analogue to the physical mode of control theory: sensor/amplification/action. Light-induced isomerization of Azo acts as the light sensor to trigger the macroscopic sol-gel transition of PNIPAm assemblies. Such transition works as the amplification, which significantly affects the ionic movements, resulting in high-amplitude switching behavior. A photoswitchable ionic conductive device was demonstrated as action in this paper. Under UV irradiation, the sol-like state of Azo/PNIPAm/[C₂mim][NTf₂] provided a higher ion conduction (around 1 mS/cm) while being exposed to visible light, and a lower ion conduction (0.04 mS/cm) was observed in the gel state. This photoswitchable ion conductivity device was integrated to a well-designed logic gate to switch circuits on or off. This confirms the possible practical application of the sol-gel device, which outputs stable and detectable electrical signals. The research here demonstrates a simple but effective strategy to control the ionic movements, which can be applied in optoelectronic devices. The principle can be used to design different types of molecular optoelectronic switches.

Robotic DNA Nanostructures

Over the past decade, DNA nanotechnology has spawned a broad variety of functional nanostructures tailored toward the enabled state at which applications are coming increasingly in view. One of the branches of these applications is in synthetic biology, where the intrinsic programmability of the DNA nanostructures may pave the way for smart task-specific molecular robotics. In brief, the synthesis of the user-defined artificial DNA nano-objects is based on employing DNA molecules with custom lengths and sequences as building materials that predictably assemble together by obeying Watson-Crick base pairing rules. The general workflow of creating DNA nanoshapes is getting more and more straightforward, and some objects can be designed automatically from the top down. The versatile DNA nano-objects can serve as synthetic tools at the interface with biology, for example, in therapeutics and diagnostics as dynamic logic-gated nanopills, light-, pH-, and thermally driven devices. Such diverse apparatuses can also serve as optical polarizers, sensors and capsules, autonomous cargo-sorting robots, rotary machines, precision measurement tools, as well as electric and magnetic-field directed robotic arms. In this review, we summarize the recent progress in robotic DNA nanostructures, mechanics, and their various implementations.

Dynamic DNA Assemblies in Biomedical Applications

Deoxyribonucleic acid (DNA) has been widely used to construct homogeneous structures with increasing complexity for biological and biomedical applications due to their powerful functionalities. Especially, dynamic DNA assemblies (DDAs) have demonstrated the ability to simulate molecular motions and fluctuations in bionic systems. DDAs, including DNA robots, DNA probes, DNA nanochannels, DNA templates, etc., can perform structural transformations or predictable behaviors in response to corresponding stimuli and show potential in the fields of single molecule sensing, drug delivery, molecular assembly, etc. A wave of exploration of the principles in designing and usage of DDAs has occurred, however, knowledge on these concepts is still limited. Although some previous reviews have been reported, systematic and detailed reviews are rare. To achieve a better understanding of the mechanisms in DDAs, herein, the recent progress on the fundamental principles regarding DDAs and their applications are summarized. The relative assembly principles and computer-aided software for their designing are introduced. The advantages and disadvantages of each software are discussed. The motional mechanisms of the DDAs are classified into exogenous and endogenous stimuli-triggered responses. The special dynamic behaviors of DDAs in biomedical applications are also summarized. Moreover, the current challenges and future directions of DDAs are proposed.

Laser-induced formation of "craters" and "hills" in azobenzene-containing polymethacrylate films

Functional organic polymer materials with an ability to change their surface topography in response to external contactless stimuli, like light irradiation, have attracted considerable attention. This work is devoted to the study of contactless control of the surface topography and the formation of the surface features in the amorphousized and liquid crystalline films of two azobenzene-containing polymers. The investigated polymers are side-chain polymethacrylates containing azobenzene chromophores with two lateral methyl substituents in ortho-positions and differing in the length of flexible spacer with six and ten methylene units. Two lateral methyl substituents at the azobenzene chromophore ensure high photoresponses of these polymeric samples in the whole visible spectral range. Irradiation of the polymethacrylate films by focused polarized light of green (532 nm) and red (633 nm) lasers induces a specific photodeformation of the film surface. In the case of the green light formation of circular "craters" with anisotropic borders was found, whereas for the red light highly asymmetric "hills" were observed. The possible mechanisms of the surface topography formation and their features are discussed.

Guanosine Assembly Enabled Gold Nanorods with Dual Thermo- and Photoswitchable Plasmonic Chiroptical Activity

Noble metal nanostructures with plasmonic circular dichroism (PCD) have attracted interest, and a modulation of PCD is of great importance for their potential applications. Herein, we propose a supramolecular strategy for achieving dual thermal and photoswitchable PCD. When guanosine (G), deoxyguanosine (dG), and boric acid modified achiral gold nanorods (GNRs) were coassembled into a hydrogel, hybrid nanofibers with PCD were produced. When the hydrogel was heated, the nanofiber was disassembled and the PCD disappeared. As the hydrogel was thermally reversible, a thermo-controlled PCD could be realized. The hybrid hydrogel also showed photoswitchable PCD. When the gel was irradiated with an IR laser, the PCD disappeared. It can be restored by being placed at room temperature. Moreover, the hybrid gel was selectively responsive to the circularly polarized light (CPL). For (G/dG)-GNR hybrid assemblies, the R-CPL irradiation showed photothermal efficiency higher than that of L-CPL, which made it useful for an IR-irradiation-controlled release of drug molecules.

Information Coding in a Reconfigurable DNA Origami Domino Array

DNA nanostructures with programmable nanoscale patterns has been achieved in the past decades, and molecular information coding (MIC) on those designed nanostructures has gained increasing attention for information security. However, achieving steganography and cryptography synchronously on DNA nanostructures remains a challenge. Herein, we demonstrated MIC in a reconfigurable DNA origami domino array (DODA), which can reconfigure intrinsic patterns but keep the DODA outline the same for steganography. When a set of keys (DNA strands) are added, the cryptographic data can be translated into visible patterns within DODA. More complex cryptography with the ASCII code within a programmable 6×6 lattice is demonstrated to demosntrate the versatility of MIC in the DODA. Furthermore, an anti-counterfeiting approach based on conformational transformation-mediated toehold strand displacement reaction is designed to protect MIC from decoding and falsification.

DNA Origami as Emerging Technology for the Engineering of Fluorescent and Plasmonic-Based Biosensors

DNA nanotechnology is a powerful and promising tool for the development of nanoscale devices for numerous and diverse applications. One of the greatest potential fields of application for DNA nanotechnology is in biomedicine, in particular biosensing. Thanks to the control over their size, shape, and fabrication, DNA origami represents a unique opportunity to assemble dynamic and complex devices with precise and predictable structural characteristics. Combined with the addressability and flexibility of the chemistry for DNA functionalization, DNA origami allows the precise design of sensors capable of detecting a large range of different targets, encompassing RNA, DNA, proteins, small molecules, or changes in physico-chemical parameters, that could serve as diagnostic tools. Here, we review some recent, salient developments in DNA origami-based sensors centered on optical detection methods (readout) with a special emphasis on the sensitivity, the selectivity, and response time. We also discuss challenges that still need to be addressed before this approach can be translated into robust diagnostic devices for bio-medical applications.

DNA-Modulated Plasmon Resonance: Methods and Optical Applications

The near-field effects in the vicinity of metallic nanoparticle surfaces, as induced by electromagnetic radiation with specific wavelength, give rise to a variety of novel optical properties and attractive applications because of surface plasmons, which are the coherent oscillations of conduction electrons on a metal surface. The interdisciplinary field of plasmonics has witnessed vigorous growth, promoting research on the modulation of plasmon resonance by constructing advanced plasmonic nanoarchitectures with controllable size, morphology, or interparticle coupling. Among diversified tools, deoxyribonucleic nucleic acid (DNA) possesses prominent superiority as a result of its designability, programmability, addressability, and ease of nanomaterial modification. In this review, we focus on the methods and optical applications of plasmon resonance modulation accomplished by DNA nanotechnology. Recent developments in the construction of DNA-mediated plasmonic nanoarchitecture and key ongoing research directions utilizing unique optical features are highlighted. Obstacles and challenges in this field are pointed out, followed by preliminary suggestions on some areas of opportunity that deserve attention.

Switching the Optical Chirality in Magnetoplasmonic Metasurfaces Using Applied Magnetic Fields

Chiral nanophotonic devices are promising candidates for chiral molecule sensing, polarization of diverse nanophotonics, and display technologies. Active chiral nanophotonic devices, where the optical chirality can be controlled by an external stimulus has triggered great research interest. However, efficient modulation of the optical chirality has been challenging. Here, we demonstrate switching of the extrinsic chirality by applied magnetic fields in a magnetoplasmonic metasurface device based on a magneto-optical oxide material, Ce₁Y₂Fe₅O₁₂ (Ce:YIG). Due to the low optical loss and strong magneto-optical effect of Ce:YIG, we experimentally demonstrated giant and continuous far-field circular dichroism (CD) modulation by applied magnetic fields from -0.6 ± 0.2° to +1.9 ± 0.1° at 950 nm wavelength under glancing incident conditions. The far-field CD modulation is due to both magneto-optical circular dichroism and near-field modulation of the superchiral fields by applied magnetic fields. Finally, we demonstrate magnetic-field-tunable chiral imaging in millimeter-scale magnetoplasmonic metasurfaces fabricated using self-assembly.

Light-Controlled, Toehold-Mediated Logic Circuit for Assembly of DNA Tiles

Inspired by cytoskeletal structures that respond sensitively to environmental changes and chemical inputs, we report a strategy to trigger and finely control the assembly of stimulus-responsive DNA nanostructures with light under isothermal conditions. The strategy is achieved via integrating an upstream light-controlled, toehold-mediated DNA strand displacement circuit with a downstream DNA tile self-assembly process. By rationally designing an upstream DNA strand module, we further transform the upstream DNA strand displacement circuit to an "AND gate" circuit to control the assembly of DNA nanostructures. This example represents the demonstration of the spatial and temporal assembly of DNA nanostructures using a noninvasive chemical input. Such a light-controlled DNA logic circuit not only adds a new element to the tool box of DNA nanotechnology but also inspires us to assemble complex and responsive nanostructures.

Light-Responsive Colloidal Crystals Engineered with DNA

A novel method for synthesizing and photopatterning colloidal crystals via light-responsive DNA is developed. These crystals are composed of 10-30 nm gold nanoparticles interconnected with azobenzene-modified DNA strands. The photoisomerization of the azobenzene molecules leads to reversible assembly and disassembly of the base-centered cubic (bcc) and face-centered cubic (fcc) crystalline nanoparticle lattices. In addition, UV light is used as a trigger to selectively remove nanoparticles on centimeter-scale thin films of colloidal crystals, allowing them to be photopatterned into preconceived shapes. The design of the azobenzene-modified linking DNA is critical and involves complementary strands, with azobenzene moieties deliberately staggered between the bases that define the complementary code. This results in a tunable wavelength-dependent melting temperature (Tm ) window (4.5-15 °C) and one suitable for affecting the desired transformations. In addition to the isomeric state of the azobenzene groups, the size of the particles can be used to modulate the Tm window over which these structures are light-responsive.

Chiromagnetic Plasmonic Nanoassemblies with Magnetic Field Modulated Chiral Activity

Chiral plasmonic nanoassemblies, which exhibit outstanding chiroptical activity in the visible or near-infrared region, are popular candidates in molecular sensing, polarized nanophotonics, and biomedical applications. Their optical chirality can be modulated by manipulating chemical molecule stimuli or replacing the building blocks. However, instead of irreversible chemical or material changes, real-time control of optical activity is desired for reversible and noninvasive physical regulating methods, which is a challenging research field. Here, the directionally and reversibly switching optical chirality of magneto-plasmonic nanoassemblies is demonstrated by the application of an external magnetic field. The gold-magnetic nanoparticles core-satellite (Au@Fe₃ O₄ ) nanostructures exhibit chiral activity in the UV-visible range, and the circular dichroism signal is 12 times greater under the magnetic field. Significantly, the chiral signal can be reversed by regulating the direction of the applied magnetic field. The attained magnetic field-regulated chirality is attributed to the large contributions of the magnetic dipole moments to polarization rotation. This magnetic field-modulated optical activity may be pivotal for photonic devices, information communication, as well as chiral metamaterials.

Stereospecific interactions between chiral inorganic nanomaterials and biological systems

Chirality is ubiquitous in nature and plays mysterious and essential roles in maintaining key biological and physiological processes.

Supramolecular chiroptical switches

Recent progress in chiroptical switches including on/off, amplification, and inversion of the chiral signals such as ECD and CPL in supramolecular assemblies is shown.

Photo-switching of blunt-end stacking between DNA strands immobilized on gold nanoparticles

End-to-end stacking of DNAs on gold nanoparticles was switched by terminal base pairing/unpairing triggered by the photo-isomerization of an azobenzene moiety nearby the DNA terminal.

Reconfigurable Plasmonic Diastereomers Assembled by DNA Origami

Herein, we report self-assembled reconfigurable plasmonic diastereomers based on DNA nanotechnology. Up to three plasmonic chiral centers were organized by dynamic DNA origami platforms. Meanwhile, each chiral center could be individually controlled to switch between left-handed and right-handed states. Thus, complex and reconfigurable chiral plasmonic diastereomers with eight plasmonic stereoisomers were achieved, driven by programmed DNA reactions. With these plasmonic diastereomers, we demonstrated the existence of strong cross-talk near-field coupling among chiral centers, and the coupling of chiral centers could substantially contribute to the overall CD signals. Our work provides an important bottom-up approach for building complex and dynamic chiral plasmonics and for probing the interactions of plasmonic chiral centers.

Reconfigurable Chiral Plasmonics beyond Single Chiral Centers

Understanding how the geometrical property of chirality is transferred into the physical properties of chiral materials is becoming increasingly important in various research fields, including plasmonics. Advances in DNA nanotechnology, especially DNA origami techniques, have enabled routine fabrication of complex chiral plasmonic assemblies. However, most of the work undertaken to date has involved plasmonic enantiomers. The concept of multiple chiral centers in stereochemistry provides simple guidelines for generating multiple chiral configurations beyond enantiomers. In this issue of ACS Nano, Wang et al. report DNA origami-based assembly and characterization of reconfigurable plasmonic chiral stereoisomers with up to three chiral centers. In this Perspective, we explore the implication of these results for further development of functional chiral plasmonic systems.