Ordering Gold Nanoparticles with DNA Origami Nanoflowers

Localized Plasmonic Heating for Single-Molecule DNA Rupture Measurements in Optical Tweezers

To date, studies on the thermodynamic and kinetic processes that underlie biological function and nanomachine actuation in biological- and biology-inspired molecular constructs have primarily focused on photothermal heating of ensemble systems, highlighting the need for probes that are localized within the molecular construct and capable of resolving single-molecule response. Here we present an experimental demonstration of wavelength-selective, localized heating at the single-molecule level using the surface plasmon resonance of a 15 nm gold nanoparticle (AuNP). Our approach is compatible with force-spectroscopy measurements and can be applied to studies of the single-molecule thermodynamic properties of DNA origami nanomachines as well as biomolecular complexes. We further demonstrate wavelength selectivity and establish the temperature dependence of the reaction coordinate for base-pair disruption in the shear-rupture geometry, demonstrating the utility and flexibility of this approach for both fundamental studies of local (nanometer-scale) temperature gradients and rapid and multiplexed nanomachine actuation.

Chemically Conjugated Branched Staples for Super-DNA Origami

DNA origami, comprising a long folded DNA scaffold and hundreds of linear DNA staple strands, has been developed to construct various sophisticated structures, smart devices, and drug delivery systems. However, the size and diversity of DNA origami are usually constrained by the length of DNA scaffolds themselves. Herein, we report a new paradigm of scaling up DNA origami assembly by introducing a novel branched staple concept. Owing to their covalent characteristics, the chemically conjugated branched DNA staples we describe here can be directly added to a typical DNA origami assembly system to obtain super-DNA origami with a predefined number of origami tiles in one pot. Compared with the traditional two-step coassembly system (yields <10%), a much greater yield (>80%) was achieved using this one-pot strategy. The diverse superhybrid DNA origami with the combination of different origami tiles can be also efficiently obtained by the hybrid branched staples. Furthermore, the branched staples can be successfully employed as the effective molecular glues to stabilize micrometer-scale, super-DNA origami arrays (e.g., 10 × 10 array of square origami) in high yields, paving the way to bridge the nanoscale precision of DNA origami with the micrometer-scale device engineering. This rationally developed assembly strategy for super-DNA origami based on chemically conjugated branched staples presents a new avenue for the development of multifunctional DNA origami-based materials.

Bulk Electrosynthesis of Patchy Particles with Highly Controlled Asymmetric Features

Asymmetric modification of particles with various patches of different composition and size at predefined positions is an important challenge in contemporary surface chemistry, as such particles have numerous potential applications, ranging from materials science and (photo)catalysis to self-assembly and drug delivery. However, approaches allowing the synthesis of this kind of complex objects in the bulk of a solution in a straightforward way are currently lacking. In this context, bipolar electrochemistry (BE) is a powerful technique for the asymmetric modification of conducting objects. Herein, this approach is used for the highly controlled modification of particles with different metal patches, generated at specific locations of isotropic objects. The synthesis is carried out in the bulk of the solution and leads to predefined patterns of increasing complexity, including even a specific chiral arrangement of the patches.

DNA-mediated regioselective encoding of colloids for programmable self-assembly

How far we can push chemical self-assembly is one of the most important scientific questions of the century. Colloidal self-assembly is a bottom-up technique for the rational design of functional materials with desirable collective properties. Due to the programmability of DNA base pairing, surface modification of colloidal particles with DNA has become fundamental for programmable material self-assembly. However, there remains an ever-lasting demand for surface regioselective encoding to realize assemblies that require specific, directional, and orthogonal interactions. Recent advances in surface chemistry have enabled regioselective control over the formation of DNA bonds on the particle surface. In particular, the structural DNA nanotechnology provides a simple yet powerful design strategy with unique regioselective addressability, bringing the complexity of colloidal self-assembly to an unprecedented level. In this review, we summarize the state-of-art advances in DNA-mediated regioselective surface encoding of colloids, with a focus on how the regioselective encoding is introduced and how the regioselective DNA recognition plays a crucial role in the self-assembly of colloidal structures. This review highlights the advantages of DNA-based regioselective modification in improving the complexity of colloidal assembly, and outlines the challenges and opportunities for the construction of more complex architectures with tailored functionalities.

DNA-directed assembly of nanomaterials and their biomedical applications

In the past decades, DNA has been widely used in the field of nanostructures due to its unique programmable properties. Besides being used to form its own diverse structures such as the assembly of DNA origami, DNA can also be used for the assembly of nanostructures with other materials. In this review, different strategies for the functionalization of DNA on nanoparticle surfaces are listed, and the roles of DNA in the assembly of nanostructures as well as the influencing factors are discussed. Finally, the biomedical applications of DNA-assembled nanostructures were summarized. This review provided new insight into the application of DNA in nanostructure assembly.

DNA-Guided Metallization of Nanomaterials and Their Biomedical Applications

Precise control of the structure of metallic nanomaterials is critical for the advancement of nanobiotechnology. As DNA (deoxyribonucleic acid) can readily modify various moieties, such as sulfhydryl, carboxyl, and amino groups, using DNA as a directing ligand to modulate the morphology of nanomaterials is a promising strategy. In this review, we focus on the use of DNA as a template to control the morphology of metallic nanoparticles and their biomedical applications, discuss the use of DNA for the metallization of gold and silver, explore the factors that influence the process, and outline its biomedical applications. This review aims to provide valuable insights into the DNA-guided growth of nanomaterials. The challenges and future directions are also discussed.

Structure-Dependent Electrical Conductance of DNA Origami Nanowires

Exploring the structural and electrical properties of DNA origami nanowires is an important endeavor for the advancement of DNA nanotechnology and DNA nanoelectronics. Highly conductive DNA origami nanowires are a desirable target for creating low-cost self-assembled nanoelectronic devices and circuits. In this work, the structure-dependent electrical conductance of DNA origami nanowires is investigated. A silicon nitride (Si₃ N₄ ) on silicon semiconductor chip with gold electrodes was used for collecting electrical conductance measurements of DNA origami nanowires, which are found to be an order of magnitude less electrically resistive on Si₃ N₄ substrates treated with a monolayer of hexamethyldisilazane (HMDS) (∼10¹³ ohms) than on native Si₃ N₄ substrates without HMDS (∼10¹⁴ ohms). Atomic force microscopy (AFM) measurements of the height of DNA origami nanowires on mica and Si₃ N₄ substrates reveal that DNA origami nanowires are ∼1.6 nm taller on HMDS-treated substrates than on the untreated ones indicating that the DNA origami nanowires undergo increased structural deformation when deposited onto untreated substrates, causing a decrease in electrical conductivity. This study highlights the importance of understanding and controlling the interface conditions that affect the structure of DNA and thereby affect the electrical conductance of DNA origami nanowires.

Tunable 2D diffusion of DNA nanostructures on lipid membranes

DNA nanotechnology facilitates the synthesis of biomimetic models for studying biological systems. This work uses lipid bilayers as platforms for two-dimensional single-particle tracking of the dynamics of DNA nanostructures. Three different DNA origami structures adhere to the membrane through hybridization with cholesterol-modified strands. Their two-dimensional diffusion coefficient is modulated by changing the concentration of monovalent and divalent salts and the number of anchors. In addition, the diffusion coefficient is tuned by targeting cholesterol-modified anchor strands with strand-displacement reactions. We demonstrate a responsive system with changing diffusivity by selectively displacing membrane-bound anchor strands. We also show the programmed release of origami structures from the lipid membranes.

Molecular Structure of Single-Stranded DNA on the ZnS Surface of Quantum Dots

DNA-based nanoparticle assemblies have emerged as leading candidates in the development of bioimaging materials, photonic devices, and computing materials. Here, we combine atomistic simulations and experiments to characterize the wrapping mechanism of chimeric single-stranded DNA (ssDNA) on CdSe-ZnS (core-shell) quantum dots (QDs) at different ratios of the phosphorothioate (PS) modification of the bases. We use an implicit solvent, all-atom ssDNA model to match the experimentally calculated ssDNA conformation at low salt concentrations. Through simulation, we find that 3-mercaptopropionic acid (MPA) induces electrostatic repulsion and O-(2-mercaptoethyl)-Ó-methyl-hexa (ethylene glycol) (mPEG) induces steric exclusion, and both reduce the binding affinity of ssDNA. In both simulation and experiment, we find that ssDNA is closer to the QD surface when the QD size is larger. The effect of the PS-base ratio on the conformation of ssDNA is also elaborated in this work. We found through MD simulations, and confirmed by transmission electron microscopy, that the maximum valence numbers are 1, 2, and 3 on QDs of 6, 9, and 14 nm in diameter, respectively. We conclude that the maximum ssDNA valence number is linearly related to the QD size, n ∝ R, and justify this finding through an electrostatic repulsion mechanism.

Engineering surface patterns on nanoparticles: New insights on nano-bio interactions

The surface properties of nanoparticles affect their fates in biological systems. Based on nanotechnology and methodology, pioneering works have explored the effects of chemical surface patterns on the behavior of...

DNA Nanotechnology-Enabled Fabrication of Metal Nanomorphology

In recent decades, DNA nanotechnology has grown into a highly innovative and widely established field. DNA nanostructures have extraordinary structural programmability and can accurately organize nanoscale materials, especially in guiding the synthesis of metal nanomaterials, which have unique advantages in controlling the growth morphology of metal nanomaterials. This review started with the evolution in DNA nanotechnology and the types of DNA nanostructures. Next, a DNA-based nanofabrication technology, DNA metallization, was introduced. In this section, we systematically summarized the DNA-oriented synthesis of metal nanostructures with different morphologies and structures. Furthermore, the applications of metal nanostructures constructed from DNA templates in various fields including electronics, catalysis, sensing, and bioimaging were figured out. Finally, the development prospects and challenges of metal nanostructures formed under the morphology control by DNA nanotechnology were discussed.

Hierarchical Assembly of Super-DNA Origami Based on a Flexible and Covalent-Bound Branched DNA Structure

DNA origami technique provides a programmable way to construct nanostructures with arbitrary shapes. The dimension of assembled DNA origami, however, is usually limited by the length of the scaffold strand. Herein, we report a general strategy to efficiently organize multiple DNA origami tiles to form super-DNA origami using a flexible and covalent-bound branched DNA structure. In our design, the branched DNA structures (B_n: with a certain number of 2-6 branches) are synthesized by a copper-free click reaction. Equilateral triangular DNA origamis with different numbers of capture strands (T_n: T₁, T₂, and T₃) are constructed as the coassembly tiles. After hybridization with the branched DNA structures, the super-DNA origami (up to 13 tiles) can be efficiently ordered in the predesigned patterns. Compared with traditional DNA junctions (J_n: J₂-J₆, as control groups) assembled by base pairing between several DNA strands, a higher yield and more compact structures are obtained using our strategy. The highly ordered and discrete DNA origamis can further precisely organize gold nanoparticles into different patterns. This rationally developed DNA origami ordering strategy based on the flexible and covalent-bound branched DNA structure presents a new avenue for the construction of sophisticated DNA architectures with larger molecular weights.

Progress of Phototherapy Applications in the Treatment of Bone Cancer

Bone cancer including primary bone cancer and metastatic bone cancer, remains a challenge claiming millions of lives and affecting the life quality of survivors. Conventional treatments of bone cancer include wide surgical resection, radiotherapy, and chemotherapy. However, some bone cancer cells may remain or recur in the local area after resection, some are highly resistant to chemotherapy, and some are insensitive to radiotherapy. Phototherapy (PT) including photodynamic therapy (PDT) and photothermal therapy (PTT), is a clinically approved, minimally invasive, and highly selective treatment, and has been widely reported for cancer therapy. Under the irradiation of light of a specific wavelength, the photosensitizer (PS) in PDT can cause the increase of intracellular ROS and the photothermal agent (PTA) in PTT can induce photothermal conversion, leading to the tumoricidal effects. In this review, the progress of PT applications in the treatment of bone cancer has been outlined and summarized, and some envisioned challenges and future perspectives have been mentioned. This review provides the current state of the art regarding PDT and PTT in bone cancer and inspiration for future studies on PT.

Polymethylolacrylamide/AuNPs Nanocomposites: Electrochemical Synthesis and Functional Characteristics

In this study the advantages of the electrochemical approach to the formation of polymer/metal nanoparticle composites are demonstrated. The method enables one to simplify the multistage processes of traditional technologies for the production of such materials through combining all intermediate processes in one stage and reducing the total formation time to 3–10 min. The possibility of a single-stage formation of a polymethylolacrylamide/AuNPs composite through including AuNPs into an electrically non-conducting polymethylolacrylamide film (carrier) formed by electropolymerization through potentiostatic electrolysis is also demonstrated for the first time. It is established that the addition of tetrachloroauric acid (HAuCl₄·4H₂O) into a monomeric composition containing acrylamide, formaldehyde, N,N′-methylene-bis-acrylamide, zinc chloride, and H₂O results in simultaneous electrochemical initiation of polymerization with the formation of a polymer film on the cathode, electrolytic reduction of gold ions to Au⁰, and immobilization of AuNPs particles into the growing polymer matrix. It was found that the formation of the PMAA / AuNPs composite is energetically more favorable than the synthesis of the main PMAA film, since it proceeds at a lower cathodic potential. The inclusion of AuNPs into the polymethylolacrylamide film was confirmed visually, as well as by X-ray phase analysis, small-angle X-ray scattering, microscopy, and element analysis. The gold content in the composite increases along with the increase of the concentration of HAuCl₄ in the electrolyte. The radius of the AuNPs particles was found to range between 3 and 7 nm. The AuNPs particles are spherical in shape and can combine into larger clusters containing up to 10 or more particles. The dynamics of formation, structure, and morphology of the polymethylolacrylamide/AuNPs composite were investigated. It was revealed that gold nanoparticles are mainly concentrated in the near-electrode and near-solution layers of the composite. We found that the composite has electrocatalytic activity. The possibility of its use as a sensor for hydrogen peroxide is demonstrated.

Bottom-Up Fabrication of DNA-Templated Electronic Nanomaterials and Their Characterization

Bottom-up fabrication using DNA is a promising approach for the creation of nanoarchitectures. Accordingly, nanomaterials with specific electronic, photonic, or other functions are precisely and programmably positioned on DNA nanostructures from a disordered collection of smaller parts. These self-assembled structures offer significant potential in many domains such as sensing, drug delivery, and electronic device manufacturing. This review describes recent progress in organizing nanoscale morphologies of metals, semiconductors, and carbon nanotubes using DNA templates. We describe common substrates, DNA templates, seeding, plating, nanomaterial placement, and methods for structural and electrical characterization. Finally, our outlook for DNA-enabled bottom-up nanofabrication of materials is presented.

Designer Nanomaterials through Programmable Assembly

Nanoparticles have long been recognized for their unique properties, leading to exciting potential applications across optics, electronics, magnetism, and catalysis. These specific functions often require a designed organization of particles, which includes the type of order as well as placement and relative orientation of particles of the same or different kinds. DNA nanotechnology offers the ability to introduce highly addressable bonds, tailor particle interactions, and control the geometry of bindings motifs. Here, we discuss how developments in structural DNA nanotechnology have enabled greater control over 1D, 2D, and 3D particle organizations through programmable assembly. This Review focuses on how the use of DNA binding between nanocomponents and DNA structural motifs has progressively allowed the rational formation of prescribed particle organizations. We offer insight into how DNA-based motifs and elements can be further developed to control particle organizations and how particles and DNA can be integrated into nanoscale building blocks, so-called "material voxels", to realize designer nanomaterials with desired functions.

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.

Small molecule-induced DNA hydrogel with encapsulation and release properties

Hydrogels are networks of polymers that can be used for packaging different payload types. They are proven to be versatile materials for various biomedical applications. Implanted hydrogels with encapsulated drugs have been shown to release the therapeutic payloads at disease sites. Hydrogels are usually made through chemical polymerization reactions. Whereas, DNA is a naturally occurring biopolymer which can assemble into highly ordered structures through noncovalent interactions. Here, we have employed a small molecule, cyanuric acid (CA), to assemble polyA-tailed DNA motif into a hydrogel. Encapsulation of a small molecule chemotherapeutic drug, a fluorescent molecule, two proteins and several nanoparticle formulations has been studied. Release of doxorubicin, small fluorescent molecule and fluorescently-labeled antibodies has been demonstrated.

CD271 antibody-functionalized HGNs for targeted photothermal therapy of osteosarcoma stem cells

Cancer stem cells (CSCs) are considered to maintain the vitality of tumor cell populations through self-renewal and infinite proliferation, but their accessibility is still under investigation. In addition, CSCs are more resistant to chemotherapy and radiotherapy compared with common tumor cells. This study aimed to develop a kind of novel and feasible nanomaterial for targeted photothermal ablation of osteosarcoma stem cells, which could be a promising anticancer strategy. The osteosarcoma stem cells were extracted by serum-free culture and we further verified the stem cell properties. We evaluated the expression of CD271 by flow cytometry. PEGylated multifunctional hollow gold nanospheres (HGNs) were prepared based on CD271 monoclonal antibody. Bifunctional SH-PEG-COOH was used to facilitate the covalent linkage between HGNs and antibody. The efficient uptake and distribution of the functionalized HGNs were investigated using ICP-MS and TEM. Morphological studies and quantitative apoptosis evaluation were performed to detect the effect of photothermal therapy (PTT). Afterwards, we explored the possible mechanism by which PTT induced targeted killing of cancer stem cells. Osteosarcoma cells isolated from serum-free culture were detected to show stem cell properties. CD271 was found to be a potential novel surface marker for osteosarcoma stem cells. By conjugating with CD271 monoclonal antibody, these biomimetic nanoparticles can be targeted and absorbed by osteosarcoma stem cells. HGNs-PEG-CD271 achieved excellent cell viability inhibition compared with non-targeted PEGylated HGNs upon near-infrared (NIR) laser irradiation. The mechanism of targeted killing may be related to the apoptosis pathway and DNA double-strand injuries. CD271 was considered to be a surface biomarker for osteosarcoma stem cells. Functionalized HGNs based on CD271 antibody exhibited excellent potential for targeted PTT, which may be a promising strategy for osteosarcoma treatment.

Three-Dimensional Patterning of Nanoparticles by Molecular Stamping

Directing the formation of nanoscale architectures from nanoparticles is one of the key challenges in designing nanomaterials with prescribed functions. Atomic systems, given their ability to form molecules and crystals via directional chemical bonds, provide an inspiration for establishing approaches where nanoparticles with designed anisotropic binding modalities can be assembled into nanoscale architectures. However, fabricating such nanoparticles has been challenging due to their small dimensions and limited ways for site-specific control of their surface. To this end, we present a molecular stamping (MOST) approach to pattern DNA-coated nanoparticles with molecules at the predefined positions on a nanoparticle surface. This patterning is realized by use of a rigid and coordinative DNA frame as a molecular stamping apparatus (MOST App). The MOST App transfers multiple types of molecular "inks", DNA sequences, onto a nanoparticle surface and fixes these molecular inks into place to form a designed pattern. After a nanoparticle is released the from MOST App, it possesses single-molecule patches that can provide anisotropic bonds with distinctive affinities. We further use these stamped nanoparticles to assemble prescribed clusters, whose structure is determined by the locations of patches. Using electron microscopy and tomographic methods, we investigate the efficiency of cluster formation and the resulting spatial arrangements of nanoparticles. The presented approach provides a single-molecule and spatially determined control over nanoparticle functionalization for creating nanoparticles with designed placement of different molecules and for realizing a rational fabrication of nanomaterial architectures.

DNA-Programmed Bimodal 2D Assembly of Differently Sized Nanoparticles via Folding of Precursory Circular Chains

Gold nanoparticle (AuNP) assemblies in two-dimensions (2D) exhibit collective physical/chemical properties that are useful for various devices. However, technical issues still impede the efficient ordering of differently sized AuNPs on solid supports while avoiding phase separation. This paper describes a method to construct binary 2D assemblies by folding precursory circular chains composed of small and large AuNPs. The structural change is caused by a spontaneous, non-cross-linking assembly of fully matched double-stranded DNA-modified AuNPs (dsDNA-AuNPs) at a high ionic strength. Since larger dsDNA-AuNPs have a lower critical coagulation concentration of the supporting electrolyte, the spontaneous assembly of large AuNPs precedes that of small AuNPs in the precursory chain during evaporation. Transmission electron microscopy reveals that alternate-type AuNP chains are folded into a binary 2D structure in a mixed mode, whereas block-type chains are transformed into a binary 2D structure in a core-shell mode. The methodology could potentially be harnessed for the fabrication of binary AuNP arrays for various devices.

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

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

Valence-programmable nanoparticle architectures

Nanoparticle-based clusters permit the harvesting of collective and emergent properties, with applications ranging from optics and sensing to information processing and catalysis. However, existing approaches to create such architectures are typically system-specific, which limits designability and fabrication. Our work addresses this challenge by demonstrating that cluster architectures can be rationally formed using components with programmable valence. We realize cluster assemblies by employing a three-dimensional (3D) DNA meshframe with high spatial symmetry as a site-programmable scaffold, which can be prescribed with desired valence modes and affinity types. Thus, this meshframe serves as a versatile platform for coordination of nanoparticles into desired cluster architectures. Using the same underlying frame, we show the realization of a variety of preprogrammed designed valence modes, which allows for assembling 3D clusters with complex architectures. The structures of assembled 3D clusters are verified by electron microcopy imaging, cryo-EM tomography and in-situ X-ray scattering methods. We also find a close agreement between structural and optical properties of designed chiral architectures.

Characterizing the non-crosslinked aggregation of DNA-modified gold nanoparticles: effects of DNA length and terminal base pair

We previously reported that fully complementary DNA duplexes formed on gold nanoparticle (GNP) surfaces aggregate at high salt concentrations. We previously reported that DNA-functionalized gold nanoparticles (GNPs) aggregate by hybridization with fully complementary DNA at high salt concentrations. Although this behavior has been applied to some precise naked-eye colorimetric analyses of DNA-related molecules, the aggregation mechanism is still unclear and comprehensive studies are needed. In this paper, we reveal the key factors that influence GNP aggregation. The effects of temperature, electrolyte concentration, probe length, and particle size, which control the stabilities of double-stranded DNAs and GNPs, were investigated. Larger GNPs aggregated more easily, and GNP aggregates were easily formed with ∼15-mer-long probes, while longer probes prevented aggregation, perhaps by preventing the formation of rigid double-stranded DNA layers, compared to shorter probes. Furthermore, GNPs with purine bases at their 5' ends aggregated more easily than those with these bases at their 3' ends. This phenomenon is different from that based on the melting-temperature trend calculated using the nearest-neighbor method.

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

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

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.

Patterning Nanoparticles with DNA Molds

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

Complementary Design for Pairing between Two Types of Nanoparticles Mediated by a Bispecific Antibody: Bottom-Up Formation of Porous Materials from Nanoparticles

Recent advances in biotechnology have enabled the generation of antibodies with high affinity for the surfaces of specific inorganic materials. Herein, we report the synthesis of functional materials from multiple nanomaterials by using a small bispecific antibody recombinantly constructed from gold-binding and ZnO-binding antibody fragments. The bispecific antibody-mediated spontaneous linkage of gold and ZnO nanoparticles forms a binary gold-ZnO nanoparticle composite membrane. The relatively low melting point of the gold nanoparticles and the solubility of ZnO in dilute acidic solution then allowed for the bottom-up synthesis of a nanoporous gold membrane by means of a low-energy, low-environmental-load protocol. The nanoporous gold membrane showed high catalytic activity for the reduction of p-nitrophenol to p-aminophenol by sodium borohydride. Here, we show the potential utility of nanoparticle pairing mediated by bispecific antibodies for the bottom-up construction of nanostructured materials from multiple nanomaterials.

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.

Thiol-free oligonucleotide surface modification of gold nanoparticles for nanostructure assembly

Gold nanoparticles (AuNPs) decorated with thiol-modified DNA (HS-DNA) strands are an extensively studied, easily adjustable, and highly controllable material for constructing 3D nanostructures with various shapes and functions. However, few reproducible and robust methods involving DNA templates as a key reagent are available for obtaining 3D nanoparticle assemblies. It is still challenging to strictly control the number and location of DNA strands on the AuNP surface. Here, we introduce an efficient approach for the surface modification of AuNPs using unmodified DNA oligonucleotides by building DNA cages that trap the nanoparticles. This enables us to vary the process of nanostructure assembly and create anisotropic nanoparticles that are necessary for directed structure construction. This developed method simplifies the production process in comparison with conventional HS-DNA modification protocols and helps to precisely control the density and position of functional DNA strands designed for further hybridization with other AuNP conjugates.

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.

High-Performance Biosensing Systems Based on Various Nanomaterials as Signal Transducers

Recently, highly sensitive and selective biosensors have become necessary for improving public health and well-being. To fulfill this need, high-performance biosensing systems based on various nanomaterials, such as nanoparticles, carbon nanomaterials, and hybrid nanomaterials, are developed. Numerous nanomaterials show excellent physical properties, including plasmonic, magnetic, catalytic, mechanical and fluorescence properties and high electrical conductivities, and these unique and beneficial properties have contributed to the fabrication of high-performance biosensors with various applications, including in optical, electrical, and electrochemical detection platforms. In addition, these properties can be transformed to signals for the detection of biomolecules. In this review, various types of nanomaterial-based biosensors are introduced, and they show high sensitivity and selectivity. In addition, the potential applications of these sensors on the biosensing of several types of biomolecules are also discussed. These nanomaterials-based biosensing systems provide a significant improvement on healthcare including rapid monitoring and early detection of infectious disease for public health.

Single-stranded templates as railroad tracks for hierarchical assembly of DNA origami

DNA origami is one of the most effective tools for bottom-up construction of novel objects and devices at the nanometer-scale. However, many applications require larger structures than can be obtained with the conventional single-stranded scaffold, typically 7249 nucleotides. Here, we address this limitation by developing custom-made single-stranded scaffolds that bind pre-assembled origami tiles and induce their one-dimensional organization in high yields. Our synthetic method allows the conversion of multiple repetitive and unique sequences into correctly assembled, large backbones, and to finely tune the position and frequency of each building block. Granted with these regions, three and five origami tiles were successfully arranged in 1-D with the aid of one or two scaffolds, forming a nano-"railroad track". This new method increases length scale in DNA origami without increasing cost and complexity, and is anticipated to increase the yield of other approaches aiming to assemble large origami structures.

Salt-Induced Assembly Transformation of DNA-AuNP Conjugates Based on RCA Origami: From Linear Arrays to Nanorings

We developed a simple method to adjust the structural transformation of DNA-gold nanoparticles assemblies from linear arrays to nanorings by increasing salt concentrations. A DNA nanoladder constructing from RCA origami acted as templates to assemble periodic AuNPs arrays by a terminal thiol located on staple oligonucleotides. The linear AuNPs arrays could be transformed into nanorings only by changing the concentration of NaCl aqueous solution during the assembly process. It was proven that the electrostatic repulsion, being asymmetrically diminished by the high concentration of NaCl, caused the formation of nanoring architectures.

Three-Dimensional DNA Origami as Programmable Anchoring Points for Bioreceptors in Fiber Optic Surface Plasmon Resonance Biosensing

Many challenges in biosensing originate from the fact that the all-important nanoarchitecture of the biosensor surface, including precise density and orientation of bioreceptors, is not entirely comprehended. Here, we introduced a three-dimensional DNA origami as a bioreceptor carrier to functionalize the fiber optic surface plasmon resonance (FO-SPR) sensor with nanoscale precision. Starting from a 24-helix bundle, two distinct DNA origami structures were designed to position thrombin-specific aptamers with different densities and distances (27 and 113 nm) from the FO-SPR surface. The origami-based biosensors not only proved to be capable of reproducible, label-free thrombin detection but revealed also valuable innovative features: (1) a significantly better performance in the absence of backfilling, known as essential in the biosensing field, suggesting improved bioreceptor orientation and accessibility, and (2) a wider linear range compared to previously reported thrombin biosensors. We envisage that our method will be beneficial for both scientists and clinicians looking for new surface (bio)chemistry and improved diagnostics.

Nanoparticle self-assembly: from interactions in suspension to polymer nanocomposites

Recent experimental results using in particular small-angle scattering to characterize the self-assembly of mainly hard spherical nanoparticles into higher ordered structures ranging from fractal aggregates to ordered assemblies are reviewed. The crucial control of interparticle interactions is discussed, from chemical surface-modification, or the action of additives like depletion agents, to the generation of directional patches and the use of external fields. It is shown how the properties of interparticle interactions have been used to allow inducing and possibly controlling aggregation, opening the road to the generation of colloidal molecules or potentially metamaterials. In the last part, studies of the microstructure of polymer nanocomposites as an application of volume-spanning and stress-carrying aggregates are discussed.

Chemical and Biological Sensing Using Hybridization Chain Reaction

Since the advent of its theoretical discovery more than 30 years ago, DNA nanotechnology has been used in a plethora of diverse applications in both the fundamental and applied sciences. The recent prominence of DNA-based technologies in the scientific community is largely due to the programmable features stored in its nucleobase composition and sequence, which allow it to assemble into highly advanced structures. DNA nanoassemblies are also highly controllable due to the precision of natural and artificial base-pairing, which can be manipulated by pH, temperature, metal ions, and solvent types. This programmability and molecular-level control have allowed scientists to create and utilize DNA nanostructures in one, two, and three dimensions (1D, 2D, and 3D). Initially, these 2D and 3D DNA lattices and shapes attracted a broad scientific audience because they are fundamentally captivating and structurally elegant; however, transforming these conceptual architectural blueprints into functional materials is essential for further advancements in the DNA nanotechnology field. Herein, the chemical and biological sensing applications of a 1D DNA self-assembly process known as hybridization chain reaction (HCR) are reviewed. HCR is a one-dimensional (1D) double stranded (ds) DNA assembly process initiated only in the presence of a specific short ssDNA (initiator) and two kinetically trapped DNA hairpin structures. HCR is considered an enzyme-free isothermal amplification process, which shows substantial promise and offers a wide range of applications for in situ chemical and biological sensing. Due to its modular nature, HCR can be programmed to activate only in the presence of highly specific biological and/or chemical stimuli. HCR can also be combined with different types of molecular reporters and detection approaches for various analytical readouts. While the long dsDNA HCR product may not be as structurally attractive as the 2D and 3D DNA networks, HCR is highly instrumental for applied biological, chemical, and environmental sciences, and has therefore been studied to foster a variety of objectives. In this review, we have focused on nucleic acid, protein, metabolite, and heavy metal ion detection using this 1D DNA nanotechnology via fluorescence, electrochemical, and nanoparticle-based methodologies.

Starch-templated bio-synthesis of gold nanoflowers for in vitro antimicrobial and anticancer activities

We describe an in situ method of synthesizing highly branched gold nanoflower (AuNFs) using aqueous seed extract of Syzygium cumini (L.) Skeels as reductant in the presence of 0.3% starch. Surprisingly, when the same reaction was carried out in the absence of starch or with starch at a lower concentration (0.15%), instead of flower-like morphology quasi-spherical or polyhedral nanoparticles (AuNPs) are obtained. The nanomaterials were extensively characterized by HRTEM, FESEM, UV–Vis, FTIR, XRD, XPS and TGA analysis. The biological activities of the materials were investigated for antimicrobial activities against four bacterial strains that include one Gram positive (Staphylococcus aureus MTCC 121), two Gram negative (Escherichia coli MTCC 40 and Pseudomonas aeruginosa MTCC 4673) and one fungi (Candida albicans MTCC 227). The nanoparticles functioned as effective antimicrobial and anti-biofilm agents against all the strains under study. Controlled study revealed that, the AuNFs showed improved efficacy over conventional polyhedral AuNPs against all the microbes under study which might be attributed to the larger surface-to-volume ratio of the nanoflowers. The AuNFs also showed effective in vitro anticancer activity against a human liver cancer cell line (HepG2) with no significant cytotoxicity. Our data suggest that the AuNFs can significantly reduce the cancer cell growth with IC50 value of 20 µg mL−1.

DNA nanostructure-directed assembly of metal nanoparticle superlattices

Structural DNA nanotechnology provides unique, well-controlled, versatile, and highly addressable motifs and templates for assembling materials at the nanoscale. These methods to build from the bottom-up using DNA as a construction material are based on programmable and fully predictable Watson-Crick base pairing. Researchers have adopted these techniques to an increasing extent for creating numerous DNA nanostructures for a variety of uses ranging from nanoelectronics to drug-delivery applications. Recently, an increasing effort has been put into attaching nanoparticles (the size range of 1-20 nm) to the accurate DNA motifs and into creating metallic nanostructures (typically 20-100 nm) using designer DNA nanoshapes as molds or stencils. By combining nanoparticles with the superior addressability of DNA-based scaffolds, it is possible to form well-ordered materials with intriguing and completely new optical, plasmonic, electronic, and magnetic properties. This focused review discusses the DNA structure-directed nanoparticle assemblies covering the wide range of different one-, two-, and three-dimensional systems.

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.

DNA-based construction at the nanoscale: emerging trends and applications

The field of structural DNA nanotechnology has evolved remarkably-from the creation of artificial immobile junctions to the recent DNA-protein hybrid nanoscale shapes-in a span of about 35 years. It is now possible to create complex DNA-based nanoscale shapes and large hierarchical assemblies with greater stability and predictability, thanks to the development of computational tools and advances in experimental techniques. Although it started with the original goal of DNA-assisted structure determination of difficult-to-crystallize molecules, DNA nanotechnology has found its applications in a myriad of fields. In this review, we cover some of the basic and emerging assembly principles: hybridization, base stacking/shape complementarity, and protein-mediated formation of nanoscale structures. We also review various applications of DNA nanostructures, with special emphasis on some of the biophysical applications that have been reported in recent years. In the outlook, we discuss further improvements in the assembly of such structures, and explore possible future applications involving super-resolved fluorescence, single-particle cryo-electron (cryo-EM) and x-ray free electron laser (XFEL) nanoscopic imaging techniques, and in creating new synergistic designer materials.