Transfer of molecular recognition information from DNA nanostructures to gold nanoparticles

A dual amplified gold nanoparticle-based biosensor for ultrasensitive and selective detection of fibrin

Ultrasensitive, selective, and non-invasive detection of fibrin in human serum is critical for disease diagnosis. So far, the development of high-performance and ultrasensitive biosensors maintains core challenges for biosensing. Herein, we designed a novel ribbon nanoprobe for ultrasensitive detection of fibrin. The probe contains gold nanoparticles (AuNPs) that can not only link with homing peptide Cys-Arg-Glu-Lys-Ala (CREKA) to recognize fibrin but also carry long DNA belts to form G-quadruplex-based DNAzyme, catalyzing the chemiluminescence of luminol-hydrogen peroxide (H2O2) reaction. Combined with the second amplification procedure of rolling circle amplification (RCA), the assay exhibits excellent sensitivity with a detection limit of 0.04 fmol L-1 fibrin based on the 3-sigma. Furthermore, the biosensor shows high specificity on fibrin in samples because the structure of antibody-fibrin-homing peptide was employed to double recognize fibrin. Altogether, the simple and inexpensive approach may present a great potential for reliable detection of biomarkers.

Concept and Development of Algebraic Topological Framework Nucleic Acids

Nucleic acids are considered as promising materials for developing exquisite nanostructures from one to three dimensions. The advances of DNA nanotechnology facilitate ingenious design of DNA nanostructures with diverse shapes and sizes. Especially, the algebraic topological framework nucleic acids (ATFNAs) are functional DNA nanostructures that engineer guest molecules (e. g., nucleic acids, proteins, small molecules, and nanoparticles) stoichiometrically and spatially. The intrinsic precise properties and tailorable functionalities of ATFNAs hold great promise for biological applications, such as cell recognition and immunotherapy. This Perspective highlights the concept and development of precisely assembled ATFNAs, and outlines the new frontiers and opportunities for exploiting the structural advantages of ATFNAs for biological applications.

Light Responsive DNA Nanomaterials and Their Biomedical Applications

DNA nanomaterials have been widely employed for various biomedical applications. With rapid development of chemical modification of nucleic acid, serials of stimuli-responsive elements are included in the multifunctional DNA nanomaterials. In this review, we summarize the recent advances in light responsive DNA nanomaterials based on photocleavage/photodecage, photoisomerization, and photocrosslinking for efficient bioimaging (including imaging of small molecule, microRNA, and protein) and drug delivery (including delivery of small molecule, nucleic acid, and gene editing system). We also discuss the remaining challenges and future perspectives of the light responsive DNA nanomaterials in biomedical applications.

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.

DNA-Mediated Peptide Assembly into Protein Mimics

The design of new protein structures is challenging due to their vast sequence space and the complexity of protein folding. Here, we report a new modular DNA-templated strategy to construct protein mimics. We achieve the spatial control of multiple peptide units by conjugation with DNA and hybridization to a branched DNA trimer template followed by covalent stapling of the preorganized peptides into a single unit. A library of protein mimics with different lengths, sequences, and heptad registers has been efficiently constructed. DNA-templated protein mimics show an α-helix or coiled-coil motif formation even when they are constructed from weakly interacting peptide units. Their attached DNA handles can be used to exert dynamic control over the protein mimics' secondary and tertiary structures. This modular strategy will facilitate the development of DNA-encoded protein libraries for the rapid discovery of new therapeutics, enzymes, and antibody mimics.

Catalytic Gold Nanoparticle Assembly Programmed by DNAzyme Circuits

Assembled gold nanoparticle (AuNP) superstructures can generate unique physicochemical characteristics and be used in various applications, thus becoming an attractive research field. Recently, several DNA-assisted gold nanoparticle assembly methods have been rigorously developed that typically require a non-catalytic equimolar molecular assembly to guarantee the designed assembly. Although efficient and accurate, exploring such non-catalytic nanoparticle assemblies in the complex cellular milieu under low trigger concentrations remains challenging. Therefore, developing a catalytic method that facilitates gold nanoparticle assemblies with relatively low DNA trigger concentrations is desirable. In this report, a catalytic method to program gold nanoparticle assemblies by DNAzyme circuits is presented, where only a small number of DNA triggers are able to induce the production of a large number of the desired nanoparticle assemblies. The feasibility of using logic DNAzyme circuits to control catalytic nanoparticle assemblies is experimentally verified. Additionally, catalytic AuNP assembly systems are established with cascading and feedback functions. The work provides an alternative research direction to enrich the tool library of nanoparticle assembly and their application in biosensing and nanomedicine.

Immobilization of azide-functionalized proteins to micro- and nanoparticles directly from cell lysate

Immobilization of proteins and enzymes on solid supports has been utilized in a variety of applications, from improved protein stability on supported catalysts in industrial processes to fabrication of biosensors, biochips, and microdevices. A critical requirement for these applications is facile yet stable covalent conjugation between the immobilized and fully active protein and the solid support to produce stable, highly bio-active conjugates. Here, we report functionalization of solid surfaces (gold nanoparticles and magnetic beads) with bio-active proteins using site-specific and biorthogonal labeling and azide-alkyne cycloaddition, a click chemistry. Specifically, we recombinantly express and selectively label calcium-dependent proteins, calmodulin and calcineurin, and cAMP-dependent protein kinase A (PKA) with N-terminal azide-tags for efficient conjugation to nanoparticles and magnetic beads. We successfully immobilized the proteins on to the solid supports directly from the cell lysate with click chemistry, forgoing the step of purification. This approach is optimized to yield low particle aggregation and high levels of protein activity post-conjugation. The entire process enables streamlined workflows for bioconjugation and highly active conjugated proteins.

DNA-Based Gold Nanoparticle Assemblies: From Structure Constructions to Sensing Applications

Gold nanoparticles (Au NPs) have become one of the building blocks for superior assembly and device fabrication due to the intrinsic, tunable physical properties of nanoparticles. With the development of DNA nanotechnology, gold nanoparticles are organized in a highly precise and controllable way under the mediation of DNA, achieving programmability and specificity unmatched by other ligands. The successful construction of abundant gold nanoparticle assembly structures has also given rise to the fabrication of a wide range of sensors, which has greatly contributed to the development of the sensing field. In this review, we focus on the progress in the DNA-mediated assembly of Au NPs and their application in sensing in the past five years. Firstly, we highlight the strategies used for the orderly organization of Au NPs with DNA. Then, we describe the DNA-based assembly of Au NPs for sensing applications and representative research therein. Finally, we summarize the advantages of DNA nanotechnology in assembling complex Au NPs and outline the challenges and limitations in constructing complex gold nanoparticle assembly structures with tailored functionalities.

Tetrahedral DNA nanostructure-corbelled click chemistry-based large-scale assembly of nanozymes for ratiometric fluorescence assay of DNA methyltransferase activity

Ligation efficiency in a surface-based DNA click chemistry (CuAAC) reaction is extremely restricted by the orientation and density of probes arranged on a heterogeneous surface. Herein, we engineer DNA tetrahedral nanostructure (DTN)-corbelled click chemistry to trigger a hybridization chain reaction (HCR) assembling a large-scale of nanozymes for ratiometric fluorescence detection of DNA adenine methyltransferase (Dam). In this study, a DNA tetrahedron structure with an alkynyl modifying pendant DNA probe (Alk-DTN) is designed and assembled on a magnetic bead (MB) as a scaffold for click chemistry. When a CuO NP-encoded magnetic nanoparticle (CuO-MNP) substrate was methylated by Dam, CuO NPs were released and turned into a mass of Cu+. The Cu+ droves azido modifying lDNA (azide-lDNA) to connect with the Alk-DTN probe on the MB through the click reaction, forming an intact primer to initiate the HCR. The HCR product, a rigid structure double-stranded DNA, periodically assembles glucose oxidase mimicking gold nanoparticles (GNPs) into a large-scale of nanozymes for catalyzing the oxidation of glucose to H2O2. NH2-MIL-101 MOFs, a fluorescent indicator and a biomimetic catalyst, activated the product H2O2 to oxidize o-phenylenediamine (oPD) into visually detectable 2,3-diaminophenazine (DAP). The change of the signal ratio between DAP and NH2-MIL-101 is proportional to the methylation event corresponding to the MTase activity. In this study, the DTN enhances the efficiency of the surface-based DNA click reaction and maintains the catalytic activities of gold nanoparticle nanozymes due to the intrinsic nature of mechanical rigidity and well-controlled orientation and well-adjusted size. Large-scale assembly of nanozymes circumvents the loss of natural enzyme activity caused by chemical modification and greatly improves the amplification efficiency. The proposed biosensor displayed a low detection limit of 0.001 U mL-1 for Dam MTase due to multiple amplification and was effective in real samples and methylation inhibitor screening, providing a promising modular platform for bioanalysis.

A Spatially Programmable DNA Nanorobot Arm to Modulate Anisotropic Gold Nanoparticle Assembly by Enzymatic Excision

Programmable assembly of gold nanoparticle superstructures with precise spatial arrangement has drawn much attention for their unique characteristics in plasmonics and biomedicine. Bio-inspired methods have already provided programmable, molecular approaches to direct AuNP assemblies using biopolymers. The existing methods, however, predominantly use DNA as scaffolds to directly guide the AuNP interactions to produce intended superstructures. New paradigms for regulating AuNP assembly will greatly enrich the toolbox for DNA-directed AuNP manipulation and fabrication. Here, we developed a strategy of using a spatially programmable enzymatic nanorobot arm to modulate anisotropic DNA surface modifications and assembly of AuNPs. Through spatial controls of the proximity of the reactants, the locations of the modifications were precisely regulated. We demonstrated the control of the modifications on a single 15 nm AuNP, as well as on a rectangular DNA origami platform, to direct unique anisotropic AuNP assemblies. This method adds an alternative enzymatic manipulation to DNA-directed AuNP superstructure assembly.

The Creation of DNA Origami-Based Supramolecular Nanostructures for Cancer Therapy

DNA origami technology, a unique type of DNA nanotechnology, has attracted much attention from researchers and is applied in various fields. Through exquisite design and precise self-assembly of four kinds of deoxyribonucleotides, DNA origami nanostructures are endowed with excellent programmability and addressability and show outstanding biocompatibility in bio-related applications, especially in cancer treatment. In this review, nanomaterials based on DNA origami for cancer therapy are concluded, whereby chemotherapy and photo-assisted therapy are the main focus. Furthermore, the working mechanisms of the functional materials attached to the rigid DNA structures to enable targeted delivery and circumvent drug resistance are also discussed. DNA origami nanostructures are valuable carriers for delivering multifunctional therapeutic agents and demonstrate great potential in cancer treatment both in vitro and in vivo. It is undoubted that DNA origami technology is a promising strategy for constructing versatile nanodevices in biological fields and will excel in human healthcare.

Methods to functionalize gold nanoparticles with tandem-phosphorothioate DNA: role of physicochemical properties of the phosphorothioate backbone in DNA adsorption to gold nanoparticles

Perception of the differences in the physicochemical properties of phosphorothioate DNA (PS-DNA) and phosphodiester DNA (PO-DNA) greatly aids in understanding the AuNP-DNA binding process. Replacing one non-bridging oxygen atom of the anionic phosphodiester backbone with a sulfur atom leads to a major change in the DNA adsorption mechanism of AuNPs. In this work, we investigated and compared salt-aging, low pH-assisted, and freeze-thaw methods for conjugating phosphorothioate-modified oligonucleotides to AuNPs. The results obtained clearly demonstrate that only the pH-assisted method can successfully bind tandem phosphorothioate DNA to gold nanoparticles and sufficiently maintain the colloidal stability of AuNPs. When a phosphate group is converted to a phosphorothioate group, the negative charge of the phosphate group is located on the sulfur atom. Due to the soft nature of sulfur (a very weak H-bond acceptor), the negative charge on the sulfur atom cannot be shielded even with the gradual addition of salt to increase the ionic strength, so, the pH-assisted based method is the best for the functionalization of AuNPs with tandem-PS DNA.

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 Assembly of Plasmonic Nanostructures Enables In Vivo SERS-Based MicroRNA Detection and Tumor Photoacoustic Imaging

Controllable self-assembly of the DNA-linked gold nanoparticle (AuNP) architecture for in vivo biomedical applications remains a key challenge. Here, we describe the use of the programmed DNA tetrahedral structure to control the assembly of three different types of AuNPs (∼20, 10, and 5 nm) by organizing them into defined positioning and arrangement. A DNA-assembled "core-satellite" architecture is built by DNA sequencing where satellite AuNPs (10 and 5 nm) surround a central core AuNP (20 nm). The density and arrangement of the AuNP satellites around the core AuNP were controlled by tuning the size and amount of the DNA tetrahedron functionalized on the core AuNPs, resulting in strong electromagnetic field enhancement derived from hybridized plasmonic coupling effects. By conjugating with the Raman molecule, strong surface-enhanced Raman scattering photoacoustic imaging signals could be generated, which were able to image microRNA-21 and tumor tissues in vivo. These results provided an efficient strategy to build precision plasmonic superstructures in plasmonic-based bioanalysis and imaging.

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.

Molecular Engineering of Colloidal Atoms

Creation of architectures with exquisite hierarchies actuates the germination of revolutionized functions and applications across a wide range of fields. Hierarchical self-assembly of colloidal particles holds the promise for materialized realization of structural programing and customizing. This review outlines the general approaches to organize atom-like micro- and nanoparticles into prescribed colloidal analogs of molecules by exploiting diverse interparticle driving motifs involving confining templates, interactive surface ligands, and flexible shape/surface anisotropy. Furthermore, the self-regulated/adaptive co-assembly of simple unvarnished building blocks is discussed to inspire new designs of colloidal assembly strategies.

DNA-Patched Nanoparticles for the Self-Assembly of Colloidal Metamaterials

Colloidal metamaterials are highly desired artificial materials that recapitulate the structure of simple molecules. They exhibit exceptional functionalities conferred by the organization of and specific interaction among constituent elements. Harvesting such exquisite attributes for potential applications necessitates establishing precise control over their structural configuration with high precision. Yet, creating molecule-like small clusters of colloidal metamaterials remains profoundly challenging, as a lack of regioselectively encoded surface chemical heterogeneity prevents specific recognition interactions. Herein, we report a new strategy by harnessing magnetic-bead-assisted DNA cluster transferring to create discretely DNA cluster-patched nanoparticles for the self-assembly of colloidal metamaterials. This strategy affords broad generalizability and scalability for robustly patching DNA clusters on nanoparticles unconstrained by geometrical, dimensional, and compositional complexities commonly encountered in colloidal materials at the nano- and microscale. We direct judiciously patched nanoparticles into a wide variety of nanoassemblies and present a case study demonstrating the distinct metamaterial properties in enhancing the spontaneous emission of diamond nanoparticles. This newly invented strategy is readily implementable and extendable to construct a palette of structurally sophisticated and functionality-explicit architecture, paving the way for nanoscale manipulation of colloidal material functionalities with wide-ranging applications for biological sensing, optical engineering, and catalytic chemistry.

Recent Advances in DNA Origami-Engineered Nanomaterials and Applications

DNA nanotechnology is a unique field, where physics, chemistry, biology, mathematics, engineering, and materials science can elegantly converge. Since the original proposal of Nadrian Seeman, significant advances have been achieved in the past four decades. During this glory time, the DNA origami technique developed by Paul Rothemund further pushed the field forward with a vigorous momentum, fostering a plethora of concepts, models, methodologies, and applications that were not thought of before. This review focuses on the recent progress in DNA origami-engineered nanomaterials in the past five years, outlining the exciting achievements as well as the unexplored research avenues. We believe that the spirit and assets that Seeman left for scientists will continue to bring interdisciplinary innovations and useful applications to this field in the next decade.

Surface engineering of colloidal nanoparticles

Synthesis of engineered colloidal nanoparticles (NPs) with delicate surface characteristics leads to well-defined physicochemical properties and contributes to multifunctional applications. Surface engineering of colloidal NPs can improve their stability in diverse solvents by inhibiting the interparticle attractive forces, thus providing a prerequisite for further particle manipulation, fabrication of the following materials and biological applications. During the last decades, surface engineering methods for colloidal NPs have been well-developed by numerous researchers. However, accurate control of surface properties is still an important topic. The emerging DNA/protein nanotechnology offers additional possibility of surface modification of NPs and programmable particle self-assembly. Here, we first briefly review the recent progress in surface engineering of colloidal NPs, focusing on the improved stability by grafting suitable small molecules, polymers or biological macromolecules. We then present the practical strategies for nucleic acid surface encoding of NPs and subsequent programmable assembly. Various exciting applications of these unique materials are summarized with a specific focus on the cellular uptake, bio-toxicity, imaging and diagnosis of colloidal NPs in vivo. With the growing interest in colloidal NPs in nano-biological research, we expect that this review can play an instructive role in engineering the surface properties for desired applications.

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.

Transfer of multi-DNA patches by colloidal stamping

Patchy particles have received great attention due to their ability to develop directional and selective interactions and serve as building units for the self-assembly of innovative colloidal molecules and crystalline structures. Although synthesizing particles with multiple dissimilar patches is still highly challenging and lacks efficient methods, these building blocks would open paths towards a broader range of ordered materials with inherent properties. Herein, we describe a new approach to pattern functional DNA patches at the surface of particles, by the use of colloidal stamps. DNA inks are transferred only at the contact zones between the target particles and the stamps thanks to selective strand-displacement reactions. The produced DNA-patchy particles are ideal candidates to act as advanced precision/designer building blocks to self-assemble the next generation of colloidal materials.

Probing and Manipulating Noncovalent Interactions in Functional Polymeric Systems

Noncovalent interactions, which usually feature tunable strength, reversibility, and environmental adaptability, have been recognized as driving forces in a variety of biological and chemical processes, contributing to the recognition between molecules, the formation of molecule clusters, and the establishment of complex structures of macromolecules. The marriage of noncovalent interactions and conventional covalent polymers offers the systems novel mechanical, physicochemical, and biological properties, which are highly dependent on the binding mechanisms of the noncovalent interactions that can be illuminated via quantification. This review systematically discusses the nanomechanical characterization of typical noncovalent interactions in polymeric systems, mainly through direct force measurements at microscopic, nanoscopic, and molecular levels, which provide quantitative information (e.g., ranges, strengths, and dynamics) on the binding behaviors. The fundamental understandings of intermolecular and interfacial interactions are then correlated to the macroscopic performances of a series of noncovalently bonded polymers, whose functions (e.g., stimuli-responsiveness, self-healing capacity, universal adhesiveness) can be customized through the manipulation of the noncovalent interactions, providing insights into the rational design of advanced materials with applications in biomedical, energy, environmental, and other engineering fields.

Preparation, applications, and challenges of functional DNA nanomaterials

As a carrier of genetic information, DNA is a versatile module for fabricating nanostructures and nanodevices. Functional molecules could be integrated into DNA by precise base complementary pairing, greatly expanding the functions of DNA nanomaterials. These functions endow DNA nanomaterials with great potential in the application of biomedical field. In recent years, functional DNA nanomaterials have been rapidly investigated and perfected. There have been reviews that classified DNA nanomaterials from the perspective of functions, while this review primarily focuses on the preparation methods of functional DNA nanomaterials. This review comprehensively introduces the preparation methods of DNA nanomaterials with functions such as molecular recognition, nanozyme catalysis, drug delivery, and biomedical material templates. Then, the latest application progress of functional DNA nanomaterials is systematically reviewed. Finally, current challenges and future prospects for functional DNA nanomaterials are discussed.

Multi-Domains in a Single Lattice Formed by DNA Self-Assembly

Using sequence programmability and the characteristics of self-assembly, DNA has been utilized in the construction of various nanostructures and the placement of specific patterns on lattices. Even though many complex structures and patterns formed by DNA assembly have been reported, the fabrication of multi-domain patterns in a single lattice has rarely been discussed. Multi-domains possessing specifically designed patterns in a single lattice provide the possibility to generate multiple patterns that enhance the pattern density in a given single lattice. Here, we introduce boundaries to construct double- and quadruple-domains with specific patterns in a single lattice and verify them with atomic force microscopy. ON, OFF, and ST (stripe) patterns on a lattice are made of DNA tiles with hairpins (ON), without hairpins (OFF), and alternating DNA tiles without and with hairpins (formed as a stripe, ST). For double- and quadruple-domain lattices, linear and cross boundaries were designed to fabricate two (e.g., ON and OFF, ON and ST, and OFF and ST) and four (OFF, ST, OFF, and ON) different types of patterns in single lattices, respectively. In double-domain lattices, each linear boundary is placed between two different domains. Similarly, four linear boundaries connected with a seed tile (i.e., a cross boundary) can separate four domains in a single lattice in quadruple-domain lattices. Due to the presence of boundaries, the pattern growth directions are different in each domain. The experimentally obtained multi-domain patterns agree well with our design. Lastly, we propose the possibility of the construction of a hexadomain lattice through the mapping from hexagonal to square grids converted by using an axial coordinate system. By proposing a hexadomain lattice design, we anticipate the possibility to extend to higher numbers of multi-domains in a single lattice, thereby further increasing the information density in a given lattice.

Sorting Nanoparticles by Valency with DNA Barcoding

Self-assembly of DNA-labeled nanoparticles is an effective strategy to fabricate new nanocomposite materials and nanoscale devices from the bottom-up. To tailor the properties of the resulting material or device, one requires access to a wide range of nanoparticle sizes and shapes, as well as control over the number (valency) of DNA molecules on the nanoparticle surface. Currently, nanoparticles with a defined DNA valency can only be obtained in a narrow range of sizes, and in small quantities, limiting the properties of the resulting composite structures and their applications. Here, we leverage the digital information encoded in the number and sequence of short DNA barcodes to generate preparatory amounts of nanoparticles bearing a specific number of DNA molecules, irrespective of the identity of the nanocomponent. We show that this DNA valency sorting chromatography, which is driven by the selective affinity of Watson-Crick base pairs, is applicable to arbitrary DNA sequences and a broad range of nanoparticle sizes, shapes, and material compositions. To further demonstrate this fact, we use valency-sorted large gold nanospheres directly in self-assembly schemes to create, in one synthesis step, large amounts of several previously inaccessible molecule-like dimer and trimer nanostructures with unique optical properties. We anticipate that the expanded scope of DNA valency-defined nanoparticle reagents, and the increased scale at which they can be produced, will open new avenues for the molecularly precise manipulation of nanoscale matter.

DNA Tetrahedron Framework Guided Conjugation and Assembly of Gold Nanoparticles

Au nanoparticles (AuNPs) have been extensively used to assemble programmable structures that feature various functions. One central challenge of precisely directed assembly is to make valence-programmable building blocks. Herein, we use the DNA tetrahedron framework to stoichiometrically conjugate to Au nanoparticles, which results in monovalent building blocks at nanometer scale. We further fabricated high-order Au-tetrahedron structures to verify the ability of the blocks for building assemblies. These structures represent an exploration of an avenue to monovalent AuNPs, and provide the feasibility of precisely manipulating nanoparticles into prescribed assemblies.

Boosted Productivity in Single-Tile-Based DNA Polyhedra Assembly by Simple Cation Replacement

Cations such as divalent magnesium ion (Mg²⁺ ) play an essential role in DNA self-assembly. However, the strong electrostatic shielding effect of Mg²⁺ would be disadvantageous in some situations that require relatively weak interactions to allow a highly reversible error-correcting mechanism in the process of assembly. Herein, by substituting the conventional divalent Mg²⁺ with monovalent sodium ion (Na⁺ ), we have achieved one-pot high-yield assembly of tile-based DNA polyhedra at micromolar concentration of tiles, at least 10 times higher than the DNA concentrations reported previously. This strategy takes advantage of coexisting counterions and is expected to surmount the major obstacle to potential applications of such DNA nanostructures: large-scale production.

Bottom-up synthesis of meta-atoms as building blocks in self-assembled metamaterials : Recent advances and perspectives

Meta-atoms interact with light in interesting ways and offer a large range of exciting properties. They exhibit optical properties inaccessible by natural atoms but their fabrication is notoriously difficult because of the precision required. In this perspective, we present the current research landscape in making meta-atoms, with a focus on the most promising self-assembly approaches and main challenges to overcome, for the development of materials with novel properties at optical frequencies.

Genetically Encoded Double-Stranded DNA-Based Nanostructure Folded by a Covalently Bivalent CRISPR/dCas System

DNA nanotechnology has been widely employed in the construction of various functional nanostructures. However, most DNA nanostructures rely on hybridization between multiple single-stranded DNAs. Herein, we report a general strategy for the construction of a double-stranded DNA-ribonucleoprotein (RNP) hybrid nanostructure by folding double-stranded DNA with a covalently bivalent clustered regularly interspaced short palindromic repeats (CRISPR)/nuclease-dead CRISPR-associated protein (dCas) system. In our design, dCas9 and dCas12a can be efficiently fused together through a flexible and stimuli-responsive peptide linker. After activation by guide RNAs, the covalently bivalent dCas9-12a RNPs (staples) can precisely recognize their target sequences in the double-stranded DNA scaffold and pull them together to construct a series of double-stranded DNA-RNP hybrid nanostructures. The genetically encoded hybrid nanostructure can protect genetic information in the folded state, similar to the natural DNA-protein hybrids present in chromosomes, and elicit efficient stimuli-responsive gene transcription in the unfolded form. This rationally developed double-stranded DNA folding and unfolding strategy presents a new avenue for the development of DNA nanotechnology.

Chemically Modified DNA Nanostructures for Drug Delivery

Based on predictable, complementary base pairing, DNA can be artificially pre-designed into versatile DNA nanostructures of well-defined shapes and sizes. With excellent addressability and biocompatibility, DNA nanostructures have been widely employed in biomedical research, such as bio-sensing, bio-imaging, and drug delivery. With the development of the chemical biology of nucleic acid, chemically modified nucleic acids are also gradually developed to construct multifunctional DNA nanostructures. In this review, we summarize the recent progress in the construction and functionalization of chemically modified DNA nanostructures. Their applications in the delivery of chemotherapeutic drugs and nucleic acid drugs are highlighted. Furthermore, the remaining challenges and future prospects in drug delivery by chemically modified DNA nanostructures are discussed.

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With excellent addressability and biocompatibility, DNA nanostructures are promising candidates for bio-sensing, bio-imaging, and drug delivery

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The recent progress in chemical modifications of DNA nanostructures is summarized

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Chemically modified DNA nanostructures for efficient delivery of chemotherapeutic drugs and nucleic acid drugs are highlighted

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Challenges and prospects of future development toward chemically modified DNA nanostructures for drug delivery are discussed

Valence-controlled protein conjugation on nanoparticles via re-arrangeable multivalent interactions of tandem repeat protein chains

Tandem repeat protein chains were wrapped around nanoparticles via re-arrangeable multivalent interactions for valence controlled protein conjugation.

Heterostructures Made of Upconversion Nanoparticles and Metal-Organic Frameworks for Biomedical Applications

Heterostructure nanoparticles (NPs), constructed by two single-component NPs with distinct nature and multifunctional properties, have attracted intensive interest in the past few years. Among them, heterostructures made of upconversion NPs (UCNPs) and metal-organic frameworks (MOFs) can not only integrate the advantageous characteristics (e.g., porosity, structural regularity) of MOFs with unique upconverted optical features of UCNPs, but also induce cooperative properties not observed either for single component due to their special optical or electronic communications. Recently, diverse UCNP-MOF heterostructures are designed and synthesized via different strategies and have demonstrated appealing potential for applications in biosensing and imaging, drug delivery, and photodynamic therapy (PDT). In this review, the synthesis strategies of UCNP-MOF heterostructures are first summarized, then the authors focus mainly on discussion of their biomedical applications, particularly as PDT agents for cancer treatment. Finally, the authors briefly outlook the current challenges and future perspectives of UCNP-MOF hybrid nanocomposites. The authors believe that this review will provide comprehensive understanding and inspirations toward recent advances of UCNP-MOF heterostructures.

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.

Molecularly imprinted polypyrrole nanotubes based electrochemical sensor for glyphosate detection

An electrochemical sensor based on molecularly imprinted polypyrrole nanotubes (MIPNs) has been developed for the detection of glyphosate (Gly) with high sensitivity and specificity. Herein, the MIPNs are prepared by imprinting Gly sites on the surface of polypyrrole (PPy) nanotubes. The synthesized MIPNs have high electrical conductivity and exhibit rapid adsorption rate, enhanced affinity and specificity to Gly. An electrochemical sensor for Gly detection is fabricated by assembling MIPNs-modified screen-printed electrodes with a 3D-printed electrode holder, which is highly portable and suitable for real-time detection. The results demonstrate that the MIPNs-based electrochemical sensor for Gly exhibits a wide detection range of 2.5-350 ng/mL with a limit of detection (LOD) of 1.94 ng/mL. Besides, the Gly sensor possessed good stability, reproducibility, and excellent selectivity against other interferents. The practicability of the sensor is verified by detecting Gly in orange juice and rice beverages, indicating that the sensor is suitable for monitoring pesticides in actual food and environmental samples.

Transient Dissipative Optical Properties of Aggregated Au Nanoparticles, CdSe/ZnS Quantum Dots, and Supramolecular Nucleic Acid-Stabilized Ag Nanoclusters

Transient, dissipative, aggregation and deaggregation of Au nanoparticles (NPs) or semiconductor quantum dots (QDs) leading to control over their transient optical properties are introduced. The systems consist of nucleic acid-modified pairs of Au NPs or pairs of CdSe/ZnS QDs, an auxiliary duplex L₁/T₁, and the nicking enzyme Nt.BbvCI as functional modules yielding transient aggregation/deaggregation of the NPs and dynamically controlling over their optical properties. In the presence of a fuel strand L₁', the duplex L₁/T₁ is separated, leading to the release of T₁ and the formation of duplex L₁/L₁'. The released T₁ leads to aggregation of the Au NPs or to the T₁-induced G-quadruplex bridged aggregated CdSe/ZnS QDs. Biocatalytic nicking of the L₁/L₁' duplex fragments L₁' and the released L₁ displaces T₁ bridging the aggregated NPs or QDs, resulting in the dynamic recovery of the original NPs or QDs modules. The dynamic aggregation/deaggregation of the Au NPs is followed by the transient interparticle plasmon coupling spectral changes. The dynamic aggregation/deaggregation of the CdSe/ZnS QDs is probed by following the transient chemiluminescence generated by the hemin/G-quadruplexes bridging the QDs and by the accompanying transient chemiluminescence resonance energy transfer proceeding in the dynamically formed QDs aggregates. A third system demonstrating transient, dissipative, luminescence properties of a reaction module consisting of nucleic acid-stabilized Ag nanoclusters (NCs) is introduced. Transient dynamic formation and depletion of the supramolecular luminescent Ag NCs system via strand displacement accompanied by a nicking process are demonstrated.

The biological applications of DNA nanomaterials: current challenges and future directions

DNA, a genetic material, has been employed in different scientific directions for various biological applications as driven by DNA nanotechnology in the past decades, including tissue regeneration, disease prevention, inflammation inhibition, bioimaging, biosensing, diagnosis, antitumor drug delivery, and therapeutics. With the rapid progress in DNA nanotechnology, multitudinous DNA nanomaterials have been designed with different shape and size based on the classic Watson-Crick base-pairing for molecular self-assembly. Some DNA materials could functionally change cell biological behaviors, such as cell migration, cell proliferation, cell differentiation, autophagy, and anti-inflammatory effects. Some single-stranded DNAs (ssDNAs) or RNAs with secondary structures via self-pairing, named aptamer, possess the ability of targeting, which are selected by systematic evolution of ligands by exponential enrichment (SELEX) and applied for tumor targeted diagnosis and treatment. Some DNA nanomaterials with three-dimensional (3D) nanostructures and stable structures are investigated as drug carrier systems to delivery multiple antitumor medicine or gene therapeutic agents. While the functional DNA nanostructures have promoted the development of the DNA nanotechnology with innovative designs and preparation strategies, and also proved with great potential in the biological and medical use, there is still a long way to go for the eventual application of DNA materials in real life. Here in this review, we conducted a comprehensive survey of the structural development history of various DNA nanomaterials, introduced the principles of different DNA nanomaterials, summarized their biological applications in different fields, and discussed the current challenges and further directions that could help to achieve their applications in the future.

A self-assembled DNA nanostructure as a FRET nanoflare for intracellular ATP imaging

Due to the incorporation of gold nanoparticles (AuNPs), previously reported AuNP-based FRET nanoflares still have some problems, such as non-negligible cytotoxicity and a time-consuming preparation procedure. In this communication, a novel AuNP-free FRET nanoflare for intracellular ATP imaging is developed based on a DNA nanostructure, which is self-assembled through cyclic U-type hybridization only involving a certain number of DNA strands.

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.

DNA Origami-Based Nanoprinting for the Assembly of Plasmonic Nanostructures with Single-Molecule Surface-Enhanced Raman Scattering

Metallic nanocube ensembles exhibit tunable localized surface plasmon resonance to induce the light manipulation at the subwavelength scale. Nevertheless, precisely control anisotropic metallic nanocube ensembles with relative spatial directionality remains a challenge. Here, we report a DNA origami based nanoprinting (DOBNP) strategy to transfer the essential DNA strands with predefined sequences and positions to the surface of the gold nanocubes (AuNCs). These DNA strands ensured the specific linkages between AuNCs and gold nanoparticles (AuNPs) that generating the stereo-controlled AuNC-AuNP nanostructures (AANs) with controlled geometry and composition. By anchoring the single dye molecule in hot spot regions, the dramatic enhanced electromagnetic field aroused stronger surface enhanced Raman scattering (SERS) signal amplification. Our approach opens the opportunity for the fabrication of stereo-controlled metal nanostructures for designing highly sensitive photonic devices.

Nanomaterial Shape Influence on Cell Behavior

Nanomaterials are proven to affect the biological activity of mammalian and microbial cells profoundly. Despite this fact, only surface chemistry, charge, and area are often linked to these phenomena. Moreover, most attention in this field is directed exclusively at nanomaterial cytotoxicity. At the same time, there is a large body of studies showing the influence of nanomaterials on cellular metabolism, proliferation, differentiation, reprogramming, gene transfer, and many other processes. Furthermore, it has been revealed that in all these cases, the shape of the nanomaterial plays a crucial role. In this paper, the mechanisms of nanomaterials shape control, approaches toward its synthesis, and the influence of nanomaterial shape on various biological activities of mammalian and microbial cells, such as proliferation, differentiation, and metabolism, as well as the prospects of this emerging field, are reviewed.

Organelle-Targeted Photosensitizers for Precision Photodynamic Therapy

Subcellular organelles are the cornerstones of cells, and destroying them will cause cell dysfunction and even death. Therefore, realizing precise organelle targeting of photosensitizers (PSs) can help reduce PS dosage, minimize side effects, avoid drug resistance, and enhance therapeutic efficacy in photodynamic therapy (PDT). Organelle-targeted PSs provide a new paradigm for the construction of the next generation of PSs and may provide implementable strategies for future precision medicine. In this Review, the recent targeting strategies of different organelles and the corresponding design principles of molecular and nanostructured PSs are summarized and discussed. The current challenges and opportunities in organelle-targeted PDT are also presented.

Site-specific facet protection of gold nanoparticles inside a 3D DNA origami box: a tool for molecular plasmonics

Bare gold nanocubes and nanospheres with different sizes are incorporated into a rationally designed 3D DNA origami box. The encaged particles expose a gold surface accessible for subsequent site-specific functionalization, for example, for applications in molecular plasmonics such as SERS or SEF.

Interface and Interphase in Polymer Nanocomposites with Bare and Core-Shell Gold Nanoparticles

Metal nanoparticles are used to modify/enhance the properties of a polymer matrix for a broad range of applications in bio-nanotechnology. Here, we study the properties of polymer/gold nanoparticle (NP) nanocomposites through atomistic molecular dynamics, MD, simulations. We probe the structural, conformational and dynamical properties of polymer chains at the vicinity of a gold (Au) NP and a functionalized (core/shell) Au NP, and compare them against the behavior of bulk polyethylene (PE). The bare Au NPs were constructed via a systematic methodology starting from ab-initio calculations and an atomistic Wulff construction algorithm resulting in the crystal shape with the minimum surface energy. For the functionalized NPs the interactions between gold atoms and chemically adsorbed functional groups change their shape. As a model polymer matrix we consider polyethylene of different molecular lengths, from the oligomer to unentangled Rouse like systems. The PE/Au interaction is parametrized via DFT calculations. By computing the different properties the concept of the interface, and the interphase as well, in polymer nanocomposites with metal NPs are critically examined. Results concerning polymer density profiles, bond order parameter, segmental and terminal dynamics show clearly that the size of the interface/interphase, depends on the actual property under study. In addition, the anchored polymeric chains change the behavior/properties, and especially the chain density profile and the dynamics, of the polymer chain at the vicinity of the Au NP.