DNA-Encoded Tuning of Geometric and Plasmonic Properties of Nanoparticles Growing from Gold Nanorod Seeds

Customized Self-Assembled Gold Nanoparticle-DNA Origami Composite Templates for Shape-Directed Growth of Plasmonic Structures

The metal plasmonic nanostructure has the optical property of plasmon resonance, which holds great potential for development in nanophotonics, bioelectronics, and molecular detection. However, developing a general and straightforward method to prepare metal plasmonic nanostructures with a controllable size and morphology still poses a challenge. Herein, we proposed a synthesis strategy that utilized a customizable self-assembly template for shape-directed growth of metal structures. We employed gold nanoparticles (AuNPs) as connectors and DNA nanotubes as branches, customizing gold nanoparticle-DNA origami composite nanostructures with different branches by adjusting the assembly ratio between the connectors and branches. Subsequently, various morphologies of plasmonic metal nanostructures were created using this template shape guided strategy, which exhibited enhancement of surface-enhanced Raman scattering (SERS) signals. This strategy provides a new approach for synthesizing metallic nanostructures with multiple morphologies and opens up another possibility for the development of customizable metallic plasmonic structures with broader applications.

DNA Molecular Computation Using the CRISPR-Mediated Reaction and Surface Growth of Gold Nanoparticles

DNA has emerged as a promising tool to build logic gates for biocomputing. However, prevailing methodologies predominantly rely on hybridization reactions or structural alterations to construct DNA logic gates, which are limited in simplicity and diversity. Herein, we developed simple and smart DNA-based logic gates for biocomputing through the DNA-mediated growth of gold nanomaterials without precise structure design and probe modification. Capitalizing on their excellent plasmonic properties, the surface growth of gold nanomaterials enables distinct wavelength shifts and unique shapes, which are modulated by the composition, length, and concentration of the DNA sequences. Combined with a CRISPR-mediated reaction, we constructed DNA circuits to achieve complicated biocomputing to modulate the surface growth of gold nanomaterials. By implementing logic functions controlled by input-mediated growth of gold nanomaterials, we established YES/NOT, AND/NAND, OR/NOR, XOR, and INHIBIT gates and further constructed cascade logic circuits, parity checker for natural numbers, and gray code encoder, which are promising for DNA biocomputing.

Polyvalent Nanobody Structure Designed for Boosting SARS-CoV-2 Inhibition

Coronavirus transmission and mutations have brought intensive challenges on pandemic control and disease treatment. Developing robust and versatile antiviral drugs for viral neutralization is highly desired. Here, we created a new polyvalent nanobody (Nb) structure that shows the effective inhibition of SARS-CoV-2 infections. Our polyvalent Nb structure, called "PNS", is achieved by first conjugating single-stranded DNA (ssDNA) and the receptor-binding domain (RBD)-targeting Nb with retained binding ability to SARS-CoV-2 spike protein and then coalescing the ssDNA-Nb conjugates around a gold nanoparticle (AuNP) via DNA hybridization with a desired Nb density that offers spatial pattern-matching with that of the Nb binding sites on the trimeric spike. The surface plasmon resonance (SPR) assays show that the PNS binds the SARS-CoV-2 trimeric spike proteins with a ∼1000-fold improvement in affinity than that of monomeric Nbs. Furthermore, our viral entry inhibition assays using the PNS against SARS-CoV-2 WA/2020 and two recent variants of interest (BQ1.1 and XBB) show an over 400-fold enhancement in viral inhibition compared to free Nbs. Our PNS strategy built on a new DNA-protein conjugation chemistry provides a facile approach to developing robust virus inhibitors by using a corresponding virus-targeting Nb with a desired Nb density.

Synthesis of Butterfly-Like Shaped Gold Nanomaterial: For the Regulation of Liquid-Liquid Phase-Separated Biomacromolecule Droplets

Nanotechnology is a critical tool to manipulate the sophisticated behavior of biological structures and has provided new research fields. Liquid-liquid phase-separated (LLPS) droplets gather attention as basic reaction fields in a living cell. Droplets play critical roles in regulating protein behavior, including enzyme compartmentalization, stress response, and disease pathogenesis. The dynamic manipulation of LLPS droplet formation/deformation has become a crucial target in nanobiotechnology. However, the development of nanodevices specifically designed for this purpose remains a challenge. Therefore, this study presents butterfly-shaped gold nanobutterflies (GNBs) as novel nanodevices for manipulating LLPS droplet dynamics. The growth process of the GNBs is analyzed via time-lapse electroscopic imaging, time-lapse spectroscopy, and additives assays. Interestingly, GNBs demonstrate the ability to induce LLPS droplet formation in systems such as adenosine triphosphate/poly-l-lysine and human immunoglobulin G, whereas spherical and rod-shaped gold nanoparticles exhibit no such capability. This indicates that the GNB concave surface interacts with the droplet precursors facilitating the LLPS droplet formation. Near-infrared-laser irradiation applied to GNBs enables on-demand deformation of the droplets through localized heat effects. GNB regulates the enzymatic reaction of lysozymes. The innovative design of GNBs presents a promising strategy for manipulating LLPS dynamics and offers exciting prospects for future research.

Gap-enhanced gold nanodumbbells with single-particle surface-enhanced Raman scattering sensitivity

Gap-enhanced Raman tags (GERTs) have been widely used for surface-enhanced Raman scattering (SERS) imaging due to their excellent SERS performances. Here, we reported a synthetic strategy for novel gap-enhanced dumbbell-like nanoparticles with anisotropic shell coatings. Controlled shell growth at the tips of gold nanorods was achieved by using cetyltrimethylammonium bromide (CTAB) as a capping agent. A mechanism related to the shape-directing effects of CTAB was proposed to explain the findings. Optimized gap-enhanced gold dumbbells exhibited highly enhanced SERS responses compared to rod cores, with an enhancement ratio of 101.5. We further demonstrated that gap-enhanced AuNDs exhibited single-particle SERS sensitivity with an acquisition time as fast as 0.1 s per spectrum, showing great potential for high-speed SERS imaging.

DNA-Encoded Bidirectional Regulation of the Peroxidase Activity of Pt Nanozymes for Bioanalysis

Rational regulation of nanozyme activity can promote biochemical sensing by expanding sensing strategies and improving sensing performance, but the design of effective regulatory strategies remains a challenge. Herein, a rapid DNA-encoded strategy was developed for the efficient regulation of Pt nanozyme activity. Interestingly, we found that the catalytic activity of Pt nanozymes was sequence-dependent, and its peroxidase activity was significantly enhanced only in the presence of T-rich sequences. Thus, different DNA sequences realized bidirectional regulation of Pt nanozyme peroxidase activity. Furthermore, the DNA-encoded strategy can effectively enhance the stability of Pt nanozymes at high temperatures, freezing, and long-term storage. Meanwhile, a series of studies demonstrated that the presence of DNA influenced the reduction degree of H₂PtCl₆ precursors, which in turn affected the peroxidase activity of Pt nanozymes. As a proof of application, the sensor array based on the Pt nanozyme system showed superior performance in the accurate discrimination of antioxidants. This study obtained the regulation rules of DNA on Pt nanozymes, which provided theoretical guidance for the development of new sensing platforms and new ideas for the regulation of other nanozyme activities.

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.

DNA-Programmed Tuning of the Growth and Enzyme-Like Activity of a Bimetallic Nanozyme and Its Biosensing Applications

Nanozymes, which combine the merits of both nanomaterials and natural enzymes, have aroused tremendous attention as new representatives of artificial enzyme mimics. However, it still remains to be a great challenge to rationally engineer the morphologies and surface properties of nanostructures that lead to the desired enzyme-like activities. Here, we report a DNA-programming seed-growth strategy to mediate the growth of platinum nanoparticles (PtNPs) on gold bipyramids (AuBPs) for the synthesis of a bimetallic nanozyme. We find that the preparation of a bimetallic nanozyme is in a sequence-dependent manner, and the encoding of a polyT sequence allows the successful formation of bimetallic nanohybrids with greatly enhanced peroxidase-like activity. We further observe that the morphologies and optical properties of T15-mediated Au/Pt nanostructures (Au/T15/Pt) change over the reaction time, and the nanozymatic activity can be tuned by controlling the experimental conditions. As a concept application, Au/T15/Pt nanozymes are used to establish a simple, sensitive, and selective colorimetric assay for the determination of ascorbic acid (AA), alkaline phosphatase (ALP), and the inhibitor sodium vanadate (Na₃VO₄), demonstrating excellent analytical performance. This work provides a new avenue for the rational design of bimetallic nanozymes for biosensing applications.

Growth Reaction of Gold Nanorods in the Presence of Mutated Peptides and Amine-Modified Single-Stranded Nucleic Acids

Conformation of biomolecules like DNA, peptides and amino acids play vital role during nanoparticle growth. Herein, we have experimentally explored the effect of different noncovalent interaction between a 5'-amine modified DNA sequence (NH₂ -C₆ H₁₂ -5'-ACATCAGT-3', PMR) and arginine during the seed-mediated growth reaction of gold nanorods (GNRs). Amino acid-mediated growth reaction of GNRs results in a snowflake-like gold nanoarchitecture. However, in case of Arg, prior incubation of GNRs with PMR selectively produces sea urchin-like gold suprastructures, via strong hydrogen bonding and cation-π interaction between PMR and Arg. This distinctive structure formation strategy has been extended to study the structural modulation caused by two structurally close α-helical RRR (Ac-(AAAAR)₃ A-NH₂ ) peptide and the lysine mutated KKR (Ac-AAAAKAAAAKAAAARA-NH₂ ) peptide with partial helix at the amino terminus. Simulation studies confirm that a greater number of hydrogen bonding and cation-π interaction between the Arg residues and PMR resulted in the gold sea urchin structure for RRR peptide against KKR peptide.

Identifying and Differentiating Topological G-Quadruplex Structures with DNA-Encoded Plasmonic Gold Nanoparticles

DNA G-quadruplexes (G4s) have been identified as critical elements in modulating genomic functions and many other biological processes. Their functions are highly dependent on the primary nucleotides and secondary folding structures. Therefore, to understand their functions, methods to identify and differentiate structures of G4 with speed and accuracy are required but limited. In this report, we have applied a synthetic G4 DNA-encoded nanoparticle approach to identify and differentiate G4 DNA molecules with different topologies and nucleotide residues. We found that the resulting plasmonic properties of the gold nanoparticles, monitored by UV/Vis spectroscopy, are quite sensitive to different G4 structures, including stacking layers, loop sequences, capping bases on G4s, and topological structures. Through these systematic investigations, we demonstrate that this G4-encoded gold nanoparticle approach can be used to profile the G4 structures and distinguish G4s from human telomeres. Such a method may have wide applications in G4 research.

Coumarin 6H-fused fluorescent probe for highly sensitive detection of coralyne using oligonucleotide-modified silver nanoparticles

In this study, a novel, rapid, and sensitive fluorescence sensing platform was developed for the detection of coralyne (COR) by the conjugation of coumarin 6H (C6H) fluorescent dye with oligonucleotide-modified silver nanoparticles [(dT)₃₂-AgNPs]. In the presence of COR, a remarkable and rapid decrease in the fluorescence signal of the probe with a quenching efficiency of around 62% was observed. The quenching response of the system towards COR was possibly due to the displacement of thymidine-rich deoxyoligonucleotides by COR on the surface of AgNPs. The complementary experiments with an adenine-rich single strand as well as with two different secondary structures (i.e., duplex and triplex) revealed a favorable sequence specificity of the sensing platform. The influence of key parameters including the incubation time and temperature was evaluated and optimized to achieve the highest performance. The linear range of 10-183 nM with a correlation coefficient of R = 0.9982 and a limit of detection of 5.24 nM were obtained under the optimized conditions. The selectivity of the proposed probe towards COR was revealed by the evaluation of its response to other small molecules that have molecular structures similar to COR. Finally, the successful applicability of the system was shown with the obtained average recoveries in the range of 87.28-104.52% in human urine samples.

Kinetic Reconstruction of DNA-Programed Plasmonic Metal Nanostructures with Predictable Shapes and Optical Properties

It is desirable to rationally engineer plasmonic metal nanostructures with sets of structural parameters that lead to specific functions. However, it is still challenging to predict the nanostructured outcome of a synthesis reaction by design because not only the exact kinetic path for the structural evolution is very complicated but also the relationships among various functional and structural parameters are often tangled. It is necessary to deconvolute the structure-function relationships and understand the co-evolution of structural and functional parameters as the nanostructures grow. DNA is a programable biomolecular capping ligand that was shown to be capable of precisely controlling the evolution of metal nanostructures. In this study, we systematically analyzed the evolution of two structural parameters and several functional parameters in the growth of Au-Ag nanostructures controlled by two DNA sequences. We deconvoluted the contributions from the two structural parameters in affecting the plasmonic properties in different kinetic and geometric domains. We further designed new nanostructures by exchanging DNA sequences in the growth environment, which also changed their evolution pathways. The resulting structural and functional parameters could be predictively tuned by the timing of the exchange. This study demonstrates the powerful toolbox provided by programable biomolecules in producing novel nanostructures in a predictable manner. It also shows that by understanding the kinetic evolution of the structural parameters and their relationships with the function parameters, it is possible to design the precise combinations of structural and functional parameters in the nanostructured products.

Characterization of Labeled Gold Nanoparticles for Surface-Enhanced Raman Scattering

Noble metal nanoparticles (NP) such as gold (AuNPs) and silver nanoparticles (AgNPs) can produce ultrasensitive surface-enhanced Raman scattering (SERS) signals owing to their plasmonic properties. AuNPs have been widely investigated for their biocompatibility and potential to be used in clinical diagnostics and therapeutics or combined for theranostics. In this work, labeled AuNPs in suspension were characterized in terms of size dependency of their localized surface plasmon resonance (LSPR), dynamic light scattering (DLS), and SERS activity. The study was conducted using a set of four Raman labels or reporters, i.e., small molecules with large scattering cross-section and a thiol moiety for chemisorption on the AuNP, namely 4-mercaptobenzoic acid (4-MBA), 2-naphthalenethiol (2-NT), 4-acetamidothiophenol (4-AATP), and biphenyl-4-thiol (BPT), to investigate their viability for SERS tagging of spherical AuNPs of different size in the range 5 nm to 100 nm. The results showed that, when using 785 nm laser excitation, the SERS signal increases with the increasing size of AuNP up to 60 or 80 nm. The signal is highest for BPT labelled 80 nm AuNPs followed by 4-AATP labeled 60 nm AuNPs, making BPT and 4-AATP the preferred candidates for Raman labelling of spherical gold within the range of 5 nm to 100 nm in diameter.

Gold Nanorods: The Most Versatile Plasmonic Nanoparticles

Gold nanorods (NRs), pseudo-one-dimensional rod-shaped nanoparticles (NPs), have become one of the burgeoning materials in the recent years due to their anisotropic shape and adjustable plasmonic properties. With the continuous improvement in synthetic methods, a variety of materials have been attached around Au NRs to achieve unexpected or improved plasmonic properties and explore state-of-the-art technologies. In this review, we comprehensively summarize the latest progress on Au NRs, the most versatile anisotropic plasmonic NPs. We present a representative overview of the advances in the synthetic strategies and outline an extensive catalogue of Au-NR-based heterostructures with tailored architectures and special functionalities. The bottom-up assembly of Au NRs into preprogrammed metastructures is then discussed, as well as the design principles. We also provide a systematic elucidation of the different plasmonic properties associated with the Au-NR-based structures, followed by a discussion of the promising applications of Au NRs in various fields. We finally discuss the future research directions and challenges of Au NRs.

DNA-encoded bimetallic Au-Pt dumbbell nanozyme for high-performance detection and eradication of Escherichia coli O157:H7

Infectious Escherichia coli O157:H7 threatens the health of millions people each year. Thus, it is important to establish a simple and sensitive method for bacterial detection and eradication. Herein, a DNA-programming strategy is explored to synthesize anisotropic dumbbell-like Au-Pt nanoparticles with excellent catalytic and anti-bacterial activities, which were applied in the simultaneous detection and eradication of pathogenic bacteria. The DNA sequence-dependent growth of bimetallic nanoparticles is firstly studied and polyT20 has the tendency to form dumbbell-like Au-Pt bimetallic structures based on gold nanorods seeds. PolyA20 and polyC20 can also form similar structures but only at much lower DNA concentrations, which can be explained by their much higher affinity to the metal surfaces than T20. The as-prepared nanoparticles exhibit high nanozyme catalytic activity resulting from the synergistic effect of Au and Pt. Under light irradiation, the Au-Pt nanoparticles show high photothermal conversion efficiency and enhanced catalytic activity, which can be applied for the eradication and detection of E. coli O157:H7 with a robust efficacy (95%) in 5 min and provides excellent linear detection (10-10⁷ CFU/mL), with a detection limit of 2 CFU/mL. This study offered new insights into DNA-directed synthesis of nanomaterials with excellent biosensing and antibiotic applications.

Bifunctional Diblock DNA-Mediated Synthesis of Nanoflower-Shaped Photothermal Nanozymes for a Highly Sensitive Colorimetric Assay of Cancer Cells

The activity of a nanozyme is closely related to its surface area-to-volume ratio and the surrounding temperature. To acquire highly active nanozymes, one-pot metallization-like synthesis of novel nanoflower-shaped photothermal nanostructures was conducted using polyadenine-containing diblock DNA as the scaffold. The nanoflower-shaped structures with a high surface area-to-volume ratio and photothermal performance exhibited excellent peroxidase-mimicking activity, and the biorecognition capability was retained by the capping agent of diblock DNA. The functionalized nanostructures were used for a proof-of-concept colorimetric assay of cancer cells in vitro. Upon incorporation of 808 nm laser irradiation, high sensitivity and selectivity for the cancer cell assay were achieved with the lowest detection level of 10 cells/mL. Relative to spherical gold nanostructures, the nanoflower-shaped photothermal nanozyme exhibited higher assay sensitivity, paving the way for the construction of nanozyme-based colorimetric sensors for point-of-care testing.

One-Step Synthesis of Single-Stranded DNA-Bridged Iron Oxide Supraparticles as MRI Contrast Agents

Despite progress on DNA-assembled nanoparticle (NP) superstructures, their complicated synthesis procedures hamper their potential biomedical applications. Here, we present an exceptionally simple strategy for the synthesis of single-stranded DNA (ssDNA) assembled Fe₃O₄ supraparticles (DFe-SPs) as magnetic resonance contrast agents. Unlike traditional approaches that assemble DNA-conjugated NPs via Watson-Crick hybridization, our DFe-SPs are formed with a high yield through one-step synthesis and assembly of ultrasmall Fe₃O₄ NPs via ssDNA-metal coordination bridges. We demonstrate that the DFe-SPs can efficiently accumulate into tumors for sensitive MR imaging. By virtue of reversible DNA-metal coordination bridges, the DFe-SPs could be disassembled into isolated small NPs in vivo, facilitating their elimination from the body. This work opens a new avenue for the ssDNA-mediated synthesis of superstructures, which expands the repertoire of DNA-directed NP assembly for biomedical applications.

Trap Energy Upconversion-Like Near-Infrared to Near-Infrared Light Rejuvenateable Persistent Luminescence

Persistent-luminescence phosphors (PLPs) have a wide variety of applications in the fields of photonics and biophotonics due to their ultralong afterglow lifetime. However, the existing PLPs are charged and recharged with short-wavelength high-energy photons or inconvenient and potentially risky X-ray beams. To date, deep tissue penetrable NIR light has mainly been used for photostimulated afterglow emission, which continues to decay and weaken after each cycle, Herein, a new paradigm of trap energy upconversion-like near-infrared (NIR) to near-infrared light rejuvenateable persistent luminescence in bismuth-doped calcium stannate phosphors and nanoparticles is reported. In contrast to the existing PLPs and persistent-luminescence nanoparticles, the materials enable the occurrence of a reversed transition of the carriers from a deep-level energy trap to a shallow-level trap upon excitation by low-energy NIR photons. Thus these new materials can be charged circularly via deep-tissue penetrable NIR photons, which is unable to be done for existing PLPs, and emit afterglow signals. This conceptual work will lay the foundation to design new categories of NIR-absorptive-NIR-emissive PLPs and nanoparticles featuring physically harmless and deep tissue penetrable NIR light renewability and sets the stage for numerous biological applications, which have been limited by current materials.

Single plasmonic nanostructures for biomedical diagnosis

The field of single nanoparticle plasmonics has grown enormously. There is no doubt that a wide diversity of the nanoplasmonic techniques and nanostructures represents a tremendous opportunity for fundamental biomedical studies as well as sensing and imaging applications. Single nanoparticle plasmonic biosensors are efficient in label-free single-molecule detection, as well as in monitoring real-time binding events of even several biomolecules. In the present review, we have discussed the prominent advantages and advances in single particle characterization and synthesis as well as new insight into and information on biomedical diagnosis uniquely obtained using single particle approaches. The approaches include the fundamental studies of nanoplasmonic behavior, two typical methods based on refractive index change and characteristic light intensity change, exciting innovations of synthetic strategies for new plasmonic nanostructures, and practical applications using single particle sensing, imaging, and tracking. The basic sphere and rod nanostructures are the focus of extensive investigations in biomedicine, while they can be programmed into algorithmic assemblies for novel plasmonic diagnosis. Design of single nanoparticles for the detection of single biomolecules will have far-reaching consequences in biomedical diagnosis.

Plasmonically Modulated Gold Nanostructures for Photothermal Ablation of Bacteria

With the wide utilization of antibiotics, antibiotic-resistant bacteria have been often developed more frequently to cause potential global catastrophic consequences. Emerging photothermal ablation has been attracting extensive research interest for quick/effective eradication of pathogenic bacteria from contaminated surroundings and infected body. In this field, anisotropic gold nanostructures with tunable size/morphologies have been demonstrated to exhibit their outstanding photothermal performance through strong plasmonic absorption of near-infrared (NIR) light, efficient light to heat conversion, and easy surface modification for targeting bacteria. To this end, this review first introduces thermal treatment of infectious diseases followed by photothermal therapy via heat generation on NIR-absorbing gold nanostructures. Then, the usual synthesis and spectral features of diversified gold nanostructures and composites are systematically overviewed with the emphasis on the importance of size, shape, and composition to achieve strong plasmonic absorption in NIR region. Further, the innovated photothermal applications of gold nanostructures are comprehensively demonstrated to combat against bacterial infections, and some constructive suggestions are also discussed to improve photothermal technologies for practical applications.

Stabilization of DNA by sodium and magnesium ions during the synthesis of DNA-bridged gold nanoparticles

Nanostructures synthesized using DNA-conjugated gold nanoparticles have a wide range of applications in the field of biosensorics. The stability of the DNA duplex plays a critical role as it determines the final geometry of these nanostructures. The main way to control DNA stability is to maintain a high ionic strength of the buffer solution; at the same time, high salt concentrations lead to an aggregation of nanoparticles. In this study, by means of the instrumentality of DNA-bridged seeds using tris(hydroxymethyl)aminomethane as a soft reducing agent the dumbbell-like gold nanoparticles up to 35 nm were synthesized with a high concentration of sodium ions of up to 100 mM and magnesium ions up to 1 mM. We also examined at the atomic level the details of the effect of the gold nanoparticle surface, as well as Na⁺ and Mg²⁺ ions, on the stability of nucleotide pairs located in close proximity to the grafting site.

Regulating Catalytic Activity of DNA-Templated Silver Nanoclusters Based on their Differential Interactions with DNA Structures and Stimuli-Responsive Structural Transition

This work reports exquisite engineering of catalytic activity of DNA-templated silver nanoclusters (DNA-AgNCs) based on unique adsorption phenomena of DNAs on DNA-AgNCs and reversible transition between double and triple-stranded DNAs. Four DNA homopolymers exhibit different inhibition effects on the catalytic activity of DNA-AgNCs, poly adenine (polyA) > poly guanine (polyG) > poly cytosine (polyC) > poly thymine (polyT), demonstrating that polyA strands have the strongest adsorption affinity on DNA-AgNCs. Through the formation of T-A•T triplex DNAs, catalytic activity of DNA-AgNCs is restored from the deactivated state by double or single-stranded DNAs, indicating the participation of N7 groups of adenine bases in binding to DNA-AgNCs and blocking active sites. Accordingly, reversibly regulating catalytic activity of DNA-AgNCs can be realized based on DNA input-stimulated transition between duplex and triplex structures. In the end, two low-cost and facile biosensing methods are presented, which are derived from the activity-switchable platform. It is worthy to anticipate that the DNA-AgNCs with controlled catalytic activity will inspire researchers to devise more functionalized nanocatalysts and contribute to the exploration of intelligent biomedicine in the future.

Quantitative Analysis of DNA-Mediated Formation of Metal Nanocrystals

The predictive synthesis of metal nanocrystals with desired structures relies on the precise control of the crystal formation process. Using a capping ligand is an effective method to affect the reduction of metal ions and the formation of nanocrystals. However, predictively synthesizing nanostructures has been difficult to achieve using conventional capping ligands. DNA, as a class of the promising biomolecular capping ligands, has been used to generate sequence-specific morphologies in various metal nanocrystals. However, mechanistic insight into the DNA-mediated nanocrystal formation remains elusive due to the lack of quantitative experimental evidence. Herein, we quantitatively analyzed the precise control of DNA over Ag+ reduction and the structures of resulting Au-Ag core-shell nanocrystals. We derived the equilibrium binding constants between DNA and Ag+, the kinetic rate constants of sequence-specific Ag+ reduction pathways, and the percentage of active surface sites remaining on the nanocrystals after DNA passivation. These three synergistic factors influence the nucleation and growth process both thermodynamically and kinetically, which contributed to the morphological evolution of Au-Ag nanocrystals synthesized with different DNA sequences. This study demonstrates the potential of using functional DNA sequences as a versatile and tunable capping ligand system for the predictable synthesis of metal nanostructures.

Capping Ligand Size-Dependent LSPR Property Based on DNA Nanostructure-Mediated Morphological Evolution of Gold Nanorods for Ultrasensitive Visualization of Target DNA

Systematically tuning the structures and properties of noble-metal nanoparticles through biomolecule-mediated overgrowth is of significant importance for their applications in biosensing and imaging. Herein thiolated biomolecules with different concentrations and sizes (molecular weight and spatial structure) were used as a class of capping ligands to control the longitudinal surface plasmon resonance (LSPR) property of gold nanorods (GNRs). The LSPR peaks were red-shifted by increasing the capping agent concentration. The size effect could be divided to two aspects: (1) When the ligands are small molecules, the LSPR peak is blue-shifted as the size of the capping ligand increases. (2) When the ligands are macromolecular proteins, the LSPR property is similar to that of the overgrown nanoparticle (Au@gap@GNR) without thiolated biomolecules as capping agents. Interestingly, thiol-free and nonhomooligomeric DNA strands as capping agents present a similar influence in shaping the overgrowth of GNRs by varying their concentrations and sizes. In addition, the size effect of a DNA nanostructure was used to construct a Δλ_LSPR-based catalytic nucleic acid biosensor using a DNA dendritic nanostructure as a capping agent combined with LSPR signals generated from the Au@gap@GNRs with morphological evolution. More importantly, the Δλ_LSPR-based biosensor possesses three advantages in nucleic acid biosensing: (1) It is completely label- and wash-free, (2) it has an ultrahigh sensitivity and signal-to-noise ratio, and (3) it can be visualized without any instrumental aid, indicating a significant potential for ultrasensitive biosensing.

DNA-Modulated Plasmon Resonance: Methods and Optical Applications

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

Thermophoretic Detection of Exosomal microRNAs by Nanoflares

Exosomal microRNAs (miRNAs) are reliable and noninvasive biomarkers for the early diagnosis of cancer. Yet, accurate and feasible detection of exosomal miRNAs is often hampered by the low abundance of miRNAs in exosomes and the requirement for RNA extraction in large sample volumes. Here we show a thermophoretic sensor implemented with nanoflares for in situ detection of exosomal miRNAs, without resorting to either RNA extraction or target amplification. Thermophoretic accumulation of nanoflare-treated exosomes leads to an amplified fluorescence signal upon the binding of exosomal miRNAs to nanoflares, allowing for direct and quantitative measurement of exosomal miRNAs down to 0.36 fM in 0.5 μL serum samples. One of the best markers, exosomal miR-375, showed an accuracy of 85% for detection of estrogen receptor-positive breast cancer at early stages (stages I, II). This work provides a feasible tool to improve the diagnosis of cancer.

Gold Nanobones Enhanced Ultrasensitive Surface-Enhanced Raman Scattering Aptasensor for Detecting Escherichia coli O157:H7

Sensitive, robust, and highly specific detection of Escherichia coli O157:H7, one of the most hazardous foodborne pathogens and the cause of numerous diseases, is needed to ensure public health. Herein, a one-pot step method is reported for the preparation of multifunctional gold nanobones (NBs) (GNR_Apt-1+RhB) from gold nanorods (GNRs) comediated by an aptamer (Apt-1) and the signal molecule rhodamine B (RhB) for surface-enhanced Raman scattering detection of E. coli O157:H7. The characterized result showed that Apt-1 and RhB were embedded in the gold NBs, and then, this combination exhibited good recognition, excellent stability, and significant Raman signal intensity enhancement. The Raman enhancement derived from a strong electromagnetic field distribution with the locations at the apex of both ends of the GNR_Apt-1+RhB and the signal stability was because of the firm embedment of Apt-1 (poly A20 + E. coli O157:H7 aptamers) and RhB on the surface of the GNR_Apt-1+RhB. Optimization experiments established that surface-enhanced Raman-scattered RhB absorption at 1350 cm^-1 had a strong linear relationship (y = 180.30x - 61.49; R² = 0.9982) with E. coli O157:H7 concentration over the range of 10-10,000 cfu/mL with a limit of detection of 3 cfu/mL. This novel aptasensor sensitively detects E. coli O157:H7 and has great promise for food pathogenic bacteria detection.

Functional Macromolecule-Enabled Colloidal Synthesis: From Nanoparticle Engineering to Multifunctionality

The synthesis of well-defined inorganic colloidal nanostructures using functional macromolecules is an enabling technology that offers the possibility of fine-tuning the physicochemical properties of nanomaterials and has contributed to a broad range of practical applications. The utilization of functional reactive polymers and their colloidal assemblies leads to a high level of control over structural parameters of inorganic nanoparticles that are not easily accessible by conventional methods based on small-molecule ligands. Recent advances in polymerization techniques for synthetic polymers and newly exploited functions of natural biomacromolecules have opened up new avenues to monodisperse and multifunctional nanostructures consisting of integrated components with distinct chemistries but complementary properties. Here, the evolution of colloidal synthesis of inorganic nanoparticles is revisited. Then, the new developments of colloidal synthesis enabled by functional macromolecules and practical applications associated with the resulting optical, catalytic, and structural properties of colloidal nanostructures are summarized. Finally, a perspective on new and promising pathways to novel colloidal nanostructures built upon the continuous development of polymer chemistry, colloidal science, and nanochemistry is provided.

Encoding Carbon Nanotubes with Tubular Nucleic Acids for Information Storage

DNA has evolved to be a type of unparalleled material for storing and transmitting genetic information. Much recent attention has been drawn to translate the natural specificity of DNA hybridization reactions for information storage in vitro. In this work, we developed a new type of tubular nucleic acid (TNA) by condensing DNA chains on the surface of one-dimensional carbon nanotubes (CNTs). We find that DNA interacts with CNTs in a sequence-specific manner, resulting in different conformations including helix, i-motif, and G-quadruplex. Atomic force microscopic (AFM) imaging revealed that TNAs exhibit distinct patterns with characteristic height and distance that can be exploited for two-dimensional encoding on CNTs. We further demonstrate the use of TNA-CNT for information storage with visual output. This noncanonical, DNA hybridization-free strategy provides a new route to DNA-based data storage.

Functional DNA Molecules Enable Selective and Stimuli-Responsive Nanoparticles for Biomedical Applications

Nanoparticles (NPs) have enormous potential to improve disease diagnosis and treatment due to their intrinsic electronic, optical, magnetic, mechanical, and physiological properties. To realize their full potential for nanomedicine, NPs must be biocompatible and targetable toward specific biomolecules to ensure selective sensing, imaging, and drug delivery in complex environments such as living cells, tissues, animals, and human bodies. In this Account, we summarize our efforts to impart specific biocompatibility and biorecognition functionality to NPs by developing strategies to integrate inorganic and organic NPs with functional DNA (fDNA), including aptamers, DNAzymes, and aptazymes to create fDNA-NPs. These hybrid NPs take advantage of fDNA's ability to either bind targets or catalyze reactions in the presence of targets selectively and utilize their unique physicochemical properties including small size, low immunogenicity, and ease of synthesis and chemical modification in comparison with other molecules such as antibodies. By integrating inorganic NPs such as gold NPs, quantum dots, and iron oxide nanoparticles with fDNA, we designed stimuli-responsive fDNA-NPs that exhibit target induced assembly and disassembly of NPs, resulting in a variety of colorimetric, fluorescent, and magnetic resonance imaging (MRI)-based sensors for diagnostic of a broad range of analytes. To impart both biocompatibility and selectivity on inorganic NPs for targeted bioimaging, we have demonstrated DNA-mediated surface functionalization, shape-controlled synthesis, and coordinative assembly of such NPs as specific bioprobes. A highlight is provided on the construction of fDNA-based nanoprobes with light-activatable sensing and imaging functions, which provides precise control of recognition properties of fDNA with high spatiotemporal resolution. To explore the potential of organic NPs for biosensing applications, we have developed an enzyme-responsive fDNA-liposome as a universal sensing platform compatible with diverse biological targets as well as different detection methods including fluorescence, MRI, or temperature, making possible point-of-care diagnostics. To expand the application regime of organic NPs, we collaborated with the Zimmerman group to prepare single-chain block copolymer-based NPs and incorporated it with a variety of functions, including monovalent DNA for assembly, tunable surface chemistry for cellular imaging, and coordinative Cu(II) sites for catalyzing intracellular click reactions, demonstrating the potential of using organic NPs to create promising fDNA-NP systems with programmable functionalities. Furthermore, we survey our recent endeavor in integration of cell-specific aptamers with different NPs for targeted drug delivery, showing that introducing stimuli-responsive properties into NPs that target tumor microenvironments would enable safer and more effective therapy for cancers. Finally, current challenges and future perspectives in fDNA-mediated engineering of NPs for biomedical applications are discussed.

Bioapplications of DNA nanotechnology at the solid-liquid interface

DNA nanotechnology engineered at the solid-liquid interface has advanced our fundamental understanding of DNA hybridization kinetics and facilitated the design of improved biosensing, bioimaging and therapeutic platforms. Three research branches of DNA nanotechnology exist: (i) structural DNA nanotechnology for the construction of various nanoscale patterns; (ii) dynamic DNA nanotechnology for the operation of nanodevices; and (iii) functional DNA nanotechnology for the exploration of new DNA functions. Although the initial stages of DNA nanotechnology research began in aqueous solution, current research efforts have shifted to solid-liquid interfaces. Based on shape and component features, these interfaces can be classified as flat interfaces, nanoparticle interfaces, and soft interfaces of DNA origami and cell membranes. This review briefly discusses the development of DNA nanotechnology. We then highlight the important roles of structural DNA nanotechnology in tailoring the properties of flat interfaces and modifications of nanoparticle interfaces, and extensively review their successful bioapplications. In addition, engineering advances in DNA nanodevices at interfaces for improved biosensing both in vitro and in vivo are presented. The use of DNA nanotechnology as a tool to engineer cell membranes to reveal protein levels and cell behavior is also discussed. Finally, we present challenges and an outlook for this emerging field.

Plasmonic ELISA based on DNA-directed gold nanoparticle growth for Cronobacter detection in powdered infant formula samples

The traditional gold nanoparticle (AuNP) growth-based plasmonic ELISA (pELISA) strictly and directly controlled by reducing reagents can achieve high sensitivity, but it remains fragile toward the surrounding environment. This work developed a sandwich pELISA for Cronobacter detection in powdered infant formula samples by mediating AuNP growth through DNA. In this assay, DNA adsorbed on the surface of gold nanoseeds guided the anisotropic crystal growth with hydroxylamine as a reducing reagent, and the catalase-hydrogen peroxide (Cat-H₂O₂) system was introduced to bridge the DNA-directed AuNP growth and pELISA, as such DNA can be cleaved into fragments by the hydroxyl radical generated from oxidation of H₂O₂ through Fenton reagents. Under optimized conditions, the proposed pELISA can qualitatively detect Cronobacter species (Cronobacter muytjensii ATCC 51329) by the naked eye with a cut-off limit of 3 × 10⁵ cfu/mL. This method also revealed a good linear range (3 × 10² to 3 × 10⁷ cfu/mL) for quantitative detection of C. muytjensii ATCC 51329 with a limit of detection of 1.6 × 10² cfu/mL, which is approximately 162.5 times lower than that of horseradish peroxidase-based conventional ELISA (2.6 × 10⁴ cfu/mL). By taking advantage of highly stable DNA-directed AuNP growth, the proposed method shows a good performance in powdered infant formula samples spiked with different concentrations of C. muytjensii ATCC 51329 with average recoveries ranging from 90.79 to 119.09% and coefficient of variation ranging from 4.24 to 9.55%. These values corresponded to an acceptable accuracy and precision for the proposed method. In brief, this work shows potential for screening other analytes in food safety, clinical diagnostics, and environmental monitoring.

Plasmonic Photothermal Nanoparticles for Biomedical Applications

Recent advances of plasmonic nanoparticles include fascinating developments in the fields of energy, catalyst chemistry, optics, biotechnology, and medicine. The plasmonic photothermal properties of metallic nanoparticles are of enormous interest in biomedical fields because of their strong and tunable optical response and the capability to manipulate the photothermal effect by an external light source. To date, most biomedical applications using photothermal nanoparticles have focused on photothermal therapy; however, to fully realize the potential of these particles for clinical and other applications, the fundamental properties of photothermal nanoparticles need to be better understood and controlled, and the photothermal effect-based diagnosis, treatment, and theranostics should be thoroughly explored. This Progress Report summarizes recent advances in the understanding and applications of plasmonic photothermal nanoparticles, particularly for sensing, imaging, therapy, and drug delivery, and discusses the future directions of these fields.

Discovery of and Insights into DNA "Codes" for Tunable Morphologies of Metal Nanoparticles

The discovery and elucidation of genetic codes has profoundly changed not only biology but also many fields of science and engineering. The fundamental building blocks of life comprises of four simple deoxyribonucleotides and yet their combinations serve as the carrier of genetic information that encodes for proteins that can carry out many biological functions due to their unique functionalities. Inspired by nature, the functionalities of DNA molecules have been used as a capping ligand for controlling morphology of nanomaterials, and such a control is sequence dependent, which translates into distinct physical and chemical properties of resulting nanoparticles. Herein, an overview on the use of DNA as engineered codes for controlling the morphology of metal nanoparticles, such as gold, silver, and Pd-Au bimetallic nanoparticles is provided. Fundamental insights into rules governing DNA controlled growth mechanisms are also summarized, based on understanding of the affinity of the DNA nucleobases to various metals, the effect of combination of nucleobases, functional modification of DNA, the secondary structures of DNA, and the properties of the seed employed. The resulting physical and chemical properties of these DNA encoded nanomaterials are also reviewed, while perspectives into the future directions of DNA-mediated nanoparticle synthesis are provided.

Phosphorothioate DNA Mediated Sequence-Insensitive Etching and Ripening of Silver Nanoparticles

Many DNA-functionalized nanomaterials and biosensors have been reported, but most have ignored the influence of DNA on the stability of nanoparticles. We observed that cytosine-rich DNA oligonucleotides can etch silver nanoparticles (AgNPs). In this work, we showed that phosphorothioate (PS)-modified DNA (PS-DNA) can etch AgNPs independently of DNA sequence, suggesting that the thio-modifications are playing the major role in etching. Compared to unmodified DNA (e.g., poly-cytosine DNA), the concentration of required PS DNA decreases sharply, and the reaction rate increases. Furthermore, etching by PS-DNA occurs quite independent of pH, which is also different from unmodified DNA. The PS-DNA mediated etching could also be controlled well by varying DNA length and conformation, and the number and location of PS modifications. With a higher activity of PS-DNA, the process of etching, ripening, and further etching was taken place sequentially. The etching ability is inhibited by forming duplex DNA and thus etching can be used to measure the concentration of complementary DNA.

Nanogold Flower-Inspired Nanoarchitectonics Enables Enhanced Light-to-Heat Conversion Ability for Rapid and Targeted Chemo-Photothermal Therapy of a Tumor

Chemo-photothermal therapy has become a promising tool for clinical noninvasive tumor therapy, which is able to efficiently avoid drug resistance and other side effects from chemical anticarcinogenic drugs. The ability to selectively fast-heat tumor tissues over surrounding compartments is of fundamental importance and makes effective treatment of tumor margins and complex tumor geometries. Currently existing chemo-photothermal methods mainly show slow light-to-heat conversion with increased temperature up to around 45-57 °C for 5-20 min or a longer time in vitro under regular near-infrared laser irradiation, and during tumor therapy, worse performance in temperature changes are obtained due to the much longer penetration distance in vivo. Herein, nanoarchitectonics with excellent chemo-photothermal performance are first proposed for tumors via in situ decoration of nanogold flowers on graphene oxide surface with further modification of the aptamer molecule. Even with simple synthesis processes, these nanoarchitectonics demonstrate impressive increased temperatures up to 85 °C in just 2 min under 808 nm laser irradiation with regular power density. Due to the fast light-to-heat conversion ability and specific binding effect between the aptamer and tumor cells, the designed nanocarrier shows a rapid and target therapy system with a targeted chemo-photothermal tumor treatment.

Fluorescent hybrid nanospheres induced by single-stranded DNA and magnetic carbon quantum dots

Assembled DNA nanospheres were preparedviaself-assembly with magnetic CQDGd as the building blocks and negatively charged ssDNA as the assembly units.

Sequence-Specific Control of Inorganic Nanomaterials Morphologies by Biomolecules

Controlling morphologies of nanomaterials such as their shapes and surface features has been a major endeavor in the field of nanoscale science and engineering, because the morphology is a major determining factor for functional properties of nanomaterials. Compared with conventional capping ligands based on organic molecules or polymers, the programmability of biomolecules makes them attractive alternatives for morphology-controlled nanomaterials synthesis. Towards the goal of predictable control of the synthesis, many studies have been performed on using different sequences of biomolecules to generate specific nanomaterial morphology. In this review, we summarize recent studies in the past few years on using DNA and peptide sequences to control inorganic nanomaterial morphologies, focusing on both case studies and mechanistic investigations. The functional properties resulting from such a sequence-specific control are also discussed, along with strengths and limitations of different approaches to achieving the goal.

DNA-Encoded Morphological Evolution of Bimetallic Pd@Au Core-shell Nanoparticles from a High-indexed Core

DNA-mediated synthesis of nanoparticles with different morphologies has proven to be a powerful method to synthesize and access many exclusive shapes and surface properties. While previous studies employ seeds that contain relatively low-energy facets, such as a simple cubic palladium seed in the synthesis of Pd-Au bimetallic nanoparticles, few studies have investigated whether DNA molecules can still exert their influence when the synthesis uses a seed that contains high-energy facets. Seeds that are enclosed by such high-energy facets or sites are known to act as easy nucleation sites in nanoparticles growth and could potentially suppress the effect of DNA. To answer this question, we herein report DNA-encoded control of morphological evolution of bimetallic Pd@Au core-shell nanoparticles from a concave palladium nanocube seed that contains high indexed facets. Based on detailed spectroscopic and SEM studies of time-dependent growth of the bimetallic nanoparticles, we found that each of 10-mer DNA molecules (T10, G10, C10 and A10) has a unique way of interacting with both the seed's surface and the precursor. Among them, the most important factor is the binding affinity of the nucleobase to the Pd surface, with the A10 possessing the highest binding affinity and thus capable of stabilizing the seed's high energy surfaces. Furthermore, for bases with lower binding affinity (T10, G10 and C10) than A10, the growth is completely dictated by the seed's surface energy initially, but the later growth can still be influenced by the different DNA sequences, resulting in four unique morphologically different Pd@Au bimetallic nanoparticles. The effect of these DNA molecules with medium binding affinity can only be observed when there is more deposition of Au. Based on the above results, a scheme for the DNA controlled growth is proposed. Together these results have provided insights into factors governing DNA-mediated growth of core-shell structures using seeds with high-energy sites, and the insights can readily be applied to other bimetallic systems that adopt seed-mediated synthesis.