DNA‐Based Assembly of Metal Nanoparticles

Heteromultivalent DNA Enhances the Assembly Yield of Hybrid Nanoparticles and Facilitates Dynamic Disassembly for Bioanalysis Using ICP-MS

To obtain enhanced physical and biological properties, various nanoparticles are typically assembled into hybrid nanoparticles through the binding of multiple homologous DNA strands to their complementary counterparts, commonly referred to as homomultivalent assembly. However, the poor binding affinity and limited controllability of homomultivalent disassembly restrict the assembly yield and dynamic functionality of the hybrid nanoparticles. To achieve a higher binding affinity and flexible assembly choice, we utilized the paired heteromultivalency DNA to construct hybrid nanoparticles and demonstrate their excellent assembly characteristics and dynamic applications. Specifically, through heteromultivalency, DNA-functionalized magnetic beads (MBs) and gold nanoparticles (AuNPs) were efficiently assembled. By utilizing ICP-MS, the assembly efficiency of AuNPs on MBs was directly monitored, enabling quantitative analysis and optimization of heteromultivalent binding events. As a result, the enhanced assembly yield is primarily attributed to the fact that heteromultivalency allows for the maximization of effective DNA probes on the surface of nanoparticles, eliminating steric hindrance interference. Subsequently, with external oligonucleotides as triggers, it was revealed that the disassembly mechanism of hybrid nanoparticles was initiated, which was based on an increased local concentration rather than toehold-mediated displacement of paired heteromultivalency DNA probes. Capitalizing on these features, an output platform was then established based on ICP-MS signals that several Boolean operations and analytical applications can be achieved by simply modifying the design sequences. The findings provide new insights into DNA biointerface interaction, with potential applications to complex logic operations and the construction of large DNA nanostructures.

Colorimetric and Label-Free Optical Detection of Pb2+ Ions via Colloidal Gold Nanoparticles

The detection of the lead heavy metal (Pb) in water is crucial in many chemical processes, as it is associated with serious health hazards. Here, we report the selective and precise colorimetric detection of Pb2+ ions in water, exploiting the aggregation and self-assembly mechanisms of glutathione (GSH)-functionalized gold nanoparticles (GNPs). The carboxyl functional groups are able to create coordination complexes with Pb2+, inducing aggregation amongst the GSH-GNPs in the presence of Pb2+ due to the chelation of the GSH ligands. The resulting aggregation amongst the GSH-GNPs in the presence of Pb2+ increases the aggregate size depending on the available Pb2+ ions, affecting the plasmonic coupling. This causes a substantial shift in the plasmon wavelength to a longer wavelength side with increasing Pb2+ concentration, resulting in a red-to-blue colorimetric or visual change, enabling the instant determination of lead content in water.

Ion-Mediated Protein Stabilization on Nanoscopic Surfaces

The emergence of nanoparticles in biomedical applications has made their interactions with proteins inevitable. Nanoparticles conjugated with proteins and peptide-based constructs form an integral part of nanotherapeutics and have recently shown promise in treating a myriad of diseases. The proper functioning of proteins is critical to achieve their biological functions. However, interface issues result in the denaturation of proteins, and the loss of orientation and steric hindrance can adversely affect the function of the conjugate. Furthermore, surface-induced denaturation also triggers protein aggregation, resulting in amyloid-like species. Understanding the mechanistic underpinnings of protein-nanoparticle interactions and controlling their interfacial characteristics are critical and challenging due to the complex nature of the conjugates. In this milieu, we demonstrate that ionic liquids can be suitable candidates for stabilizing protein-nanoparticle interactions by virtue of their excellent protein-preserving properties. We also probe the previously unexplored mechanism of ion-mediated stabilization of the protein molecules on the nanoparticle surface. The protein-nanoparticle conjugates consist of lysozyme and choline-based ionic liquids characterized by optical and electron microscopy techniques combined with surface-sensitive plasmon-enhanced Raman spectroscopy. Furthermore, atomistic molecular dynamics simulations of the conjugates delineate interfacial interactions of the protein molecules and the modulation by the ions, particularly the conformational changes and the dynamic correlation when the protein and specific ionic liquid molecules are adsorbed on the nanoparticle surface. The combined experimental and computational studies showed the synergistic behavior of the ions of the ionic liquids, specifically the orientation and coverage of the anions aided by the cations to control the surface interactions and hence the overall protein stability. These studies pave the way for using ionic liquids, particularly their biocompatible counterparts in nanoparticle-based complexes, as stabilizing agents for biomedical applications.

Harmful Microalgae Detection: Biosensors versus Some Conventional Methods

In the last decade, there has been a steady stream of information on the methods and techniques available for detecting harmful algae species. The conventional approaches to identify harmful algal bloom (HAB), such as microscopy and molecular biological methods are mainly laboratory-based and require long assay times, skilled manpower, and pre-enrichment of samples involving various pre-experimental preparations. As an alternative, biosensors with a simple and rapid detection strategy could be an improvement over conventional methods for the detection of toxic algae species. Moreover, recent biosensors that involve the use of nanomaterials to detect HAB are showing further enhanced detection limits with a broader linear range. The improvement is attributed to nanomaterials' high surface area to volume ratio, excellent biological compatibility with biomolecules, and being capable of amplifying the electrochemical signal. Hence, this review presents the potential usage of biosensors over conventional methods to detect HABs. The methods reported for the detection of harmful algae species, ranging from conventional detection methods to current biosensor approaches will be discussed, along with their respective advantages and drawbacks to indicate the future prospects of biosensor technology for HAB event management.

Programmable Matter: The Nanoparticle Atom and DNA Bond

Colloidal crystal engineering with DNA has led to significant advances in bottom-up materials synthesis and a new way of thinking about fundamental concepts in chemistry. Here, programmable atom equivalents (PAEs), comprised of nanoparticles (the "atoms") functionalized with DNA (the "bonding elements"), are assembled through DNA hybridization into crystalline lattices. Unlike atomic systems, the "atom" (e.g., the nanoparticle shape, size, and composition) and the "bond" (e.g., the DNA length and sequence) can be tuned independently, yielding designer materials with unique catalytic, optical, and biological properties. In this review, nearly three decades of work that have contributed to the evolution of this class of programmable matter is chronicled, starting from the earliest examples based on gold-core PAEs, and then delineating how advances in synthetic capabilities, DNA design, and fundamental understanding of PAE-PAE interactions have led to new classes of functional materials that, in several cases, have no natural equivalent.

Prospects in interfaces of biomolecule DNA and nanomaterials as an effective way for improvising surface enhanced Raman scattering: A review

Surface Enhanced Raman Scattering (SERS) is a field of research that has shown promising application in the analysis of various substrate molecules by means of rough metallic surfaces. In directing the enhancement of substrate molecules in micro and nano-molar concentrations, plasmonic coupling of metal nanoparticles (NPs), morphology of metal NPs and the closely arrangement of rough metal surfaces that produces 'hot spots' can effectively increase the so-called enhancement factor (EF) that will be applicable in various fields. As the mechanistic aspects are still not clear, research has been triggered all over the world for the past two decades to have a clear understanding in chemical and electromagnetic effects. As the reproducibility of intensity of signals at low concentrations of probe molecules is of a big concern, metal NPs with various scaffolds were prepared and recently bio-molecule, DNA has been studied and showed promising advantages. This review first time highlights metal NPs with DNA interface as an effective rough metallic surface for SERS with high intensity and also with better reproducibility. Based on this review, similar kinds of scaffolds like DNA can be used to further analyze SERS activities of various metal NPs with different morphologies to have high intense signals at low concentrations of probe molecules.

From DNA Nanotechnology to Material Systems Engineering

In the past 35 years, DNA nanotechnology has grown to a highly innovative and vibrant field of research at the interface of chemistry, materials science, biotechnology, and nanotechnology. Herein, a short summary of the state of research in various subdisciplines of DNA nanotechnology, ranging from pure "structural DNA nanotechnology" over protein-DNA assemblies, nanoparticle-based DNA materials, and DNA polymers to DNA surface technology is given. The survey shows that these subdisciplines are growing ever closer together and suggests that this integration is essential in order to initiate the next phase of development. With the increasing implementation of machine-based approaches in microfluidics, robotics, and data-driven science, DNA-material systems will emerge that could be suitable for applications in sensor technology, photonics, as interfaces between technical systems and living organisms, or for biomimetic fabrication processes.

Double G-quadruplexes in a copper nanoparticle based fluorescent probe for determination of HIV genes

A DNA-templated copper nanoparticle (CuNP) probe has been developed for the determination of the human immunodeficiency virus oligonucleotide (HIV-DNA). The function of the probe relies on affinity binding-induced DNA hybridization associated with the use of double G-quadruplexes. Double-stranded DNA (dsDNA) with poly(AT-TA) bases was used as a template for synthesis of dsDNA-CuNPs. These have weak fluorescence. In the next step, two G-rich sequences that are linked to both sides of the ds-DNA are locked by HIV complementary DNA (cDNA). If HIV-DNA is introduced, it will hybridize with cDNA, thereby transforming the two G-rich sequences into G-quadruplexes. This enhances the fluorescence of the adjacent dsDNA-CuNPs. Fluorescence increases linearly in the 1 to 200 and 250-1000 nM HIV-DNA concentration range, and the detection limit is 13 pM. This enzyme-free fluorometric assay is time-saving, easily operated, and therefore has large potential in biosensing because it may be extended to various other DNA targets. Graphic abstract Double-strand DNA-templated copper nanoparticles (DNA-CuNPs) have weak fluorescence. When Human Immunodeficiency Virus oligonucleotide (HIV-DNA) is added, it completely hybridized with HIV complementary DNA (cDNA). As a result, the two exposed G-rich sequences are transformed into G-quadruplexes, and an apparent increase in the fluorescence intensity can be observed. (AA: ascorbic acid).

Colorimetric detection of HVA by self-assembly of Au nanorods with DNA double helices to give side-by-side and end-to-end structures

Simple, less time consuming and sensitive self-assembly and colorimetric detection of HVA.

Integrating Deoxyribozymes into Colorimetric Sensing Platforms

Biosensors are analytical devices that have found a variety of applications in medical diagnostics, food quality control, environmental monitoring and biodefense. In recent years, functional nucleic acids, such as aptamers and nucleic acid enzymes, have shown great potential in biosensor development due to their excellent ability in target recognition and catalysis. Deoxyribozymes (or DNAzymes) are single-stranded DNA molecules with catalytic activity and can be isolated to recognize a wide range of analytes through the process of in vitro selection. By using various signal transduction mechanisms, DNAzymes can be engineered into fluorescent, colorimetric, electrochemical and chemiluminescent biosensors. Among them, colorimetric sensors represent an attractive option as the signal can be easily detected by the naked eye. This reduces reliance on complex and expensive equipment. In this review, we will discuss the recent progress in the development of colorimetric biosensors that make use of DNAzymes and the prospect of employing these sensors in a range of chemical and biological applications.

A smart DNA–gold nanoparticle probe for detecting single-base changes on the platform of a quartz crystal microbalance

A design of DNA–gold nanoparticle probe-fueled DNA strand displacements for detecting single-base changes on the platform of a quartz crystal microbalance with random sequences was developed.

Formation of copper nanoparticles on poly(thymine) through surface-initiated enzymatic polymerization and its application for DNA detection

A DNA biosensor using polyT-templated CuNPs as the fluorescent probe and SIEP as the signal amplification strategy is proposed.

Attomolar detection of BRCA1 gene based on gold nanoparticle assisted signal amplification

In this work, we report a simple strategy for signal amplification using appropriately functionalized gold nanoparticles in an electrochemical genosensor which led to attomolar detection of breast cancer 1 (BRCA1) gene. The sensor was developed by the layer-by-layer assembly of mercaptopropionic acid (MPA), polyethylene glycol (PEG) functionalized gold nanoparticle (AuNPPEG), capture DNA (DNA-c), target BRCA1 DNA (DNA-t) and gold nanoparticle labeled reporter DNA (DNA-r.AuNP) on gold electrode. PEG functionalized gold nanoparticles on the MPA surface provided good electron conducting path nullifying the insulating effect of MPA and also act as a proper immobilization platform for the DNA-c by the large number of carboxyl groups present on the functionalized gold nanoparticles. We demonstrated that the incorporation of MPA functionalized gold nanoparticles (AuNPMPA) as an electrochemical label in this sensor design could significantly enhance the sensitivity in the detection. The DNA hybridization of DNA-r.AuNP with target probe was measured by chronoamperometry, electrochemical impedance spectroscopy (EIS), and scanning tunnelling spectroscopy (STS). Electrochemical quartz crystal microbalance (EQCM) experiments were used to support the detection and also to calculate the number of adsorbed molecules on the surface. Under optimum conditions the present sensor exhibited high sensitivity and a very low detection limit of 50attomolar DNA target (294.8attogram BRCA1gene/ml). It shows excellent selectivity against non complementary sequences and 3 base mismatch complementary targets. It also shows good reproducibility, stability and reusability and the developed sensor surface is suitable for point-of care applications.

Masking nanoparticle surfaces for sensitive and selective colorimetric detection of proteins

We have developed a convenient and efficient colorimetric detection system for protein targets using aptamer-gold nanoparticle conjugates. We take advantage of the correlation between the catalytic properties and the exposed surface area of the nanoparticles, which is inversely proportional to the amount of the aptamer-bound protein targets. As the concentration of the protein target increases, the nanoparticle surface area becomes more masked, thus increasing the reduction time of 4-nitrophenol for the color change. We also reduce the detection time by either redesigning the aptamer sequences or regulating their density. This detection system is highly selective, discriminating the target protein even at a concentration 1000 times higher than the limit of detection (LOD). Importantly, to the best of our knowledge, the LOD with the unaided eye in this work is the lowest for a colorimetric detection system using lysozyme as a model protein (16 nM). Lysozyme in chicken egg whites is directly analyzed using our detection system, whose results are in excellent agreement with the enzyme-linked immunosorbent assay (ELISA) analysis.

A triggered DNA hydrogel cover to envelop and release single cells

We develop an enzyme-triggered permeable DNA hydrogel cover to envelop and release single cells in microwells. The porous structure of the DNA hydrogel allows nutrients and waste to pass through, leading to a cell viability as high as 98%. The design provides a general method to culture, monitor, and manipulate single cells, and has potential applications in cell patterning and studying cell communication.

Reversible aggregation of DNA-decorated gold nanoparticles controlled by molecular recognition

The programmable assembly of functional nanomaterials has been extensively addressed; however, their selective reversible assembly in response to an external stimulus has been more difficult to realize. The specificity and programmable interactions of DNA have been exploited for the rational self-assembly of DNA-conjugated nanoparticles, and here we demonstrate the sequence-controlled disaggregation of DNA-modified gold nanoparticles simply by employing two complementary oligonucleotides. Target oligonucleotides with perfectly matching sequence enabled dissociation of aggregated nanoparticles, whereas oligonucleotides differing by one nucleotide did not cause disassembly of the aggregated nanoparticles. Physical aspects of this process were characterized by UV-vis absorption, light scattering, and transmission electron microscopy. This strategy for programmed disassembly of gold nanoparticles in response to biological stimuli demonstrates a fundamentally important concept anticipated to be useful for diverse applications involving molecular recognition.

DNAzyme-functionalized gold nanoparticles for biosensing

Recent progress in using DNAzyme-functionalized gold nanoparticles (AuNPs) for biosensing is summarized in this chapter. A variety of methods, including those for attaching DNA on AuNPs, detecting metal ions and small molecules by DNAzyme-functionalized AuNPs, and intracellular applications of DNAzyme-functionalized AuNPs are discussed. DNAzyme-functionalized AuNPs will increasingly play more important roles in biosensing and many other multidisciplinary applications. This chapter covers the recent advancement in biosensing applications of DNAzyme-functionalized gold nanoparticles, including the detection of metal ions, small molecules, and intracellular imaging.

Natural tubule clay template synthesis of silver nanorods for antibacterial composite coating

Halloysite is naturally available clay mineral with hollow cylindrical geometry and it is available in thousands of tons. Silver nanorods were synthesized inside the lumen of the halloysite by thermal decomposition of the silver acetate, which was loaded into halloysite from an aqueous solution by vacuum cycling. Images of individual ca. 15 nm diameter silver nanorods and nanoparticles were observed with TEM. The presence of silver inside the tubes was also verified with STEM-EDX elemental mapping. Nanorods had crystalline nature with [111] axis oriented ~68° from the halloysite tubule main axis. The composite of silver nanorods encased in clay tubes with the polymer paint was prepared, and the coating antimicrobial activity combined with tensile strength increase was demonstrated. Coating containing up 5% silver loaded halloysite did not change color after light exposure contrary to the sample prepared with loading with unshelled silver nanoparticles. Halloysite tube templates have a potential for scalable manufacturing of ceramic encapsulated metal nanorods for composite materials.

Design and application of inorganic nanoparticle superstructures: current status and future challenges

Self-assembly of inorganic nanoparticles (NPs) into superstructures, which is used as a general way to integrate functional inorganic NPs into macroscale devices, has attracted much research interest. This review will summarize the recent progress and discuss future challenges of the inorganic NP superstructures. Examples include both DNA-based and polymer-based NP assemblies with controlled positioning and geometries, and quasicrystalline ordered structures from the self-assembly of binary or ternary NPs. Different from their individual NP counterparts, these self-assembled superstructures possess unique properties, such as optical chirality and dynamic structural change under an external stimulus. Due to their diversified structures and functionalities, inorganic NP superstructures have shown a wide range of promise for applications in electronic and photonic devices, such as field-effect transistors, magnetoresistive components, optical information recording, and solar cells.

Assembly-based titration for the determination of monodisperse plasmonic nanoparticle concentrations using DNA

We present a stoichiometric titration method to determine the concentration of nanoparticles of various materials, sizes, and shapes. We have discovered that the optical response associated with the assembly formation is maximized when two types of nanoparticles attractively interact at a specific ratio, regardless of the particle type. Based on the reversible hybridization properties of two cDNA sequences used to assemble the particles, the assembly-based titration of various nanoparticles of unknown concentrations is visually demonstrated with high accuracy and reliability, which is analogous to the classic molecular titration method.

Building plasmonic nanostructures with DNA

Plasmonic structures can be constructed from precise numbers of well-defined metal nanoparticles that are held together with molecular linkers, templates or spacers. Such structures could be used to concentrate, guide and switch light on the nanoscale in sensors and various other devices. DNA was first used to rationally design plasmonic structures in 1996, and more sophisticated motifs have since emerged as effective and versatile species for guiding the assembly of plasmonic nanoparticles into structures with useful properties. Here we review the design principles for plasmonic nanostructures, and discuss how DNA has been applied to build finite-number assemblies (plasmonic molecules), regularly spaced nanoparticle chains (plasmonic polymers) and extended two- and three-dimensional ordered arrays (plasmonic crystals).

Mechanically interlocked gold and silver nanoparticles using metallosupramolecular catenane chemistry

We have employed the toolbox of metallosupramolecular chemistry to mechanically interlock gold and silver nanoparticles. A specifically designed PEGthiol-functionalized bis(phenanthroline)copper(I) complex acts to 'catenate' the nanoparticles. The interlocked assemblies were characterised by three complementary techniques: DLS, SERS and TEM.

Metal-complex/DNA conjugates: a versatile building block for DNA nanoarrays

The use of DNA networks as templates for forming nanoarrays of metallic centres shows an exciting potential to generate addressable nanostructures. Inorganic units can be photoactive, electroactive and/or can possess magnetic and catalytic properties and can adopt different spatial arrangements due to their varied coordination nature. All these properties influence both the structure and function of passive DNA scaffolds and provide DNA nanostructures as a new platform for new materials in emerging technologies, such as nanotechnology, biosensing or biocomputing.

DNA-based soft phases

This chapter reviews the state-of-the-art in the study of molecular or colloidal systems whose mutual interactions are mediated by DNA molecules. In the last decade, the robust current knowledge of DNA interactions has enabled an impressive growth of self-assembled DNA-based structures that depend crucially on the properties of DNA-DNA interactions. In many cases, structures are built on design by exploiting the programmable selectivity of DNA interactions and the modularity of their strength. The study of DNA-based materials is definitely an emerging field in condensed matter physics, nanotechnology, and material science. This chapter will consider both systems that are entirely constructed by DNA and hybrid systems in which latex or metal colloidal particles are coated by DNA strands. We will confine our discussion to systems in which DNA-mediated interactions promote the formation of "phases," that is structures extending on length scales much larger than the building blocks. Their self-assembly typically involves a large number of interacting particles and often features hierarchical stages of structuring. Because of the possibility of fine-tuning the geometry and strength of the DNA-mediated interactions, these systems are characterized by a wide variety of patterns of self-assembly, ranging from amorphous, to liquid crystalline, to crystalline in one, two, or three dimensions.

Multiplexed detection of oligonucleotides with biobarcoded gold nanoparticle probes

Applications in a variety of fields rely on the high-throughput ultrasensitive and multiplexed detection of oligonucleotides. However, the conventional microarray-based techniques that employ fluorescent dyes are hampered by several limitations; they require target amplification, fluorophore labeling, and complicated instrumentation, while the fluorophore-labeled species themselves exhibit slow binding kinetics, photo-bleaching effects, and overlapping spectral profiles. Among the emerging nanomaterials that are being used to solve these problems, oligonucleotide-gold nanoparticle conjugates (Oligo-AuNPs) have recently been highlighted due to their unique chemical and physical properties. In this chapter, a detection scheme for oligonucleotides that utilize Oligo-AuNPs is evaluated with multiple oligonucleotide targets. This scheme takes advantage of the sharp melting transitions, intense optical properties, catalytic properties, enhanced binding properties, and the programmable assembly/disassembly of Oligo-AuNPs.

Recent advances in DNA-based directed assembly on surfaces

In the last decade, "small" and "integrated" have been keywords in the field of device fabrication as the desire to exploit nanoscale phenomena and make electronic, photonic and magnetic arrays has grown. In an effort to improve resolution and control costs, much work has been dedicated to developing alternatives to conventional microfabrication technology. For this purpose, biomolecular assembly and DNA nanotechnology in particular are appealing owing to their inherent size and capacity for molecular recognition. Herein, we review recent achievements in DNA-based directed assembly on substrates. These include novel methods for patterning and depositing nanomaterials on DNA-modified surfaces as well as using synthetic DNA nanostructures such as DNA tiles and origami as templates to direct the assembly of nanoscale components. Particular attention is paid to integrating self-assembly with top-down lithography, and some possible directions for future work are discussed.

Novel DNA materials and their applications

The last two decades have witnessed the exponential development of DNA as a generic material instead of just a genetic material. The biological function, nanoscale geometry, biocompatibility, biodegradability, and molecular recognition capacity of DNA make it a promising candidate for the construction of novel functional nanomaterials. As a result, DNA has been recognized as one of the most appealing and versatile nanomaterial building blocks. Scientists have used DNA in this way to construct various amazing nanostructures, such as ordered lattices, origami, supramolecular assemblies, and even three-dimensional objects. In addition, DNA has been utilized as a guide and template to direct the assembly of other nanomaterials including nanowires, free-standing membranes, and crystals. Furthermore, DNA can also be used as structural components to construct bulk materials such as DNA hydrogels, demonstrating its ability to behave as a unique polymer. Overall, these novel DNA materials have found applications in various areas in the biomedical field in general, and nanomedicine in particular. In this review, we summarize the development of DNA assemblies, describe the innovative progress of multifunctional and bulk DNA materials, and highlight some real-world nanomedical applications of these DNA materials. We also show our insights throughout this article for the future direction of DNA materials.

On the application potential of gold nanoparticles in nanoelectronics and biomedicine

Ligand-stabilized gold nanoparticles (AuNPs) are of high interest to research dedicated to future technologies such as nanoelectronics or biomedical applications. This research interest arises from the unique size-dependent properties such as surface plasmon resonance or Coulomb charging effects. It is shown here how the unique properties of individual AuNPs and AuNP assemblies can be used to create new functional materials for applications in a technical or biological environment. While the term technical environment focuses on the potential use of AuNPs as subunits in nanoelectronic devices, the term biological environment addresses issues of toxicity and novel concepts of controlling biomolecular reactions on the surface of AuNPs.

Properties and emerging applications of self-assembled structures made from inorganic nanoparticles

Just as nanoparticles display properties that differ from those of bulk samples of the same material, ensembles of nanoparticles can have collective properties that are different to those displayed by individual nanoparticles and bulk samples. Self-assembly has emerged as a powerful technique for controlling the structure and properties of ensembles of inorganic nanoparticles. Here we review different strategies for nanoparticle self-assembly, the properties of self-assembled structures of nanoparticles, and potential applications of such structures. Many of these properties and possible applications rely on our ability to control the interactions between the electronic, magnetic and optical properties of the individual nanoparticles.

Synthesis and thermally reversible assembly of DNA-gold nanoparticle cluster conjugates

We describe the facile synthesis of stable gold nanoparticle clusters densely functionalized with DNA (DNA-AuNP clusters) using dithiothreitol and monothiol DNA and their thermally reversible assembly properties. The size of the clusters exhibits a very narrow distribution and can be easily controlled by adjusting the stoichiometry of dithiothreitol and DNA, leading to a variety of colors due to the surface plasmon resonance of the AuNP clusters. Importantly, the DNA-AuNP clusters exhibit highly cooperative melting properties with distinctive and diverse color changes depending on their size. The selective and sensitive colorimetric detection of target sequences was demonstrated based upon the unique properties of the DNA-AuNP clusters.