Homogeneous detection of unamplified genomic DNA sequences based on colorimetric scatter of gold nanoparticle probes

Fluorescence proximity assay based on a metal–organic framework platform

A novel fluorescence proximity assay (FPA) based on a metal–organic framework (MOF) platform was developed for target protein detection.

Mannitol-induced gold nanoparticle aggregation for the ligand-free detection of viral particles

Addition of osmolytes causes viruses-coated AuNPs to aggregate and not protein-coated AuNPs. Ligand-free detection of virus was developed without the need for prior knowledge of the specific virus target.

Reduced Graphene Oxide-Oligonucleotide Interfaces: Understanding Based on Electrochemical Oxidation of Guanines

Investigation into the interactions between biomolecules DNA/RNA and carbon nanomaterials is very important for applications in bioassays and bioanalysis. Graphene and graphene oxide (GO) have been successfully adopted by exploiting the binding affinity difference between single-stranded oligonucleotides (ssDNA) and double-stranded oligonucleotides (dsDNA) to graphene sheets. In this work, we describe the electrochemical DNA oxidation with [Ru(bpy)₃]²⁺ to understand the interaction between dsDNA (and corresponding ssDNA) and reduced graphene oxide (rGO). The electrochemical oxidation rate of guanine bases of ssDNA bound to rGO by electrochemically generated [Ru(bpy)₃]³⁺ was much slower than those unbound to rGO. Our study revealed that ssDNA constrained on rGO was significantly protected from the electron transfer to [Ru(bpy)₃]³⁺ because of π,π-stacking interaction between nucleobases and rGO. On the other hand, the oxidation rates of 11-, 20-, and 27-mer dsDNA bound to rGO increased relative to those of dsDNA alone, demonstrating that the guanine bases of dsDNA on the interaction with rGO became more accessible to [Ru(bpy)₃]³⁺. Our electrochemical data illustrated that dsDNA could be totally or partially dehybridized and bind to rGO to form ssDNA/rGO. Furthermore, absorption, circular dichroism spectra, and fluorescence measurements of ethidium bromide using ssDNA and dsDNA with rGO supported the dehybridization of dsDNA in the presence of rGO.

Guide to Selecting a Biorecognition Element for Biosensors

Biosensors are powerful diagnostic tools defined as having a biorecognition element for analyte specificity and a transducer for a quantifiable signal. There are a variety of different biorecognition elements, each with unique characteristics. Understanding the advantages and disadvantages of each biorecognition element and their influence on overall biosensor performance is crucial in the planning stages to promote the success of novel biosensor development. Therefore, this review will focus on selecting the optimal biorecognition element in the preliminary design phase for novel biosensors. Included is a review of the typical characteristics and binding mechanisms of various biorecognition elements, and how they relate to biosensor performance characteristics, specifically sensitivity, selectivity, reproducibility, and reusability. The goal is to point toward language needed to improve the design and development of biosensors toward clinical success.

Aptamer-functionalized AuNPs for the high-sensitivity colorimetric detection of melamine in milk samples

Although aptamer-functionalized AuNPs technology exhibits great potential in analytical and biological chemistry, direct analysis of molecules at a low concentration using colorimetric assay remains challenging. The development of intuitive methods has attracted interest for promising detection of melamine in milk samples due to a demand for stable and understandable process. In this study, we propose a rapid and facile colorimetric measurement method of melamine combined aptamer-functionalized AuNPs in contaminated milk samples. To realize the high stability and the lower limit of detection, the aptamer-functionalized surface of AuNPs via a coordinated bond was used in combination with ultra-sonication. The kinetics of this colorimetric assay based on aptamer-functionalized AuNPs was analyzed to illustrate that the higher the concentration of melamine, the faster the aggregation of AuNPs induced. The sensitivity, selectivity, limit of detection and recovery rate were sufficiently validated to understand the measurement principle of melamine using aptamer-functionalized AuNPs. The calibration curve established by the absorption peak ratio (A640 /A520) was linear in the concentration range of 0~1μM of melamine in aqueous solutions with the correlation coefficient (R²) of 0.986 and the limit of detection (LOD) of 22 nM, whereas, the correlation coefficient (R²) of 0.998 and the LOD of 14.9 nM were achieved at the concentration of melamine below 0.5 μM in milk samples. The optimized performance of this colorimetric assay of melamine using aptamer-functionalized AuNPs in milk samples was obtained with 100 μL of 13 nm AuNPs solution, 40 μL of 1 μM (100 dilutions) aptamers and the pre-reaction time of 30 min. This simple colorimetric measurement of melamine using aptamer-functionalized AuNPs provides a promising target for various applications of the sample source with complex sample matrices.

Optical assays based on colloidal inorganic nanoparticles

Colloidal inorganic nanoparticles have wide applications in the detection of analytes and in biological assays. A large number of these assays rely on the ability of gold nanoparticles (AuNPs, in the 20 nm diameter size range) to undergo a color change from red to blue upon aggregation. AuNP assays can be based on cross-linking, non-cross linking or unmodified charge-based aggregation. Nucleic acid-based probes, monoclonal antibodies, and molecular-affinity agents can be attached by covalent or non-covalent means. Surface plasmon resonance and SERS techniques can be utilized. Silver NPs also have attractive optical properties (higher extinction coefficient). Combinations of AuNPs and AgNPs in nanocomposites can have additional advantages. Magnetic NPs and ZnO, TiO2 and ZnS as well as insulator NPs including SiO2 can be employed in colorimetric assays, and some can act as peroxidase mimics in catalytic applications. This review covers the synthesis and stabilization of inorganic NPs and their diverse applications in colorimetric and optical assays for analytes related to environmental contamination (metal ions and pesticides), and for early diagnosis and monitoring of diseases, using medically important biomarkers.

Metal Nanoparticles for Diagnosis and Therapy of Bacterial Infection

Infectious diseases caused by pathogenic bacteria, especially multidrug-resistant bacteria, and their global spreading have become serious public health concerns. Early diagnosis and effective therapy can efficiently prevent deterioration and further spreading of the infections. There is an urgent need for sensitive, selective, and facile diagnosis as well as therapeutically potent treatment. The emergence of nanotechnology has provided more options for diagnosis and treatments of bacterial infections. Metal nanoparticles and metal oxide nanoparticles have drawn intense attention owing to their unique optical, magnetic, and electrical properties. These versatile metal-based nanoparticles have great potential for selective detection of bacteria and/or therapy. This review gives an overview of recent efforts on developing various metal-based nanoparticles for bacterial detection and infection therapy. It begins with an introduction of fundamental concepts and mechanisms in designing diagnostic and therapeutic strategies. Representative achievements are selected to illustrate the proof-of-concept in vitro and in vivo applications. A brief discussion of challenges and perspective outlook in this field is provided at the end of this review.

Seeded Growth Synthesis of Gold Nanotriangles: Size Control, SAXS Analysis, and SERS Performance

We studied the controlled growth of triangular prismatic Au nanoparticles with different beveled sides for surface-enhanced Raman spectroscopy (SERS) applications. First, in a seedless synthesis using 3-butenoic acid (3BA) and benzyldimethylammonium chloride (BDAC), gold nanotriangles (AuNTs) were synthesized in a mixture with gold nanooctahedra (AuNOCs) and separated by depletion-induced flocculation. Here, the influence of temperature, pH, and reducing agent on the reaction kinetics was initially investigated by UV-vis and correlated to the size and yield of AuNT seeds. In a second step, the AuNT size was increased by seed-mediated overgrowth with Au. We show for the first time that preformed 3BA-synthesized AuNT seeds can be overgrown up to a final edge length of 175 nm and a thickness of 80 nm while maintaining their triangular shape and tip sharpness. The NT morphology, including edge length, thickness, and tip rounding, was precisely characterized in dispersion by small-angle X-ray scattering and in dry state by transmission electron microscopy and field-emission scanning electron microscopy. For sensor purposes, we studied the size-dependent SERS performance of AuNTs yielding analytical enhancement factors between 0.9 × 10⁴ and 5.6 × 10⁴ and nanomolar limit of detection (10^-8-10^-9 M) for 4-mercaptobenzoic acid and BDAC. These results confirm that the 3BA approach allows the fabrication of AuNTs in a whole range of sizes maintaining the NT morphology. This enables tailoring of localized surface plasmon resonances between 590 and 740 nm, even in the near-infrared window of a biological tissue, for use as colloidal SERS sensing agents or for optoelectronic applications.

DNA-Assembled Advanced Plasmonic Architectures

The interaction between light and matter can be controlled efficiently by structuring materials at a length scale shorter than the wavelength of interest. With the goal to build optical devices that operate at the nanoscale, plasmonics has established itself as a discipline, where near-field effects of electromagnetic waves created in the vicinity of metallic surfaces can give rise to a variety of novel phenomena and fascinating applications. As research on plasmonics has emerged from the optics and solid-state communities, most laboratories employ top-down lithography to implement their nanophotonic designs. In this review, we discuss the recent, successful efforts of employing self-assembled DNA nanostructures as scaffolds for creating advanced plasmonic architectures. DNA self-assembly exploits the base-pairing specificity of nucleic acid sequences and allows for the nanometer-precise organization of organic molecules but also for the arrangement of inorganic particles in space. Bottom-up self-assembly thus bypasses many of the limitations of conventional fabrication methods. As a consequence, powerful tools such as DNA origami have pushed the boundaries of nanophotonics and new ways of thinking about plasmonic designs are on the rise.

Dithiothreitol-Regulated Coverage of Oligonucleotide-Modified Gold Nanoparticles To Achieve Optimized Biosensor Performance

DNA-modified gold nanoparticles (AuNPs) are useful signal-reporters for detecting diverse molecules through various hybridization- and enzyme-based assays. However, their performance is heavily dependent on the probe DNA surface coverage, which can influence both target binding and enzymatic processing of the bound probes. Current methods used to adjust the surface coverage of DNA-modified AuNPs require the production of multiple batches of AuNPs under different conditions, which is costly and laborious. We here develop a single-step assay utilizing dithiothreitol (DTT) to fine-tune the surface coverage of DNA-modified AuNPs. DTT is superior to the commonly used surface diluent, mercaptohexanol, as it is less volatile, allowing for the rapid and reproducible controlling of surface coverage on AuNPs with only micromolar concentrations of DTT. Upon adsorption, DTT forms a dense monolayer on gold surfaces, which provides antifouling capabilities. Furthermore, surface-bound DTT adopts a cyclic conformation, which reorients DNA probes into an upright position and provides ample space to promote DNA hybridization, aptamer assembly, and nuclease digestion. We demonstrate the effects of surface coverage on AuNP-based sensors using DTT-regulated DNA-modified AuNPs. We then use these AuNPs to visually detect DNA and cocaine in colorimetric assays based on enzyme-mediated AuNP aggregation. We determine that DTT-regulated AuNPs with lower surface coverage achieve shorter reaction times and lower detection limits relative to those for assays using untreated AuNPs or DTT-regulated AuNPs with high surface coverage. Additionally, we demonstrate that our DTT-regulated AuNPs can perform cocaine detection in 50% urine without any significant matrix effects. We believe that DTT regulation of surface coverage can be broadly employed for optimizing DNA-modified AuNP performance for use in biosensors as well as drug delivery and therapeutic applications.

Stable oligonucleotide-functionalized gold nanosensors for environmental biocontaminant monitoring

The global propagation of environmental biocontaminants such as antibiotic resistant pathogens and their antibiotic resistance genes (ARGs) is a public health concern that highlights the need for improved monitoring strategies. Here, we demonstrate the environmental stability and applicability of an oligonucleotide-functionalized gold nanosensor. The mecA ARG was targeted as model biocontaminant due to its presence in clinically-relevant pathogens and to its emergence as an environmental contaminant. mecA-specific nanosensors were tested for antibiotic resistance gene (ARG) detection in ARG-spiked effluent from four wastewater treatment plants (WWTPs). The mecA-specific nanosensors showed stability in environmental conditions and in high ionic strength ([MgCl₂]<50mM), and high selectivity against mismatched targets. Spectrophotometric detection was reproducible with an LOD of 70pM (≈4×10⁷genes/μL), even in the presence of interferences associated with non-target genomic DNA and complex WWTP effluent. This contribution supports the environmental applicability of a new line of cost-effective, field-deployable tools needed for wide-scale biocontaminant monitoring.

Tuning the Gold Nanoparticle Colorimetric Assay by Nanoparticle Size, Concentration, and Size Combinations for Oligonucleotide Detection

Gold nanoparticle (GNP)-based aggregation assay is simple, fast, and employs a colorimetric detection method. Although previous studies have reported using GNP-based colorimetric assay to detect biological and chemical targets, a mechanistic and quantitative understanding of the assay and effects of GNP parameters on the assay performance is lacking. In this work, we investigated this important aspect of the GNP aggregation assay including effects of GNP concentration and size on the assay performance to detect malarial DNA. Our findings lead us to propose three major competing factors that determine the final assay performance including the nanoparticle aggregation rate, plasmonic coupling strength, and background signal. First, increasing nanoparticle size reduces the Brownian motion and thus aggregation rate, but significantly increases plasmonic coupling strength. We found that larger GNP leads to stronger signal and improved limit of detection (LOD), suggesting a dominating effect of plasmonic coupling strength. Second, higher nanoparticle concentration increases the probability of nanoparticle interactions and thus aggregation rate, but also increases the background extinction signal. We observed that higher GNP concentration leads to stronger signal at high target concentrations due to higher aggregation rate. However, the fact the optimal LOD was found at intermediate GNP concentrations suggests a balance of two competing mechanisms between aggregation rate and signal/background ratio. In summary, our work provides new guidelines to design GNP aggregation-based POC devices to meet the signal and sensitivity needs for infectious disease diagnosis and other applications.

High-Performance Colorimetric Detection of Thiosulfate by Using Silver Nanoparticles for Smartphone-Based Analysis

Developing thiosulfate (S₂O₃^2-) sensors with silver nanoparticles (AgNPs) for analysis of aqueous solutions with the interference of other anions remains challenging. In this study, we propose a new strategy for excellent selective colorimetric detection of S₂O₃^2-. The nonmorphological transition of AgNPs leading to a color change from yellow to brown is verified by UV-vis, TEM, DLS, SEM, and XPS analyses. The sensor exhibits high sensitivity with detection limits of 1.0 μM by naked-eye determination and 0.2 μM by UV-vis spectroscopy analysis. The linear relationship (R² = 0.998) between the (A₀ - A)/A₀ values and S₂O₃^2- concentrations from 0.2 μM to 2.0 μM indicates that the fabricated AgNPs-based colorimetric sensor can be employed for quantitative assay of S₂O₃^2-. Colorimetric responses are also monitored using the built-in camera of a smartphone. The sensor shows a linear response to S₂O₃^2- in 0-20.0 μM solutions under the optimized conditions and is thus more suitable for rapid on-site tests than other detection methods. A smartphone application (app) is downloaded under Android or IOS platforms to measure the RGB (red, green, blue) values of the colorimetric sensor after exposure to the analyte. Following data processing, the RGB values are converted into concentration values by using preloaded calibration curves. Confirmatory analysis indicates that the proposed S₂O₃^2- colorimetric sensor exhibits feasibility and sensitivity for S₂O₃^2- detection in real environmental samples.

Food Quality Monitor: Paper-Based Plasmonic Sensors Prepared Through Reversal Nanoimprinting for Rapid Detection of Biogenic Amine Odorants

This paper describes the fabrication of paper-based plasmonic refractometric sensors through the embedding of metal nanoparticles (NPs) onto flexible papers using reversal nanoimprint lithography. The NP-embedded papers can serve as gas sensors for the detection of volatile biogenic amines (BAs) released from spoiled food. Commercial inkjet papers were employed as sensor substrates-their high reflectance (>80%) and smooth surfaces (roughness: ca. 4.9 nm) providing significant optical signals for reflection-mode plasmonic refractometric sensing and high particle transfer efficiency, respectively; in addition, because inkjet papers have lightweight and are burnable and flexible, they are especially suitable for developing portable, disposable, cost-effective, eco-friendly sensing platforms. Solid silver NPs (SNPs), solid gold NPs (GNPs), and hollow Au-Ag alloyed NPs (HGNs) were immobilized on a solid mold and then transferred directly onto the softened paper surfaces. The particle number density and exposure height of the embedded NPs were dependent on two imprinting parameters: applied pressure and temperature. The optimal samples exhibited high particle transfer efficiency (ca. 85%), a sufficient exposure surface area (ca. 50% of particle surface area) presented to the target molecules, and a strong resonance reflectance dip for detection. Moreover, the HGN-embedded paper displayed a significant wavelength dip shift upon the spontaneous adsorption of BA vapors (e.g., Δλ = 33 nm for putrescine; Δλ = 24 nm for spermidine), indicating high refractometric sensitivity; in contrast, no visible spectroscopic responses were observed with respect to other possibly coexisting gases (e.g., air, N₂, CO₂, water vapor) during the food storage process, indicating high selectivity. Finally, the plasmonic sensing papers were used to monitor the freshness of a food product (salmon).

Stimuli-Responsive Polymeric Nanoparticles

There is increasing evidence that stimuli-responsive nanomaterials have become significantly critical components of modern materials design and technological developments. Recent advances in synthesis and fabrication of stimuli-responsive polymeric nanoparticles with built-in stimuli-responsive components (Part A) and surface modifications of functional nanoparticles that facilitate responsiveness (Part B) are outlined here. The synthesis and construction of stimuli-responsive spherical, core-shell, concentric, hollow, Janus, gibbous/inverse gibbous, and cocklebur morphologies are discussed in Part A, with the focus on shape, color, or size changes resulting from external stimuli. Although inorganic/metallic nanoparticles exhibit many useful properties, including thermal or electrical conductivity, catalytic activity, or magnetic properties, their assemblies and formation of higher order constructs are often enhanced by surface modifications. Section B focuses on selected surface reactions that lead to responsiveness achieved by decorating nanoparticles with stimuli-responsive polymers. Although grafting-to and grafting-from dominate these synthetic efforts, there are opportunities for developing novel synthetic approaches facilitating controllable recognition, signaling, or sequential responses. Many nanotechnologies utilize a combination of organic and inorganic phases to produce ceramic or metallic nanoparticles. One can envision the development of new properties by combining inorganic (metals, metal oxides) and organic (polymer) phases into one nanoparticle designated as "ceramers" (inorganics) and "metamers" (metallic).

Chemisorption of iodine-125 to gold nanoparticles allows for real-time quantitation and potential use in nanomedicine

Gold nanoparticles have been available for many years as a research tool in the life sciences due to their electron density and optical properties. New applications are continually being developed, particularly in nanomedicine. One drawback is the need for an easy, real-time quantitation method for gold nanoparticles so that the effects observed in in vitro cell toxicity assays and cell uptake studies can be interpreted quantitatively in terms of nanoparticle loading. One potential method of quantifying gold nanoparticles in real time is by chemisorption of iodine-125, a gamma emitter, to the nanoparticles. This paper revisits the labelling of gold nanoparticles with iodine-125, first described 30 years ago and never fully exploited since. We explore the chemical properties and usefulness in quantifying bio-functionalised gold nanoparticle binding in a quick and simple manner. The gold particles were labelled specifically and quantitatively simply by mixing the two items. The nature of the labelling is chemisorption and is robust, remaining bound over several weeks in a variety of cell culture media. Chemisorption was confirmed as potassium iodide can remove the label whereas sodium chloride and many other buffers had no effect. Particles precoated in polymers or proteins can be labelled just as efficiently allowing for post-labelling experiments in situ rather than using radioactive gold atoms in the production process. We also demonstrate that interparticle exchange of I-125 between different size particles does not appear to take place confirming the affinity of the binding.

Tumor Microenvironment Modulation via Gold Nanoparticles Targeting Malicious Exosomes: Implications for Cancer Diagnostics and Therapy

Exosomes are nanovesicles formed in the endosomal pathway with an important role in paracrine and autocrine cell communication. Exosomes secreted by cancer cells, malicious exosomes, have important roles in tumor microenvironment maturation and cancer progression. The knowledge of the role of exosomes in tumorigenesis prompted a new era in cancer diagnostics and therapy, taking advantage of the use of circulating exosomes as tumor biomarkers due to their stability in body fluids and targeting malignant exosomes’ release and/or uptake to inhibit or delay tumor development. In recent years, nanotechnology has paved the way for the development of a plethora of new diagnostic and therapeutic platforms, fostering theranostics. The unique physical and chemical properties of gold nanoparticles (AuNPs) make them suitable vehicles to pursuit this goal. AuNPs’ properties such as ease of synthesis with the desired shape and size, high surface:volume ratio, and the possibility of engineering their surface as desired, potentiate AuNPs’ role in nanotheranostics, allowing the use of the same formulation for exosome detection and restraining the effect of malicious exosomes in cancer progression.

An ultrasensitive near-infrared satellite SERS sensor: DNA self-assembled gold nanorod/nanospheres structure

A gold nanorod/nanospheres structure assembled by DNA was used as an ultrasensitive near-infrared satellite SERS sensor.

Stacking modular DNA circuitry in cascading self-assembly of spherical nucleic acids

Integrated circuitries are successfully built through using the cascaded modular strategy with the assistance of stochastic simulations.

Plasmonic Metasurfaces Based on Nanopin-Cavity Resonator for Quantitative Colorimetric Ricin Sensing

In view of the toxic potential of a bioweapon threat, rapid visual recognition and sensing of ricin has been of considerable interest while remaining a challenging task up to date. In this study, a gold nanopin-based colorimetric sensor is developed realizing a multicolor variation for ricin qualitative recognition and analysis. It is revealed that such plasmonic metasurfaces based on nanopin-cavity resonator exhibit reflective color appearance, due to the excitation of standing-wave resonances of narrow bandwidth in visible region. This clear color variation is a consequence of the reflective color mixing defined by different resonant wavelengths. In addition, the colored metasurfaces appear sharp color difference in a narrow refractive index range, which makes them especially well-suited for sensing applications. Therefore, this antibody-functionalized nanopin-cavity biosensor features high sensitivity and fast response, allowing for visual quantitative ricin detection within the range of 10-120 ng mL^-1 (0.15 × 10^-9 -1.8 × 10^-9 m), a limit of detection of 10 ng mL^-1 , and the typical measurement time of less than 10 min. The on-chip integration of such nanopin metasurfaces to portable colorimetric microfluidic device may be envisaged for the quantitative studies of a variety of biochemical molecules.

Nanocomposite biosensors for point-of-care—evaluation of food quality and safety

Nanosensors have wide applications in the food industry. Nanosensors based on quantum dots for heavy metal and organophosphate pesticides detection, and nanocomposites as indicators for shelf life of fish/meat products, have served as important tools for food quality and safety assessment. Luminescent labels consisting of NPs conjugated to aptamers have been popular for rapid detection of infectious and foodborne pathogens. Various detection technologies, including microelectromechanical systems for gas analytes, microarrays for genetically modified foods, and label-free nanosensors using nanowires, microcantilevers, and resonators are being applied extensively in the food industry. An interesting aspect of nanosensors has also been in the development of the electronic nose and electronic tongue for assessing organoleptic qualities, such as, odor and taste of food products. Real-time monitoring of food products for rapid screening, counterfeiting, and tracking has boosted ingenious, intelligent, and innovative packaging of food products. This chapter will give an overview of the contribution of nanotechnology-based biosensors in the food industry, ongoing research, technology advancements, regulatory guidelines, future challenges, and industrial outlook.

Targeted Enlargement of Aptamer Functionalized Gold Nanoparticles for Quantitative Protein Analysis

The ability to selectively amplify the detection signals for targets over interferences is crucial when analyzing proteins in a complicated sample matrix. Here, we describe a targeted enlargement strategy that can amplify the light-scattering signal from aptamer-functionalized gold nanoparticles (Apt-AuNP) with high specificity for quantitative protein analysis. This strategy is achieved by labeling target proteins with competitively protected Apt-AuNP probes and enlarging the probes with gold enhancement. This competitive protection strategy could effectively eliminate nonspecific protein adsorptions from a sample matrix, leading to a highly specific labeling of the target protein. As a result, the subsequent amplification of the light-scattering signal by gold enhancement only occurs in the presence of the target protein. This strategy was successfully demonstrated by analyzing human α-thrombin in human serum samples in a Western blot format.

Light-scattering Characteristics of Metal Nanoparticles on a Single Bacterial Cell

Metal nanoparticles express unique light-scattering characteristics based on the localized surface plasmon resonance, which depends on the metal species, particle size, and aggregation state of the nanoparticles. Therefore, we focused on the light-scattering characteristics of metal nanoparticles, such as silver, gold, and copper oxide, adsorbed on a bacterium. Monodisperse silver nanoparticles expressed the strongest scattered light among them, and showed various colors of scattered light. Although a monodisperse gold nanoparticle produced monochromatic light (green color), the color of the scattered light strongly depended on the aggregation state of the nanoparticles on a bacterium. On the other hand, copper oxide nanoparticles expressed monochromatic light (blue color), regardless of their aggregation states on a bacterium. We examined details concerning the light-scattering characteristics of metal nanoparticles, and discussed the possibility of their applications to bacterial cell imaging.

Proximity ligation-induced assembly of DNAzymes for simple and cost-effective colourimetric detection of proteins with high sensitivity

A novel colourimetric method for protein assays is proposed based on proximity ligation induced assembly of Mg(2+)-dependent DNAzymes, which may offer simple, cost-effective, sensitive and selective detection of the target protein.

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.

Advances in nanomaterials and their applications in point of care (POC) devices for the diagnosis of infectious diseases

Nanotechnology has gained much attention over the last decades, as it offers unique opportunities for the advancement of the next generation of sensing tools. Point-of-care (POC) devices for the selective detection of biomolecules using engineered nanoparticles have become a main research thrust in the diagnostic field. This review presents an overview on how the POC-associated nanotechnology, currently applied for the identification of nucleic acids, proteins and antibodies, might be further exploited for the detection of infectious pathogens: although still premature, future integrations of nanoparticles with biological markers that target specific microorganisms will enable timely therapeutic intervention against life-threatening infectious diseases.

Exploiting Surface-Plasmon-Enhanced Light Scattering for the Design of Ultrasensitive Biosensing Modality

Development of new detection methodologies and amplification schemes is indispensable for plasmonic biosensors to improve the sensitivity for the detection of trace amounts of analytes. Herein, an ultrasensitive scheme for signal enhancement based on the concept of surface-plasmon-resonance-enhanced light scattering (SP-LS) was validated experimentally and theoretically. The SP-LS of gold nanoparticles' (AuNPs) tags was employed in a sandwich assay for the detection of cardiac troponin I and provided up to 2 orders of magnitude improved sensitivity over conventional AuNPs-enhanced refractometric measurements and 3 orders of magnitude improvement over label-free SPR. Simulations were also performed to provide insights into the physical mechanisms.

In-Gene Quantification of O(6)-Methylguanine with Elongated Nucleoside Analogues on Gold Nanoprobes

Exposure of DNA to chemicals can result in the formation of DNA adducts, a molecular initiating event in genotoxin-induced carcinogenesis. O(6)-Methylguanine (O(6)-MeG) is a highly mutagenic DNA adduct that forms in human genomic DNA upon reaction with methylating agents of dietary, environmental, or endogenous origin. In this work, we report the design and synthesis of novel non-natural nucleoside analogues 1'-β-[1-naphtho[2,3-d]imidazol-2(3H)-one)]-2'-deoxy-d-ribofuranose and 1'-β-[1-naphtho[2,3-d]imidazole]-2'-deoxy-d-ribofuranose and their use for quantifying O(6)-MeG within mutational hotspots of the human KRAS gene. The novel nucleoside analogues were incorporated into oligonucleotides conjugated to gold nanoparticles to comprise a DNA hybridization probe system for detecting O(6)-MeG in a sequence-specific manner on the basis of colorimetric readout of the nanoparticles. The concept described herein is unique in utilizing new nucleoside analogues with elongated hydrophobic surfaces to successfully measure in-gene abundance of O(6)-MeG in mixtures with competing unmodified DNA.

Single-stranded DNA detection by solvent-induced assemblies of a metallo-peptide-based complex

DNA detection is highly important for the sensitive sensing of different pathogenic bacteria and viruses. The major challenge is to create a sensor that can selectively detect very small concentrations of DNA without the need for amplification or complicated equipment. Different technologies such as optical, electrochemical and microgravimetric approaches can detect DNA fragments. Here we show, for the first time, the use of self-assembled nanostructures generated by a metallo-peptide as an optical sensing platform for DNA detection. The system can selectively detect single stranded DNA fragments by fluorescence measurements as it can discriminate even one base mismatch and can perform in the presence of other interfering proteins. This system may be useful in lab-on-a-chip applications.

Oriented assembly of invisible probes: towards single mRNA imaging in living cells

Due to the complexity of biological systems and the ultralow concentration of analytes, improving the signal-to-noise ratio and lowering the limit of detection to allow highly sensitive detection is key to biomolecule analysis, especially intracellular analysis. Here, we present a method for highly sensitive imaging of mRNA in living cells by using novel invisible oriented probes to construct a turn-on signal generation mechanism from zero background. Two DNA probes (S1 and S2) are asymmetrically modified on two small gold nanoparticles (AuNPs) with a diameter of 20 nm. The hybridization of the two DNA probes with a single target mRNA leads to the formation of an AuNP dimer which shows a prominent plasmonic coupling effect. It generates a strong scattering signal from zero-background under a dark-field spectral analysis system. The unique design of the oriented assembly dimer has the ability to easily discriminate the target signal from the inherent cellular background noise in intracellular detection, thus making this approach a valuable technique for imaging single survivin mRNA and monitoring the distribution of survivin mRNA in tumor cells.

Optical extinction and scattering cross sections of plasmonic nanoparticle dimers in aqueous suspension

Absolute extinction and scattering cross sections for gold nanoparticle dimers were determined experimentally using a chemometric approach involving singular-value decomposition of the extinction and scattering spectra of slowly aggregating gold nanospheres in aqueous suspension. Quantitative spectroscopic data on plasmonic nanoparticle assemblies in liquid suspension are rare, in particular for particles larger than 40 nm, and in this work we demonstrate how such data can be obtained directly from the aggregating suspension. Our method can analyse, non invasively, the evolution of several sub-populations of nanoparticle assemblies. It may be applied to other self-assembling nanoparticle systems with an evolving optical response. The colloidal systems studied here are based on 20, 50 and 80 nm gold nanospheres in aqueous solutions containing sodium lipoate. In these systems, the reversible dimerisation process can be controlled using pH and ionic strength, and this control is rationalised in terms of DLVO theory. The dimers were identified in suspension by their translational and rotational diffusion through scattering correlation spectroscopy. Moreover, their gigadalton molecular weight was measured using electrospray charge-detection mass spectrometry, demonstrating that mass spectrometry can be used to study nanoparticles assemblies of very high molecular mass. The extinction and scattering cross sections calculated in the discrete-dipole approximation (DDA) agree very well with those obtained experimentally using our approach.

Synthesis of vinyl-terminated Au nanoprisms and nanooctahedra mediated by 3-butenoic acid: direct Au@pNIPAM fabrication with improved SERS capabilities

Here we describe the first seedless synthesis of vinyl-terminated Au nanotriangular prisms (AuNTPs) and nanooctahedra (AuNOC) in aqueous media. This synthesis is performed by chemical reduction of chloroauric acid (HAuCl4) with 3-butenoic acid (3BA) in the presence of benzyldimethylammonium chloride (BDAC). The principal novelties of the presented method are the use of a mixture of 3BA and BDAC, the synthesis of gold prisms and octahedra with controllable size, and the presence of terminal double bonds on the metal surface. Initially this method produces a mixture of triangular gold nanoprisms and octahedra; however, both morphologies are successfully separated by surfactant micelle induced depletion interaction, reaching percentages up to ∼90%. Moreover, the alkene moieties present on the gold surface are exploited for the fabrication of hybrid core@shell particles. Gold octahedra and triangular prisms are easily encapsulated by free radical polymerization of N-isopropylacrylamide (NIPAM). Finally, in order to obtain a gold core with the most number of tips, AuNTP@pNIPAM microgels were subjected to gold core overgrowth, thus resulting in star-shaped nanoparticles (AuSTs@pNIPAM). We use 4-amino-benzenethiol as the model analyte for SERS investigations. As expected, gold cores with tips and high curvature sites produced the highest plasmonic responses.

Droplet Digital Enzyme-Linked Oligonucleotide Hybridization Assay for Absolute RNA Quantification

We present a continuous-flow droplet-based digital Enzyme-Linked Oligonucleotide Hybridization Assay (droplet digital ELOHA) for sensitive detection and absolute quantification of RNA molecules. Droplet digital ELOHA incorporates direct hybridization and single enzyme reaction via the formation of single probe-RNA-probe (enzyme) complex on magnetic beads. It enables RNA detection without reverse transcription and PCR amplification processes. The magnetic beads are subsequently encapsulated into a large number of picoliter-sized droplets with enzyme substrates in a continuous-flow device. This device is capable of generating droplets at high-throughput. It also integrates in-line enzymatic incubation and detection of fluorescent products. Our droplet digital ELOHA is able to accurately quantify (differentiate 40% difference) as few as ~600 RNA molecules in a 1 mL sample (equivalent to 1 aM or lower) without molecular replication. The absolute quantification ability of droplet digital ELOHA is demonstrated with the analysis of clinical Neisseria gonorrhoeae 16S rRNA to show its potential value in real complex samples.

Gold Nanoparticles for DNA/RNA-Based Diagnostics

The remarkable physicochemical properties of gold nanoparticles (AuNPs) have prompted development in exploring biomolecular interactions with AuNPs-containing systems, pursuing biomedical applications in diagnostics. Among these applications, AuNPs have been remarkably useful for the development of DNA/RNA detection and characterization systems for diagnostics, including systems suitable for point of need. Here, emphasis will be on available molecular detection schemes of relevant pathogens and their molecular characterization, genomic sequences associated with medical conditions (including cancer), mutation and polymorphism identification, and the quantification of gene expression.

Femtomolar oligonucleotide detection by a one-step gold nanoparticle-based assay

A sequence-specific oligonucleotide detection method based on the tail-to-tail aggregation of functionalized gold nanoparticles in the presence of target analytes is presented together with its optimization and capabilities for detection of single nucleotide polymorphisms (SNPs). In this single-step method, capture probes are freely accessible for hybridization, resulting in an improved assay performance compared to substrate-based assays. The analytes bring the nanoparticles close to each other via hybridization, causing a red shift of the nanoparticle plasmon peak detected by a spectrophotometer or CCD camera coupled to a darkfield imaging system. Optimal conditions for the assay were found to be (i) use of capture probes complementary to the target without any gap, (ii) maximum possible probe density on the gold nanoparticles, and (iii) 1M ionic strength buffer. The optimized assay has a 1 fM limit of detection and fM to 10 pM dynamic range, with detection of perfect match sequences being three orders of magnitude more sensitive than targets with single nucleotide mismatches.