Gold nanoparticle aggregation for quantification of oligonucleotides: optimization and increased dynamic range

Employing conductive porous hydrogen-bonded organic framework for ultrasensitive detection of peanut allergen Ara h1

Peanut allergy has garnered worldwide attention due to its high incidence rate and severe symptoms, stimulating the demand for the ultrasensitive detection method of peanut allergen. Herein, we successfully developed a novel electrochemical aptasensor for ultrasensitive detection Ara h1, a major allergenic protein present in peanuts. A conductive nickel atoms Anchored Hydrogen-Bonded Organic Frameworks (PFC-73-Ni) were utilized as excellent electrocatalysts toward hydroquinone (HQ) oxidation to generate a readable current signal. The developed electrochemical aptasensor offers wide linear range (1-120 nM) and low detection limit (0.26 nM) for Ara h1. This method demonstrated a recovery rate ranging from 95.00% to 107.42% in standard addition detection of non-peanut food samples. Additionally, the developed electrochemical method was validated with actual samples and demonstrated good consistency with the results obtained from a commercial ELISA kit. This indicates that the established Ara h1 detection method is a promising tool for peanut allergy prevention.

Plasmonic Probing of Deoxyribonucleic Acid Hybridization at the Single Base Pair Resolution

Partial DNA duplex formation greatly impacts the quality of DNA hybridization and has been extensively studied due to its significance in many biological processes. However, traditional DNA sensing methods suffer from time-consuming amplification steps and hinder the acquisition of information about single-molecule behavior. In this work, we developed a plasmonic method to probe the hybridization process at a single base pair resolution and study the relationship between the complementarity of DNA analytes and DNA hybridization behaviors. We measured single-molecule hybridization events with Au NP-modified ssDNA probes in real time and found two hybridization adsorption events: stable and transient adsorption. The ratio of these two hybridization adsorption events was correlated with the length of the complementary sequences, distinguishing DNA analytes from different complementary sequences. By using dual incident angle excitation, we recognized different single-base complementary sequences. These results demonstrated that the plasmonic method can be applied to study partial DNA hybridization behavior and has the potential to be incorporated into the identification of similar DNA sequences, providing a sensitive and quantitative tool for DNA analysis.

Highly Selective, Single-Tube Colorimetric Assay for Detection of Multiple Mutations in the Epidermal Growth Factor Receptor Gene

Many closed-tube methods are designed to detect DNA biomarkers. However, the utility of biomarkers such as a DNA mutation related to personalized medicine is limited as the operation of expensive detection instruments requires well-trained technicians. Therefore, we developed a simple and cheap colorimetric assay based on aggregation of silica-gold nanoparticle-modified probes, with linking probes, to detect mutations. This method consists of target amplification, sequence identification, and aggregation of the silica-gold nanoparticle-modified probes. All reactions are controlled by one individual and proceed sequentially, in a single tube, with no manual intervention. Approximately 10 copies of target DNA were detected with this assay, using 12 hot-spot mutations in exon 19 of EGFR gene as the example. In artificial samples, 0.1% mutant DNA can be distinguished from wild-type genomic DNA. The technology was tested on 104 clinical samples, which included 29 samples that were positive for an exon 19 deletion. The data were consistent with amplification refractory mutation system PCR, with the exception of one weakly positive sample, which was confirmed to be positive by digital PCR. The limit of detection of this colorimetric assay was verified to be better than that of amplification refractory mutation system PCR, and it provides a tool to discriminate multiple mutations in EGFR gene in clinical samples.

A universal design of turn-on fluorescent aptasensor based on luminescent MOFs: Application for the detection of bisphenol A in water, milk and chicken samples

A universal design of turn-on fluorescent aptasensor based on aptamer functionalized gold nanoparticles (AuNPs) and luminescent metal-organic frameworks (LMOFs) complex (AuNPs-Apt/NH₂-MIL-125(Ti)) was realized for bisphenol A (BPA) detection. LMOF NH₂-MIL-125(Ti) was prepared using facial hydrothermal method. BPA aptamer functionalized AuNPs were prepared and adsorbed on the surface of NH₂-MIL-125(Ti) to obtain platform of the fluorescent aptasensor. The fabrication process, sensing performance and applicability of the proposed aptasensor were characterized and investigated carefully. Linear detection range of the constructed aptasensor was from 1 × 10^-9 mol L^-1 to 1 × 10^-4 mol L^-1 with good selectivity, repeatability, stability and reproducibility under optimal experimental conditions. Meanwhile, the fluorescent aptasensor was successfully utilized for BPA detection in real samples with the recoveries of 95.80%-103.12%. The proposed aptasensor based on AuNPs-Apt/NH₂-MIL-125(Ti) holds significant potential for BPA detection in environmental and food samples, promoting the construction and application of LMOFs-based aptasensor.

Highly Sensitive Aptasensor for Detecting Cancerous Exosomes Based on Clover-like Gold Nanoclusters

Exosome-based liquid biopsy technologies play an increasingly prominent role in tumor diagnosis. However, the simple and sensitive method for counting exosomes still faces considerable challenges. In this work, the CD63 aptamer-modified DNA tetrahedrons on the gold electrode were used as recognition elements for the specific capture of exosomes. Partially complementary DNA probes act as bridges linking trapped exosomes and three AuNP-DNA signal probes. This clover-like structure can tackle the recognition and sensitivity issues arising from the undesired AuNP aggregation event. When cancerous exosomes are present in the system, the high accumulation of methylene blue molecules from DNA-AuNP nanocomposites on the surface of the electrode leads to an intense current signal. According to the results, the aptasensor responds to MCF-7 cell-derived exosomes in the concentration range from 1.0 × 10³ to 1.0 × 10⁸ particles·μL^-1, with the detection limit of 158 particles·μL^-1. Furthermore, the aptasensor has been extended to serum samples from breast cancer patients and exhibited excellent specificity. To sum it up, the aptasensor is sensitive, straightforward, less expensive, and fully capable of receiving widespread application in clinics for tumor monitoring.

An optical aptasensor for real-time quantification of endotoxin: From ensemble to single-molecule resolution

Endotoxin is a deadly pyrogen, rendering it crucial to monitor with high accuracy and efficiency. However, current endotoxin detection relies on multistep processes that are labor-intensive, time-consuming, and unsustainable. Here, we report an aptamer-based biosensor for the real-time optical detection of endotoxin. The endotoxin sensor exploits the distance-dependent scattering of gold nanoparticles (AuNPs) coupled to a gold nanofilm. This is enabled by the conformational changes of an endotoxin-specific aptamer upon target binding. The sensor can be used in an ensemble mode and single-particle mode under dark-field illumination. In the ensemble mode, the sensor is coupled with a microspectrometer and exhibits high specificity, reliability (i.e., linear concentration to signal profile in logarithmic scale), and reusability for repeated endotoxin measurements. Individual endotoxins can be detected by monitoring the color of single AuNPs via a color camera, achieving single-molecule resolution. This platform can potentially advance endotoxin detection to safeguard medical, food, and pharmaceutical products.

Nanomaterial and interface advances in immunoassay biosensors

Biosensors have been used for a remarkable array of applications, including infectious diseases, environmental monitoring, cancer diagnosis, food safety, and numerous others. In particular, the global COVID-19 pandemic has exposed a need for rapid tests, so the type of biosensor that has gained considerable interest recently are immunoassays, which are used for rapid diagnostics. The performance of paper-based lateral flow and dipstick immunoassays is influenced by the physical properties of the nanoparticles (NPs), NP-antibody conjugates, and paper substrate. Many materials innovations have enhanced diagnostics by increasing sensitivity or enabling unique readouts. However, negative side effects can arise at the interface between the biological sample and biomolecules and the NP or paper substrate, such as non-specific adsorption and protein denaturation. In this Perspective, we discuss the immunoassay components and highlight chemistry and materials innovations that can improve sensitivity. We also explore the range of bio-interface issues that can present challenges for immunoassays.

Functional-Group Effect of Ligand Molecules on the Aggregation of Gold Nanoparticles: A Molecular Dynamics Simulation Study

In this paper, atomistic molecular dynamics simulations are performed for the systems consisting of functionalized gold nanoparticles (NPs) in a toluene medium. Gold NPs are coated with ligand molecules that have different terminal groups, that is, polar carboxyl (COOH), hydroxyl (OH), amine (NH₂), and nonpolar methyl (CH₃). These functional groups are selected to understand the relation between the aggregation behavior of functionalized gold NPs in toluene and the polarity of terminal groups of ligand molecules. The center-of-mass distances between NP pairs, the radial distribution functions, the mean square displacements, the radius of gyration, and the number of hydrogen bonds (H-bond) between ligand molecules are computed. Our simulation results indicate that functionalized gold NPs exhibit different aggregation/dispersion behaviors depending upon the terminal group of ligands.

Rapid Detection of Neisseria gonorrhoeae Genomic DNA Using Gold Nanoprobes Which Target the Gonococcal DNA Uptake Sequence

The rapid spread of antimicrobial resistant Neisseria gonorrhoeae continues to pose a serious threat to global health. To successfully treat and control gonococcal infections, rapid diagnosis is critical. Currently, nucleic acid amplification tests are the recommended diagnostic, however, these are both technically demanding and time consuming, making them unsuitable for resource-poor clinics. Consequently, there is a substantial need for an affordable, point-of-care diagnostic to use in these settings. In this study, DNA-functionalised gold nanoparticles (gold nanoprobes), with the ability to specifically detect the DNA Uptake Sequence (DUS) of Neisseria gonorrhoeae, were prepared. Using complementary annealing, the gold nanoprobes were shown to hybridise to genomic gonococcal DNA, causing a significant shift in their salt stability. By exploiting the shift in nanoprobe stability under the presence of target DNA, a solution-based colorimetric diagnostic for gonococcal DNA was prepared. Detection of purified genomic DNA was achieved in under 30 minutes, with a detection limit of 15.0 ng. Significantly, testing with DNA extracted from an off-target control organism suggested specificity for Neisseria. These results highlight the potential of DUS-specific gold nanoprobes in the rapid point-of-care diagnosis of gonococcal infections.

Gold nanoparticle-based optical nanosensors for food and health safety monitoring: recent advances and future perspectives

Modern society has been facing serious health-related problems including food safety, diseases and illness. Hence, it is urgent to develop analysis methods for the detection and control of food contaminants, disease biomarkers and pathogens. As the traditional instrumental methods have several disadvantages, including being time consuming, and having high cost and laborious procedures, optical nanosensors have emerged as promising alternative or complementary approaches to those traditional ones. With the advantages of simple preparation, high surface-to-volume ratio, excellent biocompatibility, and especially, unique optical properties, gold nanoparticles (AuNPs) have been demonstrated as excellent transducers for optical sensing systems. Herein, we provide an overview of the synthesis of AuNPs and their excellent optical properties that are ideal for the development of optical nanosensors based on local surface plasmon resonance (LSPR), colorimetry, fluorescence resonance energy transfer (FRET), and surface-enhanced Raman scattering (SERS) phenomena. We also review the sensing strategies and their mechanisms, as well as summarizing the recent advances in the monitoring of food contaminants, disease biomarkers and pathogens using developed AuNP-based optical nanosensors in the past seven years (2015-now). Furthermore, trends and challenges in the application of these nanosensors in the determination of those analytes are discussed to suggest possible directions for future developments.

Experimental Study on the Compatibility and Characteristics of a Dual-Target Microbubble Loaded with Anti-miR-33

Objective

To prepare a new type of dual-target microbubble loaded with anti-miR-33 (ANM33).

Methods

Carrier core nanobubbles (NBs) were prepared by thin film hydration, and microbubbles loaded with PM1 (PCNBs) were prepared by grafting DSPE-PEG2000-maleimide-PM1 onto the NB surface. ANM33 was connected via electrostatic adsorption and covalent bonding, and hyaluronic acid (HA) was covalently connected. PM1 and HA were the targets, and ANM33 was the intervention drug. To evaluate the general physical and chemical properties of the prepared dual-target microbubbles loaded with ANM33 (HA-PANBs), we observed their morphology, particle size and surface potential while monitoring their stability and in vitro imaging ability, evaluated their toxic effect on cells and verified their ability to target cells.

Results

HA-PANBs had a regular morphology and good stability. The average particle size measured by a Malvern potentiometer was 1421.75±163.23 nm, and the average surface potential was −5.51±1.87 mV. PM1 and ANM33 were effectively connected to the NBs. The PM1, ANM33, and HA binding reached 89.0±1.1%, 65.02±5.0%, and 61.4±3.5%, respectively, and the maximum binding reached 2 µg, 5 µg, and 7 µg/10⁸ microbubbles, respectively. HA-PANBs had no obvious toxic effects on cells, and their ability to continuously enhance imaging in vitro persisted for more than 15 minutes, obviously targeting foam cells in the early stage of AS.

Conclusion

HA-PANBs are ideal ultrasound contrast agents. The successful, firm connection of PM1 and HA to the NBs significantly increased the amount of carried ANM33. When microbubbles prepared with 2:4:7 PM1:ANM33:HA were used as a contrast agent, they had a high ANM33 carrying capacity, stable physical properties, and significantly enhanced imaging and targeting of foam cells in the early stage of AS.

Multi-Functionalized Nanomaterials and Nanoparticles for Diagnosis and Treatment of Retinoblastoma

Retinoblastoma is a rare type of cancer, and its treatment, as well as diagnosis, is challenging, owing to mutations in the tumor-suppressor genes and lack of targeted, efficient, cost-effective therapy, exhibiting a significant need for novel approaches to address these concerns. For this purpose, nanotechnology has revolutionized the field of medicine with versatile potential capabilities for both the diagnosis, as well as the treatment, of retinoblastoma via the targeted and controlled delivery of anticancer drugs via binding to the overexpressed retinoblastoma gene. Nanotechnology has also generated massive advancements in the treatment of retinoblastoma based on the use of surface-tailored multi-functionalized nanocarriers; overexpressed receptor-based nanocarriers ligands (folate, galactose, and hyaluronic acid); lipid-based nanocarriers; and metallic nanocarriers. These nanocarriers seem to benchmark in mitigating a plethora of malignant retinoblastoma via targeted delivery at a specified site, resulting in programmed apoptosis in cancer cells. The effectiveness of these nanoplatforms in diagnosing and treating intraocular cancers such as retinoblastoma has not been properly discussed, despite the increasing significance of nanomedicine in cancer management. This article reviewed the recent milestones and future development areas in the field of intraocular drug delivery and diagnostic platforms focused on nanotechnology.

Plasmonic Nanoparticles: Basics to Applications (I)

This review presents the main characteristics of metal nanoparticles (NPs), especially consisting of noble metal such as Au and Ag, and brief information on their synthesis methods. The physical and chemical properties of the metal NPs are described, with a particular focus on the optically variable properties (surface plasmon resonance based properties) and surface-enhanced Raman scattering of plasmonic materials. In addition, this chapter covers ways to achieve advances by utilizing their properties in the biological studies and medical fields (such as imaging, diagnostics, and therapeutics). These descriptions will help researchers new to nanomaterials for biomedical diagnosis to understand easily the related knowledge and also will help researchers involved in the biomedical field to learn about the latest research trends.

Colorimetric-based detection of Ureaplasma urealyticum using gold nanoparticles

Ureaplasma urealyticum (uu) is one of the most common agents of urogenital infections and is associated with complications such as infertility, spontaneous abortion and other sexually transmitted diseases. Here, a DNA sensor based on oligonucleotide target-specific gold nanoparticles (AuNPs) was developed, in which the dispersed and aggregated states of oligonucleotide-functionalised AuNPs were optimised for the colorimetric detection of a polymerase chain reaction (PCR) amplicon of U. urealyticum DNA. A non-cross-linking approach utilising a single Au-nanoprobe specific of the urease gene was utilised and the effect of a PCR product concentration gradient evaluated. Results from both visual and spectral analyses showed that target-Au-nanoprobe hybrids were stable against aggregation after adding the inducer. Furthermore, when a non-target PCR product was used, the peak position shifted and salt-induced aggregation occurred. The assay's limit of detection of the assay was 10 ng with a dynamic range of 10-60 ng. This procedure provides a rapid, facile and low-cost detection format, compared to methods currently used for the identification of U. urealyticum.

Dark-Field Microwells toward High-Throughput Direct miRNA Sensing with Gold Nanoparticles

MicroRNA (miRNA) is a class of short RNA that is emerging as an ideal biomarker, as its expression level has been found to correlate with different types of diseases including diabetes and cancer. The detection of miRNA is highly beneficial for early diagnostics and disease monitoring. However, miRNA sensing remains difficult because of its small size and low expression levels. Common techniques such as quantitative real-time polymerase chain reaction (qRT-PCR), in situ hybridization and Northern blotting have been developed to quantify miRNA in a given sample. Nevertheless, these methods face common challenges in point-of-care practice as they either require complicated sample handling and expensive equipment, or suffer from low sensitivity. Here we present a new tool based on dark-field microwells to overcome these challenges in miRNA sensing. This miniaturized device enables the readout of a gold nanoparticle assay without the need of a dark-field microscope. We demonstrate the feasibility of the dark-field microwells to detect miRNA in both buffer solution and cell lysate. The dark-field microwells allow affordable miRNA sensing at a high throughput which make them a promising tool for point-of-care diagnostics.

Uranium (VI) detection in groundwater using a gold nanoparticle/paper-based lateral flow device

The contamination in groundwater due to the presence of uranium is nowadays a subject of concern due to the severe health problems associated with renal failure, genotoxicity and cancer. The standard methods to detect uranium require time-consuming processes and expensive non-portable equipment, so these measurements are rarely performed in-field, which increases the time until water samples are analysed. Furthermore, the few portable methods available do not allow quantitative analysis and the detection limit is often not low enough to reach the recommendations for drinking water (30 ppb or 126 nM of uranium). For the first time, we propose a portable, fast, inexpensive and sensitive paper-based biosensor able to detect in situ U(VI) in water samples: U(VI) selective gold nanoparticle-based lateral flow strips. Antibody-coated gold nanoparticles are used as labels in the proposed lateral flow system because of their biocompatibility; in addition, these nanoparticles provide high sensitivity due to their intense plasmonic effect. The antibody used in the assay recognizes soluble U(VI) complexed to the chelator, 2,9-dicarboxyl-1,10-phenanthroline (DCP). Because of the small size of the U(VI)-DCP complex, this assay employs a competitive format that reaches a limit of detection of 36.38 nM, lower than the action level (126 nM) established by the World Health Organization and the U.S. Environmental Protection Agency for drinking waters.

Cross-linking gold nanoparticles aggregation method based on localised surface plasmon resonance for quantitative detection of miR-155

MiR-155 plays a critical role in the formation of cancers and other diseases. In this study, the authors aimed to design and fabricate a biosensor based on cross-linking gold nanoparticles (AuNPs) aggregation for the detection and quantification of miR-155. Also, they intended to compare this method with SYBR Green real-time polymerase chain reaction (PCR). Primers for real-time PCR, and two thiolated capture probes for biosensor, complementary with miR-155, were designed. Citrate capped AuNPs (18.7 ± 3.6 nm) were synthesised and thiolated capture probes immobilised to AuNPs. The various concentrations of synthetic miR-155 were measured by this biosensor and real-time PCR method. Colorimetric changes were studied, and the calibration curves were plotted. Results showed the detection limit of 10 nM for the fabricated biosensor and real-time PCR. Also, eye detection using colour showed the weaker detection limit (1 µM), for this biosensor. MiR-133b as the non-complementary target could not cause a change in both colour and UV-visible spectrum. The increase in hydrodynamic diameter and negative zeta potential of AuNPs after the addition of probes verified the biosensor accurately fabricated. This fabricated biosensor could detect miR-155 simpler and faster than previous methods.

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.

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.

Multicolored silver nanoparticles for multiplexed disease diagnostics: distinguishing dengue, yellow fever, and Ebola viruses

Rapid point-of-care (POC) diagnostic devices are needed for field-forward screening of severe acute systemic febrile illnesses. Multiplexed rapid lateral flow diagnostics have the potential to distinguish among multiple pathogens, thereby facilitating diagnosis and improving patient care. Here, we present a platform for multiplexed pathogen detection using multi-colored silver nanoplates. This design requires no external excitation source and permits multiplexed analysis in a single channel, facilitating integration and manufacturing.

Understanding aggregation-based assays: nature of protein corona and number of epitopes on antigen matters

In this study, we systematically examine how the nature of the protein corona on NPs, formed from either antibody or antigen, and how the number of binding sites or epitopes on the antigen affect aggregation.

Gold-nanoparticle-based colorimetric discrimination of cancer-related point mutations with picomolar sensitivity

Point mutations in the Kirsten rat sarcoma viral oncogene homologue (KRAS) gene are being increasingly recognized as important diagnostic and prognostic markers in cancer. In this work, we describe a rapid and low-cost method for the naked-eye detection of cancer-related point mutations in KRAS based on gold nanoparticles. This simple colorimetric assay is sensitive (limit of detection in the low picomolar range), instrument-free, and employs nonstringent room temperature conditions due to a combination of DNA-conjugated gold nanoparticles, a probe design which exploits cooperative hybridization for increased binding affinity, and signal enhancement on the surface of magnetic beads. Additionally, the scheme is suitable for point-of-care applications, as it combines naked-eye detection, small sample volumes, and isothermal (PCR-free) amplification.

Nanoparticles in the ocular drug delivery

Ocular drug transport barriers pose a challenge for drug delivery comprising the ocular surface epithelium, the tear film and internal barriers of the blood-aqueous and blood-retina barriers. Ocular drug delivery efficiency depends on the barriers and the clearance from the choroidal, conjunctival vessels and lymphatic. Traditional drug administration reduces the clinical efficacy especially for poor water soluble molecules and for the posterior segment of the eye. Nanoparticles (NPs) have been designed to overcome the barriers, increase the drug penetration at the target site and prolong the drug levels by few internals of drug administrations in lower doses without any toxicity compared to the conventional eye drops. With the aid of high specificity and multifunctionality, DNA NPs can be resulted in higher transfection efficiency for gene therapy. NPs could target at cornea, retina and choroid by surficial applications and intravitreal injection. This review is concerned with recent findings and applications of NPs drug delivery systems for the treatment of different eye diseases.