Label-free colorimetric aptasensor for IgE using DNA pseudoknot probe

Aptamers and Nanobodies as New Bioprobes for SARS-CoV-2 Diagnostic and Therapeutic System Applications

The global challenges posed by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) pandemic have underscored the critical importance of innovative and efficient control systems for addressing future pandemics. The most effective way to control the pandemic is to rapidly suppress the spread of the virus through early detection using a rapid, accurate, and easy-to-use diagnostic platform. In biosensors that use bioprobes, the binding affinity of molecular recognition elements (MREs) is the primary factor determining the dynamic range of the sensing platform. Furthermore, the sensitivity relies mainly on bioprobe quality with sufficient functionality. This comprehensive review investigates aptamers and nanobodies recently developed as advanced MREs for SARS-CoV-2 diagnostic and therapeutic applications. These bioprobes might be integrated into organic bioelectronic materials and devices, with promising enhanced sensitivity and specificity. This review offers valuable insights into advancing biosensing technologies for infectious disease diagnosis and treatment using aptamers and nanobodies as new bioprobes.

A label-free aptamer-based colorimetric biosensor for rapid gliadin detection in foods: a focus on pasta, bread and cookies

Despite numerous advancements in gluten detection, a substantial need remains for innovative, cost-effective, in situ methods that can be employed without complex analytical instruments. Addressing this demand, this study introduces a pioneering label-free colorimetric biosensor for the in situ detection of gliadin, a major component of gluten, which is a prevalent trigger of food allergies. Our novel approach employs the strategic coating of gold nanoparticles (AuNP) with gliadin-specific aptamers. In the absence of gliadin, these aptamers stably disperse AuNP, preventing their aggregation. However, upon the introduction of gliadin and in the presence of sodium chloride, AuNP aggregate, yielding a measurable colorimetric signal that facilitates the precise quantification of gliadin. Under rigorously optimized conditions, this AuNP/aptamer-based colorimetric biosensor demonstrated exceptional sensitivity and selectivity, with a detection limit of 32.1 ng mL-1 and a linear response range of 0-300 ng mL-1. Critically, the sensor maintained reliable performance when applied to real-world food samples, including gluten-free bread, cookies, and pasta. Due to its simplicity, selectivity, speed, and cost-effectiveness, this assay represents a significant advancement over current gluten detection methods. Moreover, the developed AuNP/aptamer-based colorimetric biosensor design holds promising potential for adaptation to detect other food allergens or protein toxins through selective aptamer modifications.

Paper-based upconversion fluorescence aptasensor for the quantitative detection of immunoglobulin E in human serum

Immunoglobulin E (IgE), a biomarker of allergic diseases, plays a critical role in allergic mechanism. Because of its low abundance in serum, the demand of developing sensitive, selective and simple methods for IgE detection is still very urgent. Paper-based analytical devices using upconversion nanoparticles (UCNPs) as the label can be promising point-of-care test (POCT) methods in rapid diagnosis, owing to their NIR-excitation and visible light emission nature, which can avoid the interference of autofluorescence and scattering light from biological samples and paper substrates. In this work, we proposed a paper-based analytical device for the sensitive, selective and accurate detection of total immunoglobulin E (IgE) in human serum. The assay was based on resonance energy transfer between UCNPs and organic dye tetramethylrhodamine (TAMRA), and IgE aptamer with stem-loop structure was used as the recognizing probe. The existence of IgE change the conformation of IgE aptamer, enlarge the distance between donor and acceptor, and block the energy transfer process. Thus, the luminescence of UCNPs recovered with an IgE concentration independent manner. A linear calibration was obtained in the range of 0.5-50 IU/mL, with a detection limit of 0.13 IU/mL. The results of our method were well correlated with that of commercial ELISA kit (20 human serum samples). This work suggests promising prospect of the paper-based UC-LRET analytical devices in real samples and may promote the application of paper-based analytical devices in clinical diagnosis.

Aptamers against Immunoglobulins: Design, Selection and Bioanalytical Applications

Nucleic acid aptamers show clear promise as diagnostic reagents, as highly specific strands were reported against a large variety of biomarkers. They have appealing benefits in terms of reproducible generation by chemical synthesis, controlled modification with labels and functionalities providing versatile means for detection and oriented immobilization, as along with high biochemical and temperature resistance. Aptamers against immunoglobulin targets-IgA, IgM, IgG and IgE-have a clear niche for diagnostic applications, therefore numerous aptamers have been selected and used in combination with a variety of detection techniques. The aim of this review is to overview and evaluate aptamers selected for the recognition of antibodies, in terms of their design, analytical properties and diagnostic applications. Aptamer candidates showed convincing performance among others to identify stress and upper respiratory tract infection through SIgA detection, for cancer cell recognition using membrane bound IgM, to detect and treat hemolytic transfusion reactions, autoimmune diseases with IgG and detection of IgE for allergy diseases. However, in general, their use still lags significantly behind what their claimed benefits and the plethora of application opportunities would forecast.

Aptamers as Versatile Molecular Tools for Antibody Production Monitoring and Quality Control

Antibody drugs have been used to treat many diseases, and to date, this has been the most rapidly growing drug class. However, the lack of suitable methods for real-time and high-throughput monitoring of antibody production and quality control has been a hindrance to the further advancement of antibody drugs or biosimilars. Therefore, we herein report a versatile tool for one-step fluorescence monitoring of antibody production by using aptamer probes selected through the in vitro SELEX method. In this case, DNA aptamers were selected against the humanized IgG1 antibody drug trastuzumab with high specificity and affinity with a K_d value of aptamer CH1S-3 of 10.3 nM. More importantly, the obtained aptamers were able to distinguish native from heat-treated, whereas antibodies failed this test. On the basis of the advantages of rapid detection for aptamers, we designed aptamer molecular beacons for direct and sensitive detection of trastuzumab in complex samples. Unlike traditional antibody-based ELISA, the signal was observed directly upon interaction with the target without the need for time-consuming binding and multiple washing steps. To further highlight biomedical applications, the use of aptamers as potential tools for quality control and traceless purification of antibody drugs was also demonstrated. Thus, aptamers are shown to be promising alternatives for antibody production monitoring, quality control, and purification, providing technical support to accelerate antibody drug development.

Advances in aptasensor technology

Aptasensors form a class of biosensors that function on the basis of a biological recognition. An aptasensor is advantageous because it incorporates a unique biologic recognition element, i.e., an aptamer, coupled to a transducer to convert a biological interaction to readable signals that can be easily processed and reported. In such biosensors, the specificity of aptamers is comparable to and sometimes even better than that of antibodies. Using the SELEX technique, aptamers with high specificity and affinity to various targets can be isolated from large pools of different oligonucleotides. Nowadays, new modifications of the SELEX technique and, as a result, easy generation and synthesis of aptamers have led to the wide application of these materials as biological receptors in biosensors. In this regard, aptamers promise a bright future. In the present research a brief account is initially provided of the recent developments in aptasensors for various targets. Then, immobilization methods, design strategies, current limitations and future directions are discussed for aptasensors.

Gold Nanoparticle-Based Colorimetric Strategies for Chemical and Biological Sensing Applications

Gold nanoparticles are popularly used in biological and chemical sensors and their applications owing to their fascinating chemical, optical, and catalytic properties. Particularly, the use of gold nanoparticles is widespread in colorimetric assays because of their simple, cost-effective fabrication, and ease of use. More importantly, the gold nanoparticle sensor response is a visual change in color, which allows easy interpretation of results. Therefore, many studies of gold nanoparticle-based colorimetric methods have been reported, and some review articles published over the past years. Most reviews focus exclusively on a single gold nanoparticle-based colorimetric technique for one analyte of interest. In this review, we focus on the current developments in different colorimetric assay designs for the sensing of various chemical and biological samples. We summarize and classify the sensing strategies and mechanism analyses of gold nanoparticle-based detection. Additionally, typical examples of recently developed gold nanoparticle-based colorimetric methods and their applications in the detection of various analytes are presented and discussed comprehensively.

Self-Assembly of Functional Nucleic Acid-Based Colorimetric Competition Assay for the Detection of Immunoglobulin E

In this work, we have developed a simple and rapid colorimetric assay for the detection of immunoglobulin E (IgE) using functional nucleic acids (FNAs) and a solid-phase competition enzyme-linked immunosorbent assay (ELISA). The FNAs including aptamer of recombinant IgE, G-quadruplex and its complementary fragments were immobilized on 96-well microplates to achieve recognition and detection of IgE in biological samples. The G-quadruplex DNAzyme catalyzed 2,2'-Azino-bis (3-ethylbenzothiazoline-6-sulfonic acid (ABTS)-hemin-H2O2 system was used to improve the sensitivity of colorimetric assay. In the presence of IgE, the hairpin structure and G-quadruplex would be destroyed, resulting in the inactivation of DNAzyme and subsequent reduction of its absorbance. This cost-effective approach detected IgE in the linear range from 5.0 pg/mL to 500 ng/mL, with the limit of detection (LOD) of 2.0 pg/mL, under optimal conditions. Moreover, the developed method was successfully applied to the rapid detection of IgE in human urine, indicating a great potentiality of this approach in clinical diagnosis and other biomedical applications.

Reversion of gold nanoparticle aggregates for the detection of Cu2+ and its application in immunoassays

A high concentration of copper is a hazardous element to organisms and human health. Although various strategies have been reported for the sensitive detection of copper, a facile and rapid detection of aqueous copper has seldom been addressed to date. Here, we present an easy and accessible colorimetric method to detect Cu²⁺ using the redispersion of cysteamine-modified gold nanoparticles (CA-AuNPs). Initially, CA caused the aggregation of AuNPs due to the electrostatic interaction and aggregated AuNPs can be regenerated in basic medium. The subsequent addition of Cu²⁺ to the CA-AuNP dispersion could effectively trigger the aggregation of CA-AuNPs, resulting from the coordination reactivity between the deprotonated CA and Cu²⁺. This strategy resulted in a detection limit (LOD) of 1.52 μM in drinking water, which is below the U.S. Environmental Protection Agency permissible limit (20 μM). To demonstrate the broad application of CA-AuNPs, we further applied this method to plasmonic immunoassays based on the competitive interaction of Cu²⁺ between CA-AuNPs and enzymes. The LOD of the Down syndrome biomarker hyperglycosylated human chorionic gonadotropin (H-hCG) was 0.125 mIU mL^-1, which is better than that of commercial immunoassays. Importantly, the determination of H-hCG in serum indicates its applicability for the measurement of real samples. Our assay agrees well with the current immunoassay systems and thus it can easily be expanded to a more common sensing platform for different types of biotargets by changing the corresponding antibodies.

DNA aptamer-based colorimetric detection platform for Salmonella Enteritidis

Food safety is a major issue to protect public health and a key challenge is to find detection methods for identification of hazards in food. Food borne infections affects millions of people each year and among pathogens, Salmonella Enteritidis is most widely found bacteria causing food borne diseases. Therefore, simple, rapid, and specific detection methods are needed for food safety. In this study, we demonstrated the selection of DNA aptamers with high affinity and specificity against S. Enteritidis via Cell Systematic Evolution of Ligands by Exponential Enrichment (Cell-SELEX) and development of sandwich type aptamer-based colorimetric platforms for its detection. Two highly specific aptamers, crn-1 and crn-2, were developed through 12 rounds of selection with K_d of 0.971µM and 0.309µM, respectively. Both aptamers were used to construct sandwich type capillary detection platforms. With the detection limit of 10³ CFU/mL, crn-1 and crn-2 based platforms detected target bacteria specifically based on color change. This platform is also suitable for detection of S. Enteritidis in complex food matrix. Thus, this is the first to demonstrate use of Salmonella aptamers for development of the colorimetric aptamer-based detection platform in its identification and detection with naked eye in point-of-care.

DNA base-stacking assay utilizing catalytic hairpin assembly-induced gold nanoparticle aggregation for colorimetric protein sensing

A label-free and enzyme-free colorimetric sensing platform for the amplified detection of fibronectin was developed based on an ingenious combination of catalytic hairpin assembly and a base stacking hybridization-based gold nanoparticle aggregation strategy.

Aptamer-based colorimetric detection of proteins using a branched DNA cascade amplification strategy and unmodified gold nanoparticles

A branched DNA amplification strategy was employed to design a colorimetric aptameric biosensor using unmodified gold nanoparticles (AuNPs). First, a programmed DNA dendritic nanostructure was formed using two double-stranded substrate DNAs and two single-stranded auxiliary DNAs as assembly components via a target-assisted cascade amplification reaction, and it was then captured by DNA sensing probe-stabilized AuNPs. The release of sensing probes from AuNPs led to the formation of unstable AuNPs, promoting salt-induced aggregation. By integrating the signal amplification capacity of the branched DNA cascade reaction and unmodified AuNPs as a sensing indicator, this amplified colorimetric sensing strategy allows protein detection with high sensitivity (at the femtomole level) and selectivity. The limit of detection of this approach for VEGF was lower than those of other aptamer-based detection methods. Moreover, this assay provides modification-free and enzyme-free protein detection without sophisticated instrumentation and might be generally applicable to the detection of other protein targets in the future.

A review on immobilised aptamers for high throughput biomolecular detection and screening

The discovery of Systematic Evolution of Ligands by Exponential Enrichment (SELEX) assay has led to the generation of aptamers from libraries of nucleic acids. Concomitantly, aptamer-target recognition and its potential biomedical applications have become a major research endeavour. Aptamers possess unique properties that make them superior biological receptors to antibodies with a plethora of target molecules. Some specific areas of opportunities explored for aptamer-target interactions include biochemical analysis, cell signalling and targeting, biomolecular purification processes, pathogen detection and, clinical diagnosis and therapy. Most of these potential applications rely on the effective immobilisation of aptamers on support systems to probe target species. Hence, recent research focus is geared towards immobilising aptamers as oligosorbents for biodetection and bioscreening. This article seeks to review advances in immobilised aptameric binding with associated successful milestones and respective limitations. A proposal for high throughput bioscreening using continuous polymeric adsorbents is also presented.

Colorimetric detection of human chorionic gonadotropin using catalytic gold nanoparticles and a peptide aptamer

We combined catalytic gold nanoparticles (AuNPs) with an hCG-specific peptide aptamer to create a simple, sensitive, label-free colorimetric assay for hCG. The applications of this colorimetric biosensor may be expanded by changing the peptide aptamer.

A simple label-free electrochemical aptasensor for dopamine detection

A simple and label-free electrochemical biosensor based on a dopamine DNA aptamer was developed for the sensitive and selective detection of dopamine.