Capillary gel electrophoresis-coupled aptamer enzymatic cleavage protection strategy for the simultaneous detection of multiple small analytes

Recent advances in nucleic acid signal amplification-based aptasensors for sensing mycotoxins

Mycotoxin contamination in food products may cause serious health hazards and economic losses. The effective control and accurate detection of mycotoxins have become a global concern. Even though a variety of methods have been developed for mycotoxin detection, most conventional methods suffer from complicated operation procedures, low sensitivity, high cost, and long assay time. Therefore, the development of simple and sensitive methods for mycotoxin assay is highly needed. The introduction of nucleic acid signal amplification technology (NASAT) into aptasensors significantly improves the sensitivity and facilitates the detection of mycotoxins. Herein, we give a comprehensive review of the recent advances in NASAT-based aptasensors for assaying mycotoxins and summarize the principles, features, and applications of NASAT-based aptasensors. Moreover, we highlight the challenges and prospects in the field, including the simultaneous detection of multiple mycotoxins and the development of portable devices for field detection.

Capillary electrophoresis-based immunoassay and aptamer assay: A review

Over the last two decades, the group of techniques called affinity probe CE has been widely used for the detection and the determination of several types of biomolecules with high sensitivity. These techniques combine the low sample consumption and high separation power of CE with the selectivity of the probe to the target molecule. The assays can be defined according to the type of probe used: CE immunoassays, with an antibody as the probe, or aptamer-based CE, with an aptamer as the probe. Immunoassays are generally divided into homogeneous and heterogeneous groups, and homogeneous variant can be further performed in competitive or noncompetitive formats. Interacting partners are free in solution at homogeneous assay, as opposed to heterogeneous analyses, where one of them is immobilized onto a solid support. Highly sensitive fluorescence, chemiluminescence or electrochemical detections were typically used in this type of study. The use of the aptamers as probes has several advantages over antibodies such as shorter generation time, higher thermal stability, lower price, and lower variability. The aptamer-based CE technique was in practice utilized for the determination of proteins in biological fluids and environmentally or clinically important small molecules. Both techniques were also transferred to microchip. This review is focused on theoretical principles of these techniques and a summary of their applications in research.

Application of Capillary Electrophoresis with Laser-Induced Fluorescence to Immunoassays and Enzyme Assays

Capillary electrophoresis using laser-induced fluorescence detection (CE-LIF) is one of the most sensitive separation tools among electrical separation methods. The use of CE-LIF in immunoassays and enzyme assays has gained a reputation in recent years for its high detection sensitivity, short analysis time, and accurate quantification. Immunoassays are bioassay platforms that rely on binding reactions between an antigen (analyte) and a specific antibody. Enzyme assays measure enzymatic activity through quantitative analysis of substrates and products by the reaction of enzymes in purified enzyme or cell systems. These two category analyses play an important role in the context of biopharmaceutical analysis, clinical therapy, drug discovery, and diagnosis analysis. This review discusses the expanding portfolio of immune and enzyme assays using CE-LIF and focuses on the advantages and disadvantages of these methods over the ten years of existing technology since 2008.

Use of capillary electrophoresis to select a DNA aptamer that recognizes swine anaphylatoxin C5a

Complement factor 5a is a potent proinflammatory mediator that contributes to the pathogenesis of numerous inflammatory diseases. Protein-based C5a inhibitors have proven to be clinically valuable. Aptamers, which are oligonucleic acid chains or polypeptides, can bind to target molecules and hence have the potential to be used for detection and blockade of targets. Here, we describe the discovery that the single-stranded DNA aptamer S1 can bind specifically to swine C5a, which can then be quickly selected for with capillary electrophoresis for high-throughput sequencing. Aptamer S1 bound specifically to swine C5a with a dissociation constant of 4 μM as measured by surface plasmon resonance (SPR). Moreover, aptamer S1 inhibited C5a-induced chemotaxis of neutrophils in vitro. Our study suggests that the S1 aptamer has great potential to be a key structure in the development of effective therapeutic agents against inflammatory diseases.

Selection and Biosensor Application of Aptamers for Small Molecules

Small molecules play a major role in the human body and as drugs, toxins, and chemicals. Tools to detect and quantify them are therefore in high demand. This review will give an overview about aptamers interacting with small molecules and their selection. We discuss the current state of the field, including advantages as well as problems associated with their use and possible solutions to tackle these. We then discuss different kinds of small molecule aptamer-based sensors described in literature and their applications, ranging from detecting drinking water contaminations to RNA imaging.

A combinatorial approach to the repertoire of RNA kissing motifs; towards multiplex detection by switching hairpin aptamers

Loop–loop (also known as kissing) interactions between RNA hairpins are involved in several mechanisms in both prokaryotes and eukaryotes such as the regulation of the plasmid copy number or the dimerization of retroviral genomes. The stability of kissing complexes relies on loop parameters (base composition, sequence and size) and base combination at the loop–loop helix - stem junctions. In order to identify kissing partners that could be used as regulatory elements or building blocks of RNA scaffolds, we analysed a pool of 5.2 × 10⁶ RNA hairpins with randomized loops. We identified more than 50 pairs of kissing RNA hairpins. Two kissing motifs, 5′CCNY and 5′RYRY, generate highly stable complexes with K_Ds in the low nanomolar range. Such motifs were introduced in the apical loop of hairpin aptamers that switch between unfolded and folded state upon binding to their cognate target molecule, hence their name aptaswitch. The aptaswitch–ligand complex is specifically recognized by a second RNA hairpin named aptakiss through loop–loop interaction. Taking advantage of our kissing motif repertoire we engineered aptaswitch–aptakiss modules for purine derivatives, namely adenosine, GTP and theophylline and demonstrated that these molecules can be specifically and simultaneously detected by surface plasmon resonance or by fluorescence anisotropy.

ELAKCA: Enzyme-Linked Aptamer Kissing Complex Assay as a Small Molecule Sensing Platform

We report herein a novel sandwich-type enzyme-linked assay for the "signal-on" colorimetric detection of small molecules. The approach (referred to as enzyme-linked aptamer kissing complex assay (ELAKCA)) relied on the kissing complex-based recognition of the target-bound hairpin aptamer conformational state by a specific RNA hairpin probe. The aptamer was covalently immobilized on a microplate well surface to act as target capture element. Upon small analyte addition, the folded aptamer was able to bind to the biotinylated RNA hairpin module through loop-loop interaction. The formed ternary complex was then revealed by the introduction of the streptavidin-horseradish peroxidase conjugate that catalytically converted the 3,3',5,5'-tetramethylbenzidine substrate into a colorimetric product. ELAKCA was successfully designed for two different systems allowing detecting the adenosine and theophylline molecules. The potential practical applicability in terms of biological sample analysis (human plasma), temporal stability, and reusability was also reported. Owing to the variety of both hairpin functional nucleic acids, kissing motifs, and enzyme-based signaling systems, ELAKCA opens up new prospects for developing small molecule sensing platforms of wide applications.

Recent Advances for the Detection of Ochratoxin A

Ochratoxin A (OTA) is one of the mycotoxins secreted by Aspersillus and Penicillium that can easily colonize various grains like coffee, peanut, rice, and maize. Since OTA is a chemically stable compound that can endure the physicochemical conditions of modern food processing, additional research efforts have been devoted to develop sensitive and cost-effective surveillance solutions. Although traditional chromatographic and immunoassays appear to be mature enough to attain sensitivity up to the regulation levels, alternative detection schemes are still being enthusiastically pursued in an attempt to meet the requirements of rapid and cost-effective detections. Herein, this review presents recent progresses in OTA detections with minimal instrumental usage, which have been facilitated by the development of OTA aptamers and by the innovations in functional nanomaterials. In addition to the introduction of aptamer-based OTA detection techniques, OTA-specific detection principles are also presented, which exclusively take advantage of the unique chemical structure and related physicochemical characteristics.

A Luminescent Cocaine Detection Platform Using a Split G-Quadruplex-Selective Iridium(III) Complex and a Three-Way DNA Junction Architecture

In this study, a series of 10 in-house cyclometalated iridium(III) complexes bearing different auxiliary ligands were tested for their selectivity toward split G-quadruplex in order to construct a label-free switch-on cocaine detection platform employing a three-way junction architecture and a G-quadruplex motif as a signal output unit. Through two rounds of screening, we discovered that the iridium(III) complex 7 exhibited excellent selectivity toward the intermolecular G-quadruplex motif. A detection limit as low as 30 nM for cocaine can be achieved by this sensing approach with a linear relationship between luminescence intensity and cocaine concentration established from 30 to 300 nM. Furthermore, this sensing approach could detect cocaine in diluted oral fluid. We hope that our simple, signal-on, label-free oligonucleotide-based sensing method for cocaine using a three-way DNA junction architecture could act as a useful platform in bioanalytical research.

Capillary electrophoresis applied to DNA: determining and harnessing sequence and structure to advance bioanalyses (2009-2014)

This review of capillary electrophoresis methods for DNA analyses covers critical advances from 2009 to 2014, referencing 184 citations. Separation mechanisms based on free-zone capillary electrophoresis, Ogston sieving, and reptation are described. Two prevalent gel matrices for gel-facilitated sieving, which are linear polyacrylamide and polydimethylacrylamide, are compared in terms of performance, cost, viscosity, and passivation of electroosmotic flow. The role of capillary electrophoresis in the discovery, design, and characterization of DNA aptamers for molecular recognition is discussed. Expanding and emerging techniques in the field are also highlighted.