The DNA aptamers that specifically recognize ricin toxin are selected by two in vitro selection methods

Sensitive Detection and Differentiation of Biologically Active Ricin and Abrin in Complex Matrices via Specific Neutralizing Antibody-Based Cytotoxicity Assay

Ricin and abrin are highly potent plant-derived toxins, categorized as type II ribosome-inactivating proteins. High toxicity, accessibility, and the lack of effective countermeasures make them potential agents in bioterrorism and biowarfare, posing significant threats to public safety. Despite the existence of many effective analytical strategies for detecting these two lethal toxins, current methods are often hindered by limitations such as insufficient sensitivity, complex sample preparation, and most importantly, the inability to distinguish between biologically active and inactive toxin. In this study, a cytotoxicity assay was developed to detect active ricin and abrin based on their potent cell-killing capability. Among nine human cell lines derived from various organs, HeLa cells exhibited exceptional sensitivity, with limits of detection reaching 0.3 ng/mL and 0.03 ng/mL for ricin and abrin, respectively. Subsequently, toxin-specific neutralizing monoclonal antibodies MIL50 and 10D8 were used to facilitate the precise identification and differentiation of ricin and abrin. The method provides straightforward and sensitive detection in complex matrices including milk, plasma, coffee, orange juice, and tea via a simple serial-dilution procedure without any complex purification and enrichment steps. Furthermore, this assay was successfully applied in the unambiguous identification of active ricin and abrin in samples from OPCW biotoxin exercises.

Assessment of the structural change of DNA by binding with a small molecule based on capillary sieving electrophoresis

In this study, capillary sieving electrophoresis (CSE) using polymer solutions was used to evaluate the structural changes in nucleic acids upon complexation with small molecules. As the model target and nucleic acids, L-tyrosinamide (Tyr-Am) and its aptamer, which is a type of DNA specifically binding to Tyr-Am, were selected. CSE was conducted using a capillary filled with background solution (BGS) containing hydroxypropyl cellulose (HPC) as a sieving matrix. When Tyr-Am or tyrosine was added to the BGS in CSE, the ratio of mobility differences of the Tyr-Am-aptamer complex increased compared to that of the free aptamer without the addition of Tyr-Am. In contrast, when other amino acids or their analogs were added, results showed no apparent change or decreases in electrophoretic mobility. These results indicate that the proposed method can be applied to assess structural changes in nucleic acids that target small molecules.

A DNA walker triggered isothermal amplification method based on freezing construction of AuNP probes and its application in ricin detection

DNA molecular machines are widely used in the fields of biosensors and biological detection. Among them, DNA walkers have attracted much attention due to their simple design and controllability. Herein, we attempt to develop a DNA walker triggered exponential amplification method and explore its application. The AuNP probes in the DNA walker are constructed by a freezing technology, instead of the time-consuming and complex synthesis process of the traditional method. Meanwhile, after the "recognition-cleavage-relative motion" cycle of this DNA walker reaction, the exponential amplification reaction is initiated, and leads to the fluorescence recovery of the molecular beacon. Taking ricin as a target, this new method shows a limit of detection of 2.25 pM by selecting aptamers with strong binding affinity, and exhibits a wide detection range, satisfactory specificity, and excellent stability in practical application. Therefore, our method provides a universal sensing platform and has great prospects in the fields of biosensors, food safety detection, and clinical diagnostics.

Neutralizing Monoclonal Antibody, mAb 10D8, Is an Effective Detoxicant against Abrin-a Both In Vitro and In Vivo

Abrin is a types II ribosome-inactivating protein (RIP) isolated from Abrus precatorious seeds, which comprises a catalytically active A chain and a lectin-like B chain linked by a disulfide bond. Four isotoxins of abrin have been reported with similar amino-acid composition but different cytotoxicity, of which abrin-a is the most potent toxin. High lethality and easy availability make abrin a potential bioterrorism agent. However, there are no antidotes available for managing abrin poisoning, and treatment is only symptomatic. Currently, neutralizing antibodies remain the most effective therapy against biotoxin poisoning. In this study, we prepared, identified, and acquired a high-affinity neutralizing monoclonal antibody (mAb) 10D8 with a potent pre- and post-exposure protective effect against cytotoxicity and animal toxicity induced by abrin-a or abrin crude extract. The mAb 10D8 could rescue the mouse injected intraperitoneally with a 25 × LD₅₀ dose of abrin-a from lethality and prevent tissue damages. Results indicated that 10D8 does not prevent the binding and internalization of abrin-a to cells but inhibits the enzymatic activity of abrin-a and reduces protein synthesis inhibition of cells. The high affinity, good specificity, and potent antitoxic efficiency of 10D8 make it a promising candidate for therapeutic antibodies against abrin.

The Application of Microfluidic Technologies in Aptamer Selection

Aptamers are sequences of single-strand oligonucleotides (DNA or RNA) with potential binding capability to specific target molecules, which are increasingly used as agents for analysis, diagnosis, and medical treatment. Aptamers are generated by a selection method named systematic evolution of ligands by exponential enrichment (SELEX). Numerous SELEX methods have been developed for aptamer selections. However, the conventional SELEX methods still suffer from high labor intensity, low operation efficiency, and low success rate. Thus, the applications of aptamer with desired properties are limited. With their advantages of low cost, high speed, and upgraded extent of automation, microfluidic technologies have become promising tools for rapid and high throughput aptamer selection. This paper reviews current progresses of such microfluidic systems for aptamer selection. Comparisons of selection performances with discussions on principles, structure, operations, as well as advantages and limitations of various microfluidic-based aptamer selection methods are provided.

Fractionation of Single-stranded DNAs with/without Stable Preorganized Structures Using Capillary Sieving Electrophoresis for Aptamer Selection

Aptamers, single-stranded DNAs/RNAs with a strong and specific interaction towards a target molecule, have wide applications in the fields of medicine and biosensors. In conventional aptamer selection methods, it is difficult to obtain "preorganized" and/or "induced-fit" type of aptamers selectively. In this study, separation and fractionation of single-stranded DNAs with/without stable preorganized structures were carried out using capillary sieving electrophoresis. The fractionated DNAs showed different mobilities and thermodynamic stabilities of their secondary structures; this outcome is deemed to be necessary for the synthesis of novel aptasensors with a desirable sensing mechanism.

[Highly toxic type Ⅱ ribosome-inactivating proteins ricin and abrin and their detection methods: a review]

Type Ⅱ ribosome-inactivating proteins (RIPs) are an important class of protein toxins that consist of A and B chains linked by an interchain disulfide bond. The B-chain with lectin-like activity is responsible for binding to the galactose-containing receptors on eukaryotic cell surfaces, which is essential for A-chain internalization by endocytosis. The A-chain has N-glycosidase activity that irreversibly depurinates a specific adenine from 28S ribosomal RNA (28S rRNA) and terminates protein synthesis. The synergistic effect of the A-B chain inactivates the ribosome, inhibits protein synthesis, and exhibits high cytotoxicity. Ricin and abrin that are expressed by the plants Ricinus communis and Abrus precatorius, respectively, are typical type Ⅱ RIPs. The toxicity of ricin and abrin are 385 times and 2885 times, respectively, more that of the nerve agent VX. Owing to their ease of preparation, wide availability, and potential use as a bioterrorism agent, type Ⅱ RIPs have garnered increasing attention in recent years. Ricin is listed as a prohibited substance under schedule 1A of the Chemical Weapons Convention (CWC). The occurrence of ricin-related bioterrorism incidents in recent years has promoted the development of accurate, sensitive, and rapid detection and identification technology for type Ⅱ RIPs. Significant progress has been made in the study of toxicity mechanisms and detection methods of type Ⅱ RIPs, which primarily involve qualitative and quantitative analysis methods including immunological assays, mass spectrometry analysis methods, and toxin activity detection methods based on depurination and cytotoxicity. Immunoassays generally involve the specific recognition of antigens and antibodies, which is based on oligonucleotide molecular recognition elements called aptamers. These methods are fast and highly sensitive, but for highly homologous proteins in complex samples, they provide false positive results. With the rapid development of biological mass spectrometry detection technology, techniques such as electrospray ionization (ESI) and matrix-assisted laser desorption ionization (MALDI) are widely used in the identification of proteins. These methods not only provide accurate information on molecular weight and structure of proteins, but also demonstrate accurate quantification. Enzyme digestion combined with mass spectrometry is the predominantly used detection method. Accurate identification of protein toxins can be achieved by fingerprint analysis of enzymatically digested peptides. For analysis of protein toxins in complex samples, abundant peptide markers are obtained using a multi-enzyme digestion strategy. Targeted mass spectrometry analysis of peptide markers is used to obtain accurate qualitative and quantitative information, which effectively improves the accuracy and sensitivity of the identification of type Ⅱ RIP toxins. Although immunoassay and mass spectrometry detection methods can provide accurate identification of type Ⅱ RIPs, they cannot determine whether the toxins will retain potency. The widely used detection methods for activity analysis of type Ⅱ RIPs include depurination assay based on N-glycosidase activity and cytotoxicity assay. Both the methods provide simple, rapid, and sensitive analysis of type Ⅱ RIP toxicity, and complement other detection methods. Owing to the importance of type Ⅱ RIP toxins, the Organization for the Prohibition of Chemical Weapons (OPCW) has proposed clear technical requirements for the identification and analysis of relevant samples. We herein reviewed the structural characteristics, mechanism of action, and the development and application of type Ⅱ RIP detection methods; nearly 70 studies on type Ⅱ RIP toxins and their detection methods have been cited. In addition to the technical requirements of OPCW for the unambiguous identification of biotoxins, the trend of future development of type Ⅱ RIP-based detection technology has been explored.

PEI-assisted boronate affinity magnetic nanoparticle-based SELEX for efficient in vitro evolution of saponin-binding aptamers

Branched polyethyleneimine assisted boronate affinity magnetic nanoparticle-based aptamer evolution platform.

Immunoaffinity Extraction and Alternative Approaches for the Analysis of Toxins in Environmental, Food or Biological Matrices

The evolution of instrumentation in terms of separation and detection allowed a real improvement of the sensitivity and analysis time. However, the analysis of ultra-traces of toxins in complex samples requires often a step of purification and even preconcentration before their chromatographic analysis. Therefore, immunoaffinity sorbents based on specific antibodies thus providing a molecular recognition mechanism appear as powerful tools for the selective extraction of a target molecule and its structural analogs to obtain more reliable and sensitive quantitative analysis in environmental, food or biological matrices. This review focuses on immunosorbents that have proven their efficiency in selectively extracting various types of toxins of various sizes (from small mycotoxins to large proteins) and physicochemical properties. Immunosorbents are now commercially available, and their use has been validated for numerous applications. The wide variety of samples to be analyzed, as well as extraction conditions and their impact on extraction yields, is discussed. In addition, their potential for purification and thus suppression of matrix effects, responsible for quantification problems especially in mass spectrometry, is presented. Due to their similar properties, molecularly imprinted polymers and aptamer-based sorbents that appear to be an interesting alternative to antibodies are also briefly addressed by comparing their potential with that of immunosorbents.

An overview and future prospects on aptamers for food safety

Introduction

Many bacteria are responsible for infections in humans and plants, being found in vegetables, water, and medical devices. Most bacterial detection methods are time-consuming and take days to give the result. Aptamers are a promising alternative for a quick and reliable measurement technique to detect bacteria present in food products. Selected aptamers are DNA or RNA oligonucleotides that can bind with bacteria or other molecules with affinity and specificity for the target cells by the SELEX or cell-SELEX technique. This method is based on some rounds to remove the non-ligand oligonucleotides, leaving the aptamers specific to bind to the selected bacteria. Compared with conventional methodologies, the detection approach using aptamers is a rapid, low-cost form of analysis.

Objective

This review summarizes obtention methods and applications of aptamers in the food industry and biotechnology. Besides, different techniques with aptamers are presented, which enable more effective target detection.

Conclusion

Applications of aptamers as biosensors, or the association of aptamers with nanomaterials, may be employed in analyses by colorimetric, fluorescence, or electrical devices. Additionally, more efficient ways of sample preparation are presented, which can support food safety to provide human health, with a low-cost method for contaminant detection.

Key points • Aptamers are promising for detecting contaminants outbreaks. • Studies are needed to identify aptamers for different targets.

Evolution of multi-functional capillary electrophoresis for high-efficiency selection of aptamers

Aptamers have drawn considerable attention as newly emerging molecular recognition elements in clinical diagnostics, drug delivery, therapeutics, environmental monitoring, and food safety analyses. As the in vitro screening antibody analogs, aptamers are enabled to recognize various types of targets with high affinity and specificity like or even superior to antibodies. However, the restrictions and inefficiency of selection have been hampering their wider application. Among various modified systematic evolution of ligands by exponential enrichment (SELEX) methods, capillary electrophoresis (CE)-SELEX holds multiple functions and advantages with the powerful qualitative and quantitative analysis capabilities, less consumption of sample and analytical reagent, natural binding environment, higher screening efficiency, and availability in multiple modes. This review summarizes the key developments in the area of CE-SELEX by leading research groups, including our teams' ten years of research and experience to help researchers fully understand and utilize CE-SELEX. Aptamers' history, applications, as well as the SELEX developments, have been briefly described; the advantages of CE-SELEX are highlighted compared with the conventional SELEX methods. Further, we describe some essential CE-SELEX models and provide an overview of the CE-SELEX, including the targets and ssDNA library, every technical point in the selection process, and post-SELEX protocol. We expect this review will inspire more researchers to have insight into the screening problems from CE-SELEX viewpoint and will help to improve the selection efficiency and probability of success to meet the growing needs of aptamers' discovery in bioanalytical and medical fields.

Ultrasensitive On-Site Detection of Biological Active Ricin in Complex Food Matrices Based on Immunomagnetic Enrichment and Fluorescence Switch-On Nanoprobe

Ricin is a highly toxic protein largely existing in castor beans, which could be used as a warfare agent due to its unique properties. As a deadenylase, inactivation of ricin means a loss of its toxic threat. Therefore, developing simple, accurate, and sensitive on-site detection of biologically active ricin in wide types of complex matrices is most valuable. Here, antifouling polymer brush modified magnetic beads were prepared first and post modified with ricin monoclonal antibody (the MB@P(C-H)-mAb_ricin) to efficiently capture ricin from various foods and biological matrices. Active ricin obtained in this manner were sequentially determined by a new designed AuNP/QDs nanoassembly. In this double strand oligodeoxynucleotides (dsODN) linked core-satellite nanoprobe, the fluorescence of satellite QDs was extensively quenched by AuNPs due to the dipole-metal interaction. Active ricin can react with its specific depurination substrates which had been inserted in the dsODN linkers. This reaction would trigger the separation of QDs from Au cores by cutting multiple adenines, and then result in the restoration of QDs fluorescence. By coupling with the magnetic enrichment, this AuNP/QDs nanoprobe provided a qualitative result for active ricin in the range from 10.0 to 100.0 ng mL^-1 with the limit of detection as low as 7.46 ng mL^-1. Compared with previously proposed methods, this on-site detection strategy offered an easy to handle on-site test for trace amounts of active ricin in a wide range of complex matrices.

Recent progress in the development of recognition bioelements for polychlorinated biphenyls detection: Antibodies and aptamers

Polychlorinated biphenyls (PCBs) are persistent pollutants, which have expanded in foods and the environment. Detection of PCBs is considered essential due to recognized side-effects of PCBs on health and the public concerns in this regard. On the other hand, due to the trace levels of these organic chlorine compounds, reliable and sensitive assays must be developed. Recognition elements are essential parts of analytical detection assays and sensors of PCBs since these elements are involved in the selective identification of the analytes of interest. Understanding the fundamentals of the recognition elements of PCBs and the benefits of the sensor strategies result in the development of next-generation recognition devices. This review aimed to highlight the recent progress in the recognition elements as key parts of biosensors. We initially, focused on the developed antibody-based biosensors for the detection of PCBs, followed by discussing the aptamers as novel recognition elements. Furthermore, the recent advancement in the development of aptamer-based solid phase extractions has been evaluated. These findings could contribute to improving the design of commercial PCB-kits in the future.

Online reaction based single-step capillary electrophoresis-systematic evolution of ligands by exponential enrichment for ssDNA aptamers selection

Capillary electrophoresis-systematic evolution of ligands by exponential enrichment (CE-SELEX) has proven to be an effective technique for aptamers selection. In this study, we present an online reaction based convenient single-step CE-SELEX (ssCE-SELEX) mode with human thrombin (H-Thr) as a model target. The selection progress was monitored through bulk K_d analysis, which showed more than a 1000-fold improvement over the initial library after two rounds of selection. Three selected candidate sequences presented high binding affinities against H-Thr with nanomolar (nM) K_d determined by nonequilibrium capillary electrophoresis of equilibrium mixtures (NECEEM, 56.4-177.1 nM) and CE based non-linear fitting (CE-NLF, 98.2-199.7 nM). They also exhibited high specificities towards H-Thr compared with bovine thrombin, IgG, lysozyme, and lactoferrin. Meanwhile, the K_d results by isothermal titration calorimetry (ITC) confirmed the effective CE in measuring the aptamer affinity. In addition, three candidates were applied as aptasensors in the AuNPs based colorimetric assay, which showed visible color change and good linear relationships (R² > 0.93) with H-Thr concentration. Furthermore, molecular dynamics (MD) simulation was performed to validate the binding of the three candidates with H-Thr by binding sites and binding free energy. The ssCE-SELEX method avoids off-line incubation, saves time and sample, and may provide a universal and convenient method for aptamers selection.

Critical Review: DNA Aptasensors, Are They Ready for Monitoring Organic Pollutants in Natural and Treated Water Sources?

There is a growing need to monitor anthropogenic organic contaminants detected in water sources. DNA aptamers are synthetic single-stranded oligonucleotides, selected to bind to target contaminants with favorable selectivity and sensitivity. These aptamers can be functionalized and are used with a variety of sensing platforms to develop sensors, or aptasensors. In this critical review, we (1) identify the state-of-the-art in DNA aptamer selection, (2) evaluate target and aptamer properties that make for sensitive and selective binding and sensing, (3) determine strengths and weaknesses of alternative sensing platforms, and (4) assess the potential for aptasensors to quantify environmentally relevant concentrations of organic contaminants in water. Among a suite of target and aptamer properties, binding affinity is either directly (e.g., organic carbon partition coefficient) or inversely (e.g., polar surface area) correlated to properties that indicate greater target hydrophobicity results in the strongest binding aptamers, and binding affinity is correlated to aptasensor limits of detection. Electrochemical-based aptasensors show the greatest sensitivity, which is similar to ELISA-based methods. Only a handful of aptasensors can detect organic pollutants at environmentally relevant concentrations, and interference from structurally similar analogs commonly present in natural waters is a yet-to-be overcome challenge. These findings lead to recommendations to improve aptasensor performance.

Insight into the Molecular Mechanisms of AuNP-Based Aptasensor for Colorimetric Detection: A Molecular Dynamics Approach

Colorimetric aptasensor based on assembly of salt-induced gold nanoparticles (AuNPs) is a promising biosensor. However, the molecular mechanism of the aptasensor is far from being fully understood. Herein, molecular dynamics (MD) simulation was used to investigate molecular interactions in the detection of ochratoxin A (OTA) including the following: (i) the molecular recognition of the anti-OTA aptamer, (ii) OTA-aptamer interactions in monovalent (Na⁺) and divalent (Mg²⁺) electrolytes, (iii) the binding mode of citrate on the AuNP surface, (iv) interactions of the aptamer with citrate-capped AuNPs, and (v) a detailed mechanism of the aptasensor. Our MD simulations revealed a specific binding of the OTA-aptamer complex, compared with OTB and warfarin. Compared with Na⁺, Mg²⁺ ions exerted a more effective attractive force between OTA and anti-OTA aptamer. Three different binding modes of citrate on AuNP surfaces were found. The kinetics of the adsorption of unfolded aptamers onto the citrate-capped AuNP was also elucidated. Most importantly, our MD simulation revealed an insightful analysis of the molecular mechanisms in the AuNP-based aptasensor and paved the way for the design of a novel colorimetric aptasensor for other target molecules, which is not limited to OTA detection.

Fast on-Site Visual Detection of Active Ricin Using a Combination of Highly Efficient Dual-Recognition Affinity Magnetic Enrichment and a Specific Gold Nanoparticle Probe

Ricin, a highly toxic protein, is a controlled substance by both the Chemical Weapons Convention (CWC) and the Biological Weapons Convention (BWC). Therefore, fast precaution of potential ricin toxin plays an important role in national security and public safety. Herein, a simple, sensitive, and accurate visual detection of active ricin in complex samples is presented by combining magnetic affinity enrichment with a specific gold nanoparticle (AuNP) probe. In the first step, a dual-recognition magnetic absorbent was fabricated by simultaneously incorporating two different affinity ligands (concanavalin A and galactosamine) on low-foul polymer brushes grafted magnetic beads, which showed remarkable multivalent synergy binding capacity for ricin even under complex interfering environments. Subsequently, a homoadenine-constituted oligodeoxynucleotide named poly(21dA) was conjugated to AuNPs (the poly(21dA)-AuNPs), which served as a specific depurination substrate of active ricin. Coralyne can trigger the intact poly(21dA)-AuNPs aggregate by forming a non-Watson-Crick homoadenine/coralyne complex, but the poly(21dA)-AuNPs after reacting with active ricin failed to form this complex due to the loss of adenines. Based on these facts, active ricin can be detected as low as 12.5 ng mL^-1 with the naked eyes. This detection strategy could be well-applied in various ricin-spiked complex matrices. The features such as ready operation, facile readout, and easy accessibility make the assay a better choice for fast on-site active ricin detection.

Complexes of Oligoribonucleotides with D-Mannitol Inhibit Hemagglutinin-Glycan Interaction and Suppress Influenza A Virus H1N1 (A/FM/1/47) Infectivity In Vitro

The influenza virus hemagglutinin (HA) mediates both receptor (glycan) binding and membrane fusion for cell entry and has been the basis for subtyping influenza viruses. The oligoribonucleotides-d-mannitol (ORNs-d-M) complexes possess an anti-influenza activity in vitro and in vivo. In the present studies, we have found that ORNs-d-M interferes with hemagglutinin (HA)–glycan interaction and suppress viral infection in host cells. HA–glycan interactions were evaluated to indirectly quantify the amount of influenza virus titer by an agglutination assay. Influenza virus infectivity was determined by TCID₅₀ assay. The direct virucidal action of the complexes was evaluated by both cytopathic effects (CPE) reduction assay and cell MTT assay. We found that ORNs-d-M hinders interaction between HA and glycan. These complexes decreased the infectivity of influenza virus and had a direct virucidal action. ORNs-d-M reduces influenza virus infectivity, affecting the HA–glycan interaction in vitro. By suppressing the influenza viral infection, the ORNs-d-M can have direct virucidal action.

Ultrasensitive detection of ochratoxin A using aptasensors

Regarding teratogenic, carcinogenic, and immunotoxic nature of ochratoxin A (OTA), selective and sensitive monitoring of this molecule in food samples is of great importance. In recent years, various methods have been introduced for detection of OTA. However, they are usually time-consuming, labor-intensive and expensive. Therefore, these parameters limited their usage. The emerging method of detection, aptasensor, has attracted more attention for OTA detection, due to distinctive advantages including high sensitivity, selectivity and simplicity. In this review, the new developed aptasensors for detection of OTA have been investigated. We also highlighted advantages and disadvantages of different types of OTA aptasensors. This review also takes into consideration the goal to find out which designs are the most rational ones for highly sensitive detection of OTA.

Advances in the development of aptamer drug conjugates for targeted drug delivery

A key goal of modern medicine is target-specific therapeutic intervention. However, most drugs lack selectivity, resulting in 'off-target' side effects. To address the requirements of 'targeted therapy,' aptamers, which are artificial oligonucleotides, have been used as novel targeting ligands to construct aptamer drug conjugates (ApDC) that can specifically bind to a broad spectrum of targets, including diseased cells. Accordingly, the application of aptamers in targeted drug delivery has attracted broad interest due to their impressive selectivity and affinity, low immunogenicity, easy synthesis with high reproducibility, facile modification, and relatively rapid tissue penetration with no toxicity. Functionally, aptamers themselves can be used as macromolecular drugs, and they are also commonly used in biomarker discovery and targeted drug delivery. In this review, we will highlight the most recent advances in the development of aptamers and aptamer conjugates, and discuss their potential in targeted therapy. WIREs Nanomed Nanobiotechnol 2017, 9:e1438. doi: 10.1002/wnan.1438 For further resources related to this article, please visit the WIREs website.

Tetraphenylethene derivative modified DNA oligonucleotide for in situ potassium ion detection and imaging in living cells

The monitoring of K⁺ is very important and emergency because of their unique relationship in various disease diagnosis and treatment. G-quadruplex analogue is a classical recognition unit for K⁺ detection and has been widely applied in K⁺ relevant research. Common fluorescent dyes were employed for design of G-quadruplex structure-based K⁺ probes which suffered from the aggregation-caused quenching effect, and possibly limited the biological applications in living systems. Herein, we report an aggregation-induced emission (AIE) effect-based fluorescent probe for cellular K⁺ analysis and imaging. Benefitting from the K⁺ triggered AIE phenomenon, the designed TPE derivative modified guanine (G)-rich oligonucleotide fluorescent probe (TPE-oligonucleotide probe) exhibits high sensitivity (∼10-fold higher than most reported G-quadruplex-based probes) with extended photostability which facilitates the prolonged fluorescence observations of K⁺ in living cells. On the basis of these advantages, the TPE-oligonucleotide probe serves as a promising candidate for the functional study and analysis of K⁺.

Aptamer Selection Technology and Recent Advances

Over the last decade, aptamers have begun to find their way from basic research to diverse commercial applications. The development of diagnostics is even more widespread than clinical applications because aptamers do not have to be extensively modified to enhance their in vivo stability and pharmacokinetics in diagnostic assays. The increasing attention has propelled the technical progress of the in vitro selection technology (SELEX) to enhance the efficiency of developing aptamers for commercially interesting targets. This review highlights recent progress in the technical steps of a SELEX experiment with a focus on high-throughput next-generation sequencing and bioinformatics. Achievements have been made in the optimization of aptamer libraries, separation schemes, amplification of the selected libraries and the identification of aptamer sequences from enriched libraries.

Hybrid Approach Combining Boronate Affinity Magnetic Nanoparticles and Capillary Electrophoresis for Efficient Selection of Glycoprotein-Binding Aptamers

Capillary electrophoresis (CE) and magnetic beads have been widely used for the selection of aptamers owing to their efficient separation ability. However, these methods alone are associated with some apparent drawbacks. CE suffers from small injection volumes and thereby only a limited amount of aptamer can be collected at each round. While the magnetic beads approach is often associated with tedious procedure and nonspecific binding. Herein we present a hybrid approach that combines the above two classical aptamer selection methods to overcome the drawbacks associated with these methods alone. In this hybrid method, one single round selection by boronate affinity magnetic nanoparticles (BA-MNPs) was first performed and then followed by a CE selection of a few rounds. The BA-MNPs-based selection eliminated nonbinding sequences, enriching effective sequences in the nucleic acid library. While the CE selection, which was carried out in free solutions, eliminated steric hindrance effects in subsequent selection. Two typical glycoproteins, Ribonuclease B (RNase B) and alkaline phosphatase (ALP), were used as targets. This hybrid method allowed for efficient selection of glycoprotein-binding aptamers within 4 rounds (1 round of BA-MNPs-based selection and 3 rounds of CE selection) and the dissociation constants reached 10^-8 M level. The hybrid selection approach exhibited several significant advantages, including speed, affinity, specificity, and avoiding negative selection. Using one of the selected ALP-binding aptamers as an affinity ligand, feasibility for real application of the selected aptamers was demonstrated through constructing an improved enzyme activity assay.

A DNA Aptamer Against Influenza A Virus: An Effective Inhibitor to the Hemagglutinin-Glycan Interactions

Most therapeutical nucleic acid aptamers tend to inhibit protein-protein interactions and thereby function as antagonists. Attachment of the influenza virus surface glycoprotein hemagglutinin (HA) to sialic acid-containing host cell receptors (glycan) facilitates the initial stage of viral infection. Inhibition of the attachment may result in an antiviral effect on the proliferation of the influenza virus. To develop therapeutically interesting agents, we selected two single-stranded DNA (ssDNA) aptamers specific to the HA protein of H1N1 influenza virus (A/Puerto Rico/8/1934) through a procedure of systematic evolution of ligands by exponential enrichment. As it showed a higher binding affinity for HA protein (Kd = 78 ± 1 nM), aptamer 1 was tested for its ability to interfere with HA-glycan interactions using chicken red blood cell hemagglutination and microneutralization assays, which demonstrated that it significantly suppressed the viral infection in host cells. These results indicate that the isolated ssDNA aptamer may be developed as an antiviral agent against influenza through appropriate therapeutic formulation.

The application of capillary electrophoresis for assisting whole-cell aptamers selection by characterizing complete ssDNA distribution

Whole-cell SELEX faces more difficulties than SELEX against purified molecules target. In this work, we demonstrate the application of capillary electrophoresis for assisting whole-cell aptamers selection by characterizing complete ssDNA distribution. We chose three cancer cell lines U251, Hela and PC3 as target, FAM labeled Sgc8c (a 41mer aptamer) and FAM labeled 41mer random ssDNA library as ssDNA model. CE conditions of running buffer and capillary length and inner diameter as well as UV and LIF detection were optimized. The distribution percentage of Sgc8c and ssDNA library against U251, Hela and PC3 was demonstrated, the relative peak area of their complex is 8.94%, 1.05% and 0.44% for Sgc8c and 9.03%, 1.04% and 0.12% for ssDNA library respectively. Under the chosen experimental conditions, binding ability comparison of three cell lines was U251>Hela>PC3, which was validated by laser confocol microscope. For each cell, distribution percentage of ssDNA library was compared with that of Sgc8c. Finally, whole-cell complex of U251-Sgc8c was confirmed by increase incubation time and fraction CE analysis.

New Surface-Enhanced Raman Sensing Chip Designed for On-Site Detection of Active Ricin in Complex Matrices Based on Specific Depurination

Quick and accurate on-site detection of active ricin has very important realistic significance in view of national security and defense. In this paper, optimized single-stranded oligodeoxynucleotides named poly(21dA), which function as a depurination substrate of active ricin, were screened and chemically attached on gold nanoparticles (AuNPs, ∼100 nm) via the Au-S bond [poly(21dA)-AuNPs]. Subsequently, poly(21dA)-AuNPs were assembled on a dihydrogen lipoic-acid-modified Si wafer (SH-Si), thus forming the specific surface-enhanced Raman spectroscopy (SERS) chip [poly(21dA)-AuNPs@SH-Si] for depurination of active ricin. Under optimized conditions, active ricin could specifically hydrolyze multiple adenines from poly(21dA) on the chip. This depurination-induced composition change could be conveniently monitored by measuring the distinct attenuation of the SERS signature corresponding to adenine. To improve sensitivity of this method, a silver nanoshell was deposited on post-reacted poly(21dA)-AuNPs, which lowered the limit of detection to 8.9 ng mL(-1). The utility of this well-controlled SERS chip was successfully demonstrated in food and biological matrices spiked with different concentrations of active ricin, thus showing to be very promising assay for reliable and rapid on-site detection of active ricin.

Non-Equilibrium Capillary Electrophoresis of Equilibrium Mixtures-Based Affinity Separation and Selective Enrichment of a Long-Length DNA Aptamer

Non-equilibrium capillary electrophoresis of equilibrium mixtures (NECEEM) is a kinetic capillary electrophoresis method used for the affinity analysis of DNA binding to proteins or ligands as well as a rapid selection of DNA aptamers. However, long DNA strands (100-mer or more) are generally difficult to analyse by this method owing to their poor peak separation. Herein, we report optimized conditions (use of a neutral phosphate buffer with an ionic strength of 0.074 as a binding buffer and use of an 80-cm fused silica capillary with a 75-μm internal diameter) for the peak separation of a 100-mer thrombin-binding DNA aptamer-target complex and its consequent enrichment using the NECEEM-based capillary electrophoresis–systematic evolution of ligands by exponential enrichment (CE-SELEX) method.

Surface conformations of an anti-ricin aptamer and its affinity for ricin determined by atomic force microscopy and surface plasmon resonance

We used atomic force microscopy (AFM) and surface plasmon resonance (SPR) to study the surface conformations of an anti-ricin aptamer and its specific binding affinity for ricin molecules. The effect of surface modification of the Au(111) substrate on the aptamer affinity was also estimated. The AFM topography images had a resolution high enough to distinguish different aptamer conformations. The specific binding site on the aptamer molecule was clearly located by the AFM recognition images. The aptamer on a Au(111) surface modified with carboxymethylated-dextran (CD) showed both similarities to and differences from the one without CD modification. The influence of CD modification was evaluated using AFM images of various aptamer conformations on the Au(111) surface. The affinity between ricin and the anti-ricin aptamer was estimated using the off-rate values measured using AFM and SPR. The SPR measurements of the ricin sample were conducted in the range from 83.3 pM to 8.33 nM, and the limit of detection was estimated as 25 pM (1.5 ng mL(-1)). The off-rate values of the ricin-aptamer interactions were estimated using both single-molecule dynamic force spectroscopy (DFS) and SPR as (7.3 ± 0.4) × 10(-4) s(-1) and (1.82 ± 0.067) × 10(-2) s(-1), respectively. The results show that single-molecule measurements can obtain different reaction parameters from bulk solution measurements. In AFM single-molecule measurements, the various conformations of the aptamer immobilized on the gold surface determined the availability of each specific binding site to the ricin molecules. The SPR bulk solution measurements averaged the signals from specific and non-specific interactions. AFM images and DFS measurements provide more specific information on the interactions of individual aptamer and ricin molecules.

Efficient suppression of biofilm formation by a nucleic acid aptamer

Biofilms are microbial communities that are attached to a solid surface using extracellular polymeric substances. Motility and initial attachment mediated by flagella are required for biofilm formation. Therefore, blocking the motility of flagella is a potential strategy to inhibit biofilm formation. In this study, single-stranded DNA aptamers specific to the Salmonella choleraesuis were selected after 14 cycles of the systematic evolution of ligands by exponential enrichment. Among the selected aptamers, the aptamer 3 showed the highest affinity for S. choleraesuis with a dissociation constant (Kd) of 41 ± 2 nM. Aptamer 3, conjugated with magnetic beads, was then used to capture its binding target on the bacteria. After mass spectrometry and specific binding analysis, the flagellin was identified as the target captured by aptamer 3. Furthermore, inhibition experiments, inverted microscopy and atomic force microscopy demonstrated that aptamer 3 was able to control the biofilm formation and promote the inhibitory effect of an antibiotic on bacterial biofilms. Single-stranded DNA aptamers therefore have great potential as inhibitors of biofilm formation.

Current approaches in SELEX: An update to aptamer selection technology

Systematic evolution of ligands by exponential enrichment (SELEX) is a well-established and efficient technology for the generation of oligonucleotides with a high target affinity. These SELEX-derived single stranded DNA and RNA molecules, called aptamers, were selected against various targets, such as proteins, cells, microorganisms, chemical compounds etc. They have a great potential in the use as novel antibodies, in cancer theragnostics and in biomedical research. Vast interest in aptamers stimulated continuous development of SELEX, which underwent numerous modifications since its first application in 1990. Novel modifications made the selection process more efficient, cost-effective and significantly less time-consuming. This article brings a comprehensive and up-to-date review of recent advances in SELEX methods and pinpoints advantages, main obstacles and limitations. The post-SELEX strategies and examples of application are also briefly outlined in this review.

A facile label-free colorimetric aptasensor for ricin based on the peroxidase-like activity of gold nanoparticles

A facile colorimetric aptasensor for ricin based on the peroxidase-like activity of gold nanoparticles was demonstrated for the first time.

Nanomaterial-based cocaine aptasensors

Up to now, many different methods have been developed for detection of cocaine, but most of these methods are usually time-consuming, tedious and require special or expensive equipment. Therefore, the development of simple, sensitive and rapid detection methods is necessary. In the last decade, aptamers have been used as a new biosensor platform for detection of cocaine in different samples. Aptamers are artificial single-stranded DNA or RNA oligonucleotides capable of binding to specific molecular targets with high affinity and if integrated to nanomaterials, it may lead in precise methods for cocaine detection in the common laboratories. In this review, recent advances and applications of aptamer-based biosensors and nanobiosensors, have been updated, paying attention to the use of fluorescence, colorimetric and electrochemical techniques for the detection and quantitative determination of cocaine.

Low pH capillary electrophoresis application to improve capillary electrophoresis-systematic evolution of ligands by exponential enrichment

In this work, a novel low pH CE-SELEX (LpH-CE-SELEX) as a CE-SELEX variant is proposed. Transferring (Trf), bovine serum albumin (BSA) and cytochrome c (Cyt c) as model protein are incubated with a FAM labeled ssDNA library, respectively. Incubation mixture is separated in low pH CE (pH 2.6), where positively charged protein, protein-ssDNA complex and negatively charged ssDNA library migrate oppositely without EOF driven. Analysis of protein-ssDNA complex under positive voltage and unbound ssDNA library under negative voltage by CE-UV are applied for interactive evaluation. By increasing injection time, larger amount protein-ssDNA complex can be collected conveniently at the cathode end whereas ssDNA migrates to anode. Finally, stability of protein-ssDNA complex in low pH CE separation is discussed.

Capillary-driven surface-enhanced Raman scattering (SERS)-based microfluidic chip for abrin detection

Herein, we firstly demonstrate the design and the proof-of-concept use of a capillary-driven surface-enhanced Raman scattering (SERS)-based microfluidic chip for abrin detection. The micropillar array substrate was etched and coated with a gold film by microelectromechanical systems (MEMS) process to integrate into a lateral flow test strip. The detection of abrin solutions of various concentrations was performed by the as-prepared microfluidic chip. It was shown that the correlation between the abrin concentration and SERS signal was found to be linear within the range of 0.1 ng/mL to 1 μg/mL with a limit of detection of 0.1 ng/mL. Our microfluidic chip design enhanced the operability of SERS-based immunodiagnostic techniques, significantly reducing the complication and cost of preparation as compared to previous SERS-based works. Meanwhile, this design proved the superiority to conventional lateral flow test strips in respect of both sensitivity and quantitation and showed great potential in the diagnosis and treatment for abrin poisoning as well as on-site screening of abrin-spiked materials.

High Specific DNAzyme-Aptamer Sensor for Salmonella paratyphi A Using Single-Walled Nanotubes-Based Dual Fluorescence-Spectrophotometric Methods

In this work, single-stranded DNA aptamers that are highly specific to enterotoxigenic Salmonella paratyphi A were obtained from an enriched oligonucleotide pool using Systematic Evolution of Ligands by Exponential Enrichment (SELEX) to target the flagellin protein. The selected aptamers were confirmed to have high sensitivity and specificity to the flagellin. In addition, a probe (P0) containing the DNAzyme and fluorescein isothiocyanate-labeled aptamer3 sequences was employed as a dual probe for observing fluorescence and absorbance changes. The flagellin demonstrated low detection limits of 5 ng/mL by fluorescence and 20 ng/mL by spectrophotometry. Moreover, milk samples spiked with Salmonella paratyphi A were also detected, with the low detection limits increasing to 10(5) CFU/mL by fluorescence and 10(6)CFU/mL by spectrophotometry. The combination of fluorescence and spectrophotometry offers a specific, rapid, and sensitive way for detecting Salmonella paratyphi A and has potential for detecting other pathogens in food.

Transition model for ricin-aptamer interactions with multiple pathways and energy barriers

We develop a transition model to interpret single-molecule ricin-aptamer interactions with multiple unbinding pathways and energy barriers measured by atomic force microscopy dynamic force spectroscopy. Molecular simulations establish the relationship between binding conformations and the corresponding unbinding pathways. Each unbinding pathway follows a Bell-Evans multiple-barrier model. Markov-type transition matrices are developed to analyze the redistribution of unbinding events among the pathways under different loading rates. Our study provides detailed information about complex behaviors in ricin-aptamer unbinding events.

Recent trends in SELEX technique and its application to food safety monitoring

The method referred to as "systemic evolution of ligands by exponential enrichment" (SELEX) was introduced in 1990 and ever since has become an important tool for the identification and screening of aptamers. Such nucleic acids can recognize and bind to their corresponding targets (analytes) with high selectivity and affinity, and aptamers therefore have become attractive alternatives to traditional antibodies not the least because they are much more stable. Meanwhile, they have found numerous applications in different fields including food quality and safety monitoring. This review first gives an introduction into the selection process and to the evolution of SELEX, then covers applications of aptamers in the surveillance of food safety (with subsections on absorptiometric, electrochemical, fluorescent and other methods), and then gives conclusions and perspectives. The SELEX method excels by its features of in vitro, high throughput and ease of operation. This review contains 86 references.

Highly sensitive and rapid visual detection of ricin using unmodified gold nanoparticle probes

A sensitive aptamer-based colorimetric biosensor for the detection of ricin using unmodified gold nanoparticles as probe was developed.

A novel protocol for generating high-affinity ssDNA aptamers by using alternating magnetic fields

A novel non-evolutionary protocol for generating high-affinity ssDNA aptamers using alternating magnetic fields is presented and demonstrated.

Tracking the emergence of high affinity aptamers for rhVEGF165 during capillary electrophoresis-systematic evolution of ligands by exponential enrichment using high throughput sequencing

Capillary electrophoresis-systematic evolution of ligands by exponential enrichment (CE-SELEX) is a powerful technique for isolating aptamers for various targets, from large proteins to small peptides with molecular weights of several kilodaltons. One of the unique characteristics of CE-SELEX is the relatively high heterogeneity of the ssDNA pools that remains even after multiple rounds of selection. Enriched sequences or highly abundant oligonucleotide motifs are rarely reported in CE-SELEX studies. In this work, we employed 454 pyrosequencing to profile the evolution of an oligonucleotide pool through multiple rounds of CE-SELEX selection against the target recombinant human vascular endothelial growth factor 165 (rhVEGF165). High throughput sequencing allowed up to 3 × 10(4) sequences to be obtained from each selected pool and compared to the unselected library. Remarkably, the highest abundance contiguous sequence (contig) was only present in 0.8% of sequences even after four rounds of selection. Closer analyses of the most abundant contigs, the top 1000 oligonucleotide fragments, and even the eight original FASTA files showed no evidence of prevailing motifs in the selected pools. The sequencing results also provided insight into why many CE-SELEX selections obtain pools with reduced affinities after many rounds of selection (typically >4). Preferential amplification of a particular short polymerase chain reaction (PCR) product allowed this nonbinding sequence to overtake the pool in later rounds of selection suggesting that further refinement of primer design or amplification optimization is necessary. High affinity aptamers with 10(-8) M dissociation constants for rhVEGF165 were identified. The affinities of the higher abundance contigs were compared with aptamers randomly chosen from the final selection pool using affinity capillary electrophoresis (ACE) and fluorescence polarization (FP). No statistical difference in affinity between the higher abundance contigs and the randomly chosen aptamers was observed, supporting the premise that CE-SELEX selects a uniquely heterogeneous pool of high affinity aptamers.

Efficient selection of glycoprotein-binding DNA aptamers via boronate affinity monolithic capillary

Systematic evolution of ligands by exponential enrichment (SELEX) is the workhorse method for selecting aptamers that are capable of binding target molecules from a random oligonucleic acid library. However, conventional SELEX methods are associated with apparent drawbacks including labor-intensive, time-consuming, large reagent consumption and strong nonspecific binding with separation media. Herein, we report a boronate affinity monolithic capillary-based SELEX approach for rapid selection of high-specificity glycoprotein-binding DNA aptamers. Boronate affinity monolithic capillary is an advanced functional material appeared in recent years, which allows for facile capture/release of glycoproteins in a pH-switchable fashion. By using boronate affinity monolithic capillary as a platform for target immobilization and aptamer isolation, the proposed SELEX method allowed for efficient selection of glycoprotein-binding aptamers by 6 rounds and the dissociation constants were at 10(-8) M level. Because of the employment of boronate affinity monolithic capillary, the new SELEX approach overcame the above-mentioned drawbacks and provided several significant advantages, including rapid selection speed (only 2 days were needed), high specificity toward the target molecules, and minute reagent consumption.