Perspective on the Future Role of Aptamers in Analytical Chemistry

Aptamer-based assays: strategies in the use of aptamers conjugated to magnetic micro- and nanobeads as recognition elements in food control

An outlook on the current status of different strategies for magnetic micro- and nanosized bead functionalization with aptamers as prominent bioreceptors is given with a focus on electrochemical and optical apta-assays, as well as on aptamer-modified magnetic bead–based miniaturized extraction techniques in food control. Critical aspects that affect interaction of aptamers with target molecules, as well as the possible side effects caused by aptamer interaction with other molecules due to non-specific binding, are discussed. Challenges concerning the real potential and limitations of aptamers as bioreceptors when facing analytical problems in food control are addressed.

Recent Advancements in Aptamer-Based Surface Plasmon Resonance Biosensing Strategies

Surface plasmon resonance (SPR) can track molecular interactions in real time, and is a powerful as well as widely used biological and chemical sensing technique. Among the different SPR-based sensing applications, aptamer-based SPR biosensors have attracted significant attention because of their simplicity, feasibility, and low cost for target detection. Continuous developments in SPR aptasensing research have led to the emergence of abundant technical and design concepts. To understand the recent advances in SPR for biosensing, this paper reviews SPR-based research from the last seven years based on different sensing-type strategies and sub-directions. The characteristics of various SPR-based applications are introduced. We hope that this review will guide the development of SPR aptamer sensors for healthcare.

Rational design of guiding elements to control folding topology in i-motifs with multiple quadruplexes

Nucleic acids are versatile scaffolds that accommodate a wide range of precisely defined operational characteristics. Rational design of sensing, molecular computing, nanotechnology, and other nucleic acid devices requires precise control over folding conformations in these macromolecules. Here, we report a new approach that empowers well-defined conformational transitions in DNA molecular devices. Specifically, we develop tools for precise folding of multiple DNA quadruplexes (i-motifs) within the same oligonucleotide strand. To accomplish this task, we modify a DNA strand with kinetic control elements (hairpins and double stranded stems) that fold on a much faster timescale and consequently guide quadruplexes toward the targeted folding topology. To demonstrate that such guiding elements indeed facilitate formation of the targeted folding topology, we thoroughly characterize the folding/unfolding transitions through a combination of thermodynamic techniques, size exclusion chromatography (SEC) and small-angle X-ray scattering (SAXS). Furthermore, we extend SAXS capabilities to produce a direct insight on the shape and dimensions of the folded quadruplexes by computing their electron density maps from solution scattering data.

Electrochemical Biosensors for Cytokine Profiling: Recent Advancements and Possibilities in the Near Future

Cytokines are soluble proteins secreted by immune cells that act as molecular messengers relaying instructions and mediating various functions performed by the cellular counterparts of the immune system, by means of a synchronized cascade of signaling pathways. Aberrant expression of cytokines can be indicative of anomalous behavior of the immunoregulatory system, as seen in various illnesses and conditions, such as cancer, autoimmunity, neurodegeneration and other physiological disorders. Cancer and autoimmune diseases are particularly adept at developing mechanisms to escape and modulate the immune system checkpoints, reflected by an altered cytokine profile. Cytokine profiling can provide valuable information for diagnosing such diseases and monitoring their progression, as well as assessing the efficacy of immunotherapeutic regiments. Toward this goal, there has been immense interest in the development of ultrasensitive quantitative detection techniques for cytokines, which involves technologies from various scientific disciplines, such as immunology, electrochemistry, photometry, nanotechnology and electronics. This review focusses on one aspect of this collective effort: electrochemical biosensors. Among the various types of biosensors available, electrochemical biosensors are one of the most reliable, user-friendly, easy to manufacture, cost-effective and versatile technologies that can yield results within a short period of time, making it extremely promising for routine clinical testing.

Characterization of DNA aptamer-protein binding using fluorescence anisotropy assays in low-volume, high-efficiency plates

Aptamers have many useful attributes including specific binding to molecular targets. After aptamers are identified, their target binding must be characterized. Fluorescence anisotropy (FA) is one technique that can be used to characterize affinity and to optimize aptamer-target interactions. Efforts to make FA assays more efficient by reducing assay volume and time from mixing to measurement may save time and resources by minimizing consumption of costly reagents. Here, we use thrombin and two thrombin-binding aptamers as a model system to show that plate-based FA experiments can be performed in volumes as low as 2 μL per well with 20 minute incubations with minimal loss in assay precision. We demonstrate that the aptamer-thrombin interaction is best modelled with the Hill equation, indicating cooperative binding. The miniaturization of this assay has implications in drug development, as well as in the efficiency of aptamer selection workflows by allowing for higher throughput aptamer analysis.

Metal-organic frameworks as advanced materials for sample preparation of bioactive peptides

Development of novel affinity materials and separation techniques is crucial for the progress of modern proteomics and peptidomics. Detection of peptides and proteins from complex matrices still remains a challenging task due to the highly complicated biological composition, low abundance of target molecules, and large dynamic range of proteins. As an emerging area of analytical science, metal-organic framework (MOF)-based separation of proteins and peptides is attracting growing interest. This minireview summarizes the recent advances in MOF-based affinity materials for the sample preparation of proteins and peptides. Some newly emerging MOF nanoreactors for the degradation of peptides and proteins are introduced. An update of MOF-based affinity materials for the isolation of glycopeptides, phosphopeptides and low-abundance endogenous peptides in the last two years is focused on. The separation mechanism is discussed along with the chemical structures of MOFs. Finally, the remaining challenges and future development of MOFs in analyzing peptides and proteins in complicated biological samples are discussed.

SELEX-based DNA Aptamer Selection: A Perspective from the Advancement of Separation Techniques

DNA aptamers, which are short, single-stranded DNA sequences that selectively bind to target substances (proteins, cells, small molecules, metal ions), can be acquired by means of the systematic evolution of ligands by exponential enrichment (SELEX) methodology. In the SELEX procedure, one of the keys for the effective acquisition of high-affinity and functional aptamer sequences is the separation stage to isolate target-bound DNA from unbound DNA in a randomized DNA library. In this review, various remarkable advancements in separation techniques for SELEX-based aptamer selection developed in this decade, are described and discussed, including CE-, microfluidic chip-, solid phase-, and FACS-based SELEX along with other methods.

Pesticide Aptasensors-State of the Art and Perspectives

Contamination by pesticides in the food chain and the environment is a worldwide problem that needs to be actively monitored to ensure safety. Unfortunately, standard pesticide analysis based on mass spectrometry takes a lot of time, money and effort. Thus, simple, reliable, cost-effective and field applicable methods for pesticide detection have been actively developed. One of the most promising technologies is an aptamer-based biosensor or so-called aptasensor. It utilizes aptamers, short single-stranded DNAs or RNAs, as pesticide recognition elements to integrate with various innovative biosensing technologies for specific and sensitive detection of pesticide residues. Several platforms for aptasensors have been dynamically established, such as colorimetry, fluorometry, electrochemistry, electrochemiluminescence (ECL) and so forth. Each platform has both advantages and disadvantages depending on the purpose of use and readiness of technology. For example, colorimetric-based aptasensors are more affordable than others because of the simplicity of fabrication and resource requirements. Electrochemical-based aptasensors have mainly shown better sensitivity than others with exceedingly low detection limits. This paper critically reviews the progression of pesticide aptasensors throughout the development process, including the selection, characterization and modification of aptamers, the conceptual frameworks of integrating aptamers and biosensors, the ASSURED (affordable, sensitive, specific, user-friendly, rapid and robust, equipment-free and deliverable to end users) criteria of different platforms and the future outlook.

Detection of chloramphenicol with an aptamer-based colorimetric assay: critical evaluation of specific and unspecific binding of analyte molecules

A chloramphenicol (CAP)-binding aptamer of 80 nucleotides (nt) was reported in 2011. In 2014, it was truncated to 40 nt and has since been used by most researchers, although a careful binding study is still lacking. In this work, binding assays using isothermal titration calorimetry and various DNA-staining dyes were performed. By comparing the truncated aptamer with three control sequences, no specific binding of CAP was observed in each case. The secondary structures of the original and truncated aptamers were analyzed, and it was shown that the likelihood of the truncated aptamer to retain the same binding mechanism as the original sequence is low. We further examined gold nanoparticle (AuNP)-based label-free colorimetric assays. By quantifying the extinction ratio at 620 nm over that at 520 nm, a similar color response was observed regardless of the sequence of DNA, suggesting the color change mainly reflected other events such as the adsorption of CAP by the AuNPs, instead of aptamer binding to CAP. Salt-induced aggregation experiments suggested direct adsorption of CAP on AuNPs. CAP only weakly inhibited DNA adsorption by AuNPs but did not displace pre-adsorbed DNA. Therefore, CAP adsorption by AuNPs needs to be considered when designing related sensors, for example, by using non-aptamer sequences as controls. This work calls for careful confirmation of aptamer binding and control experiments for designing aptamer and AuNP-based biosensors.

Biosensors for rapid detection of Salmonella in food: A review

Salmonella is one of the main causes of foodborne infectious diseases, posing a serious threat to public health. It can enter the food supply chain at various stages of production, processing, distribution, and marketing. High prevalence of Salmonella necessitates efficient and effective approaches for its identification, detection, and monitoring at an early stage. Because conventional methods based on plate counting and real-time polymerase chain reaction are time-consuming and laborious, novel rapid detection methods are urgently needed for in-field and on-line applications. Biosensors provide many advantages over conventional laboratory assays in terms of sensitivity, specificity, and accuracy, and show superiority in rapid response and potential portability. They are now recognized as promising alternative tools and one of the most on-site applicable and end user-accessible methods for rapid detection. In recent years, we have witnessed a flourishing of studies in the development of robust and elaborate biosensors for detection of Salmonella in food. This review aims to provide a comprehensive overview on Salmonella biosensors by highlighting different signal-transducing mechanisms (optical, electrochemical, piezoelectric, etc.) and critically analyzing its recent trends, particularly in combination with nanomaterials, microfluidics, portable instruments, and smartphones. Furthermore, current challenges are emphasized and future perspectives are discussed.

Low Temperature Greatly Enhancing Responses of Aptamer Electrochemical Sensor for Aflatoxin B1 Using Aptamer with Short Stem

Aflatoxin B1 (AFB1), one of the most toxic mycotoxins, poses great health risks. Rapid and sensitive detection of AFB1 is important for food safety, environment monitoring, and health risk assessment. We report here the development of a simple and reusable electrochemical aptasensor for rapid and sensitive detection of AFB1. Main improvements were achieved through engineering an aptamer containing a short stem-loop structure and enhancing the binding affinity at a lower temperature. The DNA aptamer with a methylene blue (MB) label at one end was immobilized on a gold electrode. Upon AFB1 binding, the aptamer folded into a stem-loop structure and brought MB close to the electrode surface, resulting in increases in electric current. The aptamer having a shorter stem (2-4 bp) underwent a larger conformation change upon target binding. The sensors built with the aptamer containing a 2 bp stem generated much higher signal-on responses to AFB1 at 4 °C than at room temperature (25 °C). The improvements resulted in a detection limit of 6 pM, enabling the determination of trace AFB1 in a complex sample matrix. This study demonstrates that low temperature greatly enhances the performance of aptamer electrochemical sensors. This aptasensor is simple to construct and readily regenerated by washing with deionized water for reuse. This aptasensor strategy could be applied to the development of an electrochemical aptasensor for other targets.

Enzyme-powered cascade three-dimensional DNA machine for the ultrasensitive determination of kanamycin

DNA walking machines have been widely used in rapid and sensitive detection. In this work, we develop a single enzyme-powered DNA cascade machine for the ultrasensitive determination of kanamycin. To construct the cascade manner, two types of single-legged three-dimensional DNA walking machine are employed to implement integrated target recognition, signal transduction and signal amplification. Upon adding kanamycin to trigger the upstream machine, the sequential enzymatic cleavage drives the autonomous movement of the walking strand and produces plenty of dye-labeled fragments with fluorescence recovery. Meanwhile, these fragments also serve as walking strands to activate the downstream machine for cascade signal amplification. Taking advantage of this cascade DNA machine, ultrasensitive determination can be accomplished in 60 min. Under the optimum conditions, this method was highly selective toward kanamycin with a detection limit of 28 fM. This cascade signal amplification shows great potential for the rapid screening of antibiotics in food.

Recent advances in separation applications of polymerized high internal phase emulsions

Polymerized high internal phase emulsions as highly porous adsorption materials have received increasing attention and wide applications in separation science in recent years due to their remarkable merits such as highly interconnected porosity, high permeability, good thermal and chemical stability, and tailorable chemistry. In this review, we attempt to introduce some strategies to utilize polymerized high internal phase emulsions for separation science, and highlight the recent advances made in the applications of polymerized high internal phase emulsions for diverse separation of small organic molecules, carbon dioxide, metal ions, proteins, and other interesting targets. Potential challenges and future perspectives for polymerized high internal phase emulsion research in the field of separation science are also speculated at the end of this review.

Reduction in Dynamics of Base pair Opening upon Ligand Binding by the Cocaine-Binding Aptamer

We have used magnetization transfer NMR experiments to measure the exchange rate constant (k_ex) of the imino protons in the unbound, cocaine-bound, and quinine-bound forms of the cocaine-binding DNA aptamer. Both long-stem 1 (MN4) and short-stem 1 (MN19) variants were analyzed, corresponding to structures with a prefolded secondary structure and ligand-induced-folding versions of this aptamer, respectively. The k_ex values were measured as a function of temperature from 5 to 45°C to determine the thermodynamics of the base pair opening for MN4. We find that the base pairs close to the ligand-binding site become stronger upon ligand binding, whereas those located away from the binding site do not strengthen. With the buffer conditions used in this study, we observe imino ¹H signals in MN19 not previously seen, which leads us to conclude that in the free form, both stem 2 and parts of stem 3 are formed and that the base pairs in stem 1 become structured or more rigid upon binding. This is consistent with the k_ex values for MN19 decreasing in both stem 1 and at the ligand-binding site. Based on the temperature dependence of the k_ex values, we find that MN19 is more dynamic than MN4 in the free and both ligand-bound forms. For MN4, ligand-binding results in the reduction of dynamics that are localized to the binding site. These results demonstrate that an aptamer in which the base pairs are preformed also experiences a reduction in dynamics with ligand binding.

Gold nanoparticle aptamer assay for the determination of histamine in foodstuffs

The development of a gold nanoparticle aptamer assay is persued for rapid and sensitive determination of histamine in foodstuffs, which could be deployed for on-site use. The assay is based on a histamine-specific aptamer and gold nanoparticles and the salt-induced aggregation of the particles in the presence of histamine indicated by the color change from red to blue. Gold nanoparticle size, salt type, and concentration as well as aptamer concentration were optimized, and using optimum conditions, a limit of detection of 8 nM (~ 0.05 mg/kg) was obtained. Finally, the aptamer AuNP assay was applied to the determination of histamine in quality control fish samples. The histamine levels of these samples had previously been determined using HPLC and commercial ELISA kits by numerous independent laboratories and a good correlation was obtained. The developed AuNP assay is rapid, sensitive, and reproducible. Graphical abstract.

Dopamine and Melamine Binding to Gold Nanoparticles Dominates Their Aptamer-Based Label-Free Colorimetric Sensing

Target-directed aptamer adsorption by gold nanoparticles (AuNPs) has been widely used to develop label-free colorimetric biosensors. However, the potential interactions between target molecules and AuNPs have not been considered, which may lead to misinterpretation of analytical results. In this work, the detection of dopamine, melamine, and K⁺ was studied as model systems to address this problem. First, dopamine and two control molecules all induced the aggregation of citrate-capped AuNPs with apparent K_d's of 5.8 μM dopamine, 51.6 μM norepinephrine, and 142 μM tyramine. Isothermal titration calorimetry measured the aptamer K_d to be 1.9 μM dopamine and 16.8 μM norepinephrine, whereas tyramine cannot bind. Surface enhanced Raman spectroscopy confirmed direct adsorption of dopamine, and the adsorbed dopamine inhibited the adsorption of DNA. Using a typical salt-induced colorimetric detection protocol, a similar color response was observed regardless of the sequence of DNA, indicating the observed color change reflected the adsorption of dopamine by the AuNPs instead of the binding of dopamine by the aptamer. For this label-free sensor to work, the interaction between the target molecule and AuNPs should be very weak, while dopamine represents an example of strong interactions. For the other two systems, the melamine detection did not reflect aptamer binding either but the K⁺ detection did, suggesting melamine also strongly interacted with AuNPs, whereas K⁺ had very weak interactions with AuNPs. Since each target molecule is different, such target/AuNP interactions need to be studied case-by-case to ensure the sensing mechanism.

Truncated aptamers as selective receptors in a gluten sensor supporting direct measurement in a deep eutectic solvent

Enzyme-linked immunosorbent assays are currently the most popular methods to quantify gluten in foods. Unfortunately, the antibodies used as specific receptors in such methods are not compatible with the usual solvents for the extraction of gluten proteins. In consequence, commercial tests require a high dilution of the sample after the extraction, increasing the limit of quantification and decreasing convenience. In this work, we have rationally truncated an aptamer capable of recognizing gliadin in a deep eutectic solvent (DES). The truncated aptamer is a 19-nucleotides-long DNA that minimizes self-hybridization, allowing the development of an electrochemical sandwich-based sensor for the quantification of gluten in the DES ethaline. The sensor incorporates two identical biotin-labeled truncated aptamers, one of which is immobilized on a carbon screen-printed electrode and the other reports the binding of gliadin after incubation in streptavidin-peroxidase. This sensor can detect gliadin in DES, with a dynamic range between 1 and 100 μg/L and an intra-assay coefficient of variation of 11%. This analytical performance allows the quantification of 20 μg of gluten/kg of food when 1 g of food is extracted with 10 mL of ethaline. We demonstrate the ability of this method to achieve the measurement of gluten in food samples, after the extraction with pure ethaline. The assay is useful for the analysis of residual gluten levels in foods, thus facilitating the evaluation of any potential health risk associated with the consumption of such food by people with celiac disease or other gluten-related disorders.

Aptamer binding assays and molecular interaction studies using fluorescence anisotropy - A review

Binding of nucleic acid aptamers to specific targets and detection with fluorescence anisotropy (FA) or fluorescence polarization (FP) take advantage of the complementary features of aptamers and the fluorescence techniques. We review recent advances in affinity binding assays using aptamers and FA/FP, with an emphasis on studies of molecular interactions and identification of binding sites. Aptamers provide several benefits, including the ease of labelling fluorophores on specific sites, binding-induced changes in aptamer structures, hybridization of the aptamers to complementary sequences, changes in molecular volume upon binding of the aptamer to its target, and adsorption of aptamers onto nanomaterials. Some of these benefits have been utilized for FA/FP assays. Once the aptamer binds to its target, the resulting changes in molecular volume (size), structure, local rotation of the fluorophore, and/or the fluorescence lifetime influence changes to the FA/FP values. Measurements of these fluorescence anisotropy/polarization changes have provided insights into the molecular interactions, such as the binding affinity and the site of binding. Studies of molecular interactions conducted in homogeneous solutions, as well as those with separations, e.g., capillary electrophoresis, have been summarized in this review. Studies on mapping the position of binding in aptamers at the single nucleotide level have demonstrated a unique benefit of the FA/FP techniques and pointed to an exciting direction for future research.

Rolling Circle Amplification-Based Polyvalent Molecular Beacon Probe-Assisted Signal Amplification Strategies for Sensitive Detection of B16 Cells

We developed a simple and sensitive signal amplification method for the detection of B16 cells based on the combination of rolling circle amplification (RCA) and molecular beacons (MBs). A long-chain structure of DNA synthesized by RCA was used to turn on aptamer-based MBs. Because of the multiple complementary repeat units, the RCA scaffold hybridized tens or hundreds of MBs to form polyvalent aptamer probes. The unfold ability and the fluorescence intensity of MBs were both improved by RCA, as compared to short single chains. The cell experiment results demonstrated that RCA-based polyvalent MBs were significantly more effective than monovalent MBs in targeting B16 cells and signal sensitivity because of their multivalent effects. The establishment of this strategy would provide a powerful platform for early clinical diagnostics of cancer cells.

Functionalized DNA-spider silk nanohydrogels for controlled protein binding and release

Hydrogels are excellent scaffolds to accommodate sensitive enzymes in a protective environment. However, the lack of suitable immobilization techniques on substrates and the lack of selectivity to anchor a biocatalyst are major drawbacks preventing the use of hydrogels in bioanalytical devices. Here, nanofilm coatings on surfaces were made of a recombinant spider silk protein (rssp) to induce rssp self-assembly and thus the formation of fibril-based nanohydrogels. To functionalize spider silk nanohydrogels for bioselective binding of proteins, two different antithrombin aptamers were chemically conjugated with the rssp, thereby integrating the target-binding function into the nanohydrogel network. Human thrombin was selected as a sensitive model target, in which the structural integrity determines its activity. The chosen aptamers, which bind various exosites of thrombin, enabled selective and cooperative embedding of the protein into the nanohydrogels. The change of the aptamer secondary structure using complementary DNA sequences led to the release of active thrombin and confirmed the addressable functionalization of spider silk nanohydrogels.

Screening of multiple hemoprotein-specific aptamers and their applications for the binding, quantification, and extraction of hemoproteins in a microfluidic system

The blood hemoproteins, albumin, γ-globulin, and fibrinogen, serve as biomarkers for a variety of human diseases, including kidney and hepatorenal syndromes. Therefore, there is a need to quickly and accurately measure their concentrations in blood. Herein, nucleic acid aptamers demonstrating high affinity and specificity toward these hemoproteins were selected via systematic evolution of ligands by exponential enrichment, and their ability to capture their protein targets was assessed with sodium dodecyl sulfate-polyacrylamide gel electrophoresis followed by a tetramethyl benzidine assay. The limits of detection for the hemoproteins were all around 10-3 μM, and dissociation constant values of 131, 639, and 29nM were obtained; capture rates were measured to be 66%, 71%, and 61%, which is likely to be suitable for clinical diagnostics. Furthermore, a multi-layer microfluidic disk system featuring hemoprotein-specific aptamers for depleting hemoproteins was demonstrated. It could be a promising approach to use aptamers to replace conventional antibodies.

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.

Recent development of nucleic acid nanosensors to detect sequence-specific binding interactions: From metal ions, small molecules to proteins and pathogens

DNA carries important genetic instructions and plays vital roles in regulating biological activities in living cells. Proteins such as transcription factors binds to DNA to regulate the biological functions of DNA, and similarly many drug molecules also bind to DNA to modulate its functions. Due to the importance of protein-DNA and drug-DNA binding, there has been intense effort in developing novel nanosensors in the same length scale as DNA, to effectively study these binding interactions in details. In addition, aptamers can be artificially selected to detect metal ions and pathogens such as bacteria and viruses, making nucleic acid nanosensors more versatile in detecting a large variety of analytes. In this minireview, we first explained the different types and binding modes of protein-DNA and drug-DNA interactions in the biological systems, as well as aptamer-target binding. This was followed by the review of five types of nucleic acid nanosensors based on optical or electrochemical detection. The five types of nucleic acid nanosensors utilizing colorimetric, dynamic light scattering (DLS), surface-enhanced Raman spectroscopy (SERS), fluorescence and electrochemical detections have been recently developed to tackle some of the challenges in high-throughput screening technology for large scale analysis, which is especially useful for drug development and mass screening for pandemic outbreak such as SARS or COVID-19.