Aptamers from random sequence space: Accomplishments, gaps and future considerations

A Fluorescent Aptasensor for Sensitive and Selective Determination of Epigenetic Cancer Biomarker N1-Methyladenosine in Urine Samples

N1-methyladenosine (m1A) level in urine increases in the presence of cancer and is associated with the tumor size and stage. In the present study, we aimed to develop a method for rapid, sensitive and accurate determination of m1A in urine samples. The capture systematic evolution of ligands by exponential enrichment (SELEX) method was used to isolate aptamers that could selectively bind to m1A. We successfully isolated two sequences that have high selectivity toward m1A. The affinities against m1A were determined by isothermal titration calorimetry (ITC) and thioflavin T (ThT) assays. The N1MA1a aptamer has a Kd of 1.9±0.1 µm determined by the ThT assay and 0.75±0.04 µm determined by ITC. A strand-displacement biosensor was designed by labeling the aptamer with a carboxy fluorescein (FAM) and hybridizing it with a quencher-labeled complementary DNA strand. Using this biosensing system, m1A was detected with a detection limit of 1.9 µm. The system shows high selectivity to m1A and high tolerance to adenosine, cytidine, guanosine, thymidine, uridine and N6-methyladenosine (m6A) as well as urine constituents at their real levels in urine. The sensor has been applied to five different human urine samples showing quantitative recovery values, which indicates practical potential of this aptamer-based biosensor.

Increasing Aptamer Affinity from Millimolar to Nanomolar by Forming a Covalent Adduct for Detecting Acrylamide

Being a neurotoxin and carcinogen, acrylamide has been an important target for developing biosensors. DNA aptamers are attractive for making biosensors due to their programmable structure, low cost, and ease of modification. However, DNA aptamers have poor affinities to low-binding epitope target molecules such as acrylamide. In this work, an aptamer for acrylamide was isolated with an apparent Kd of 10.5 mM using a thioflavin T fluorescence assay and 4.7 mM using the fluorescence strand-displacement assay. To improve binding affinity, acrylamide was reacted with xanthydrol to form a covalent adduct, and a new aptamer selected for this adduct achieved a Kd of 20 nM using the strand-displacement assay, representing an improvement of 235,000-fold. Using the strand-displacement biosensor, a limit of detection of 4.2 nM was achieved for the adduct. This work demonstrates a practical route to convert low epitope targets to high-affinity targets for aptamer binding and bioanalytical applications.

Nanostructured aptasensors for ricin detection and tumor therapy: exploring aptamer-protein interactions and conformational stability in biological complexities

Aptamers are distinctive single-stranded oligonucleotides derived through in vitro evolution, and exhibit exceptional ability in binding to target proteins. Structural modifications of aptamers can profoundly regulate their interactions with proteins, thereby influencing associated cellular behavior. Recent research focused on modulating aptamer-protein interaction in complex biological environments to regulate various biological processes. However, in such crowded conditions, aptamer conformation and stability are susceptible to nuclease degradation, which can impair stable binding to target. Ricin is recognized as a significant biological toxin protein, distinguished by its widespread availability, remarkable dissemination, and resilience including wide pH tolerance, remarkable thermostability, and solubility. RTA is an enzymatic subunit of ricin, that can inactivate approximately 2000 ribosomes per minute, rapidly halting protein synthesis, making it a powerful candidate for tumor therapy. By leveraging the potent cytotoxicity of ricin, coupled with the targeting precision of aptamers and the versatility of nanomaterials, a powerful approach emerges for both targeted tumor therapy and highly sensitive detection of ricin. Although there have been some insightful reports on aptamers applied in ricin detection, a systematic discussion remains limited. In this context, we provide an in-depth overview of techniques used to analyze aptamer-ricin interactions and explore the potential of ricin-aptamer interactions in clinical diagnosis.

Controlled Nanoconfinement in a Microfluidic Modular Bead Array Device via Elastomeric Diaphragm Collapse for Enhancing Biomolecular Binding Kinetics

Nanoscale confinement strategies alleviate diffusional transport limitations to enhance target binding kinetics with receptors, motivating their utilization for screening and selecting receptors based on binding affinities with target molecules. Herein, a modular and multiplexed device for creating nanoconfinement is presented through the collapse of an elastomeric diaphragm onto microbead arrays immobilized with biomolecules, followed by repeated diaphragm withdrawal to promote bulk transport, thereby enhancing receptor binding kinetics. To repeatedly create controlled nanoconfinement over large spatial extents on the bead, the diaphragm is integrated on its top side with a strain sensor for modulating vertical displacement, while microfabricated nanoposts (≈500 nm depth) on its bottom side control the lateral extent. The modular platform enables facile assembly of beads, each immobilized with different targets into eight microwells for multiplexed screening of receptors, and facile disassembly for quantifying DNA-binding on each bead by downstream q-PCR. Nanoconfinement enhances biomolecular binding at 1 Hz diaphragm pressurization, as validated by rapid DNA immobilization (time constant of ≈6 min vs >60 min under no confinement) and through saturating the binding of target molecules with optimal aptamer candidates (88% site occupancy vs 5% under no confinement at 10 nm levels), thereby screening candidate receptors based on binding affinity parameters.

Theoretical Basis for the Highly Efficient Aptamer Selection Using Unique Molecular Identifiers

Rapid selection methods are crucial for promoting the discovery and application of aptamers across various fields. We previously reported a highly efficient aptamer selection strategy by using unique molecular identifiers (UMIs), enabling the efficient isolation of aptamers from a single cell by only one round. The strategy integrates an ultrasensitive DNA barcoding technology with high-throughput sequencing to accurately quantify aptamer candidates, thereby mitigating issues such as PCR bias and sequence overenrichment that are inherent in traditional multiround selection. Here, we conduct a systematically theoretical analysis of this strategy in the elucidation of the theoretical basis, advantages, and applicability. The feasibility and advantages of isolating aptamers from low-enriched DNA libraries was investigated at a theoretical level, showing that this strategy is effective in reducing nonspecific binding and thus increasing the success of selecting high-affinity aptamers. Our theoretical analysis supports the broad applicability of the strategy for the single-round aptamer selection, paving the way for its widespread adoption in high-efficiency aptamer discovery and aptamer-based cell atlas.

Profiling Nascent Tumor Extracellular Vesicles via Metabolic Timestamping and Aptamer-Driven Specific Click Chemistry

Tumor-derived extracellular vesicles (tEVs) are essential mediators of tumor progression and therapeutic resistance, yet their secretion dynamics and cargo composition in response to therapies remain poorly understood. Here, we present STAMP, specific click-tagging driven by aptamer for tEV labeled with a metabolic timestamp, which exploits the unique kinetics and thermodynamics of aptamer to significantly enhance the local concentration of clickable probes on tEVs for their covalent attachment to the timestamp, resulting in the selective microfluidic isolation of nascent tEVs following stimulation. In a PD-L1 antibody-treated model, we demonstrated the feasibility of STAMP and revealed a robust positive correlation between the nascent EpCAM+ EV levels and tumor volume. Proteome profiling of isolated nascent tEVs identified previously unknown upregulated vesicle proteins following immunotherapy, including key regulators of immune activation and suppression, suggesting that tumors orchestrate an intricate dual adaptive response through tEV secretion modulation to simultaneously elicit therapeutic sensitivity and resistance. Notably, among the upregulated proteins, we identified HSP70, whose enhanced presentation on tEVs promotes antitumor immunity and inhibits tumor growth. Thus, STAMP provides an effective gateway for studying EV dynamics with cell-origin accuracy and for identifying potential therapeutic targets based on EV transitions.

Computation-Enabled Structure-Based Discovery of Potent Binders for Small-Molecule Aptamers

Aptamers, functional nucleic acids recognized for their high target-binding affinity and specificity, have been extensively employed in biosensors, diagnostics, and therapeutics. Conventional screening methods apply evolutionary pressure to optimize affinity, while counter-selections are used to minimize off-target binding and improve specificity. However, aptamer specificity characterization remains limited to target analogs and experimental controls. A systematic exploration of the chemical space for aptamer-binding chemicals (targets) is crucial for uncovering aptamer versatility and enhancing target specificity in practical applications, a task beyond the scope of experimental approaches. To address this, we employed a high-throughput three-stage structure-based computational framework to identify potent binders for two model aptamers. Our findings revealed that the l-argininamide (L-Arm)-binding aptamer has a 31-fold higher affinity for the retromer chaperone R55 than for L-Arm itself, while guanethidine and ZINC10314005 exhibited comparable affinities to L-Arm. In another case, norfloxacin and difloxacin demonstrated over 10-fold greater affinity for the ochratoxin A (OTA)-binding aptamer OBA3 than OTA, introducing a fresh paradigm in aptamer-target interactions. Furthermore, pocket mutation studies highlighted the potential to tune aptamer specificity, significantly impacting the bindings of L-Arm or norfloxacin. These findings demonstrate the effectiveness of our computational framework in discovering potent aptamer binders, thereby expanding the understanding of aptamer-binding versatility and advancing nucleic acid-targeted drug discovery.

Development of a novel label-free NIR aptasensor based on triphenylmethane dyes for rapid and sensitive detection of copper ions

Heavy metal pollution, particularly from copper ions (Cu2+), poses a significant threat to both the ecological environment and human health. However, traditional copper ion analysis techniques are often hindered by the need for expensive equipment, labor-intensive sample preparation and skilled operation, which limits their effectiveness for field and real-time applications. In this work, we report a novel near-infrared aptamer sensor (NIRApt) that originates from the binding reaction between the DNA aptamer AptCu and the fluorescent small molecule crystal violet (CV), enabling rapid detection of Cu2+ through the competitive effect of Cu2+ with AptCu. This sensor shows a significant enhancement in NIR fluorescence after aptamer binding. NIRApt exhibits superior performance, requiring only three core components to achieve a fast response time and operational simplicity in less than a minute. The sensor shows high sensitivity with a detection limit as low as 61 nM, making it suitable for the detection of trace amounts of Cu2+ in diverse samples. The efficacy of NIRApt has been validated through successful applications in real water samples, highlighting its promising potential for environmental monitoring.

A Facile Label-Free Colorimetric Assay for DNase I Activity Based on the Peroxidase-Like Activity of Functional Nucleic Acids

DNase I plays a crucial role in fundamental biological processes, including gene expression, DNA repair, and apoptosis. Therefore, it is important to develop a simple and efficient method to detect DNase I activity. In this work, a colorimetric assay based on functional nucleic acid for sensitive DNase I detection was reported. The functional nucleic acids with G-rich bases exhibit peroxidase-like activity under acetic acid conditions, capable of catalyzing the oxidation of chromogenic substrate 3,3',5,5'-tetramethylbenzidine (TMB). The specific nucleic acid is designed as the substrate for DNase I, which can hydrolyze the strand and reduce the catalytic activity of the reaction system. Based on this, a sensitive, simple, efficient, and cost-effective colorimetric detection platform was constructed for the quantitative analysis of DNase I. The detection limit (3σ/s) for DNase I was 0.046 U/mL with a linear range of 0.1-1 U/mL. Moreover, the practicality of this colorimetric detection platform was demonstrated by detecting DNase I in human serum.

Aptamer-based fluorescence biosensor for rapid detection of chloramphenicol based on pyrene excimer switch

Chloramphenicol (CAP) is widely used in treating bacteria infection in animals and humans. However, the accumulation of CAP in food and environment caused serious health risk to human. Consequently, sensitive and selective detection of CAP is of great importance in environmental monitoring and food safety. Among various analytical methods, aptamer-based biosensors exhibit great potentials for CAP detection. Here, we developed an aptamer-based biosensor for rapid fluorescence detection of CAP based on pyrene excimer switch by using a newly selected short DNA aptamer with high affinity. The aptamer was labeled with pyrene molecules at both ends. The binding of CAP to the aptamer probe caused two pyrene molecules close to each other and the formation of a pyrene excimer, which induced the increase of the fluorescence signal from the pyrene excimer. CAP detection was achieved by measuring the fluorescence signal changes of the aptamer probes with dual pyrene labels. Under optimized conditions, the developed aptamer biosensor showed a detection limit of 24.4 nmol/L for CAP. The aptamer-based fluorescence sensor could quantify CAP in diluted tap water and lake water, exhibiting potentials for the application in real sample sensing of CAP.

A CRISPR/Cas12a-based competitive aptasensor for ochratoxin A detection

The serious contamination of ochratoxin A (OTA) in agricultural products has promoted the development of rapid, sensitive, and selective analytical methods for OTA monitoring. We demonstrated a competitive aptasensor for OTA detection using CRISPR/Cas12a as an effective signal amplifier. OTA competes with complementary DNA of the aptamer on the microplate to bind to the aptamer. Streptavidin bridges the biotinylated aptamer and biotinylated activator to convert the OTA input into Cas12a activation, which cleaves fluorescent DNA reporters. Under optimized experimental conditions, the aptasensor was demonstrated to work well for sensitive detection of OTA, with a linear range from 0.5 nM to 62.5 nM and a detection limit of 0.5 nM. Moreover, our method not only exhibits high selectivity, but also has satisfactory anti-interference ability against complex sample matrices. Taken together, the CRISPR/Cas12a-based competitive aptasensor offers a simple and sensitive platform for OTA detection, and it holds great promise for food security monitoring.

Fighting Mutations with Mutations: Evolutionarily Adapting a DNA Aptamer for High-Affinity Recognition of Mutated Spike Proteins of SARS-CoV-2

An on-going challenge with COVID-19, which has huge implications for future pandemics, is the rapid emergence of viral variants that makes diagnostic tools less accurate, calling for rapid identification of recognition elements for detecting new variants caused by mutations. We hypothesize that we can fight mutations of the viruses with mutations of existing recognition elements. We demonstrate this concept via rapidly evolving an existing DNA aptamer originally selected for the spike protein (S-protein) of wildtype SARS-CoV-2 to enhance the interaction with the same protein of the Omicron variants. The new aptamer, MBA5SA1, has acquired 22 mutations within its 40-nucleotide core sequence and improved its binding affinity for the S-proteins of diverse Omicron subvariants by >100-fold compared to its parental aptamer (improved from nanomolar to picomolar affinity). Deep sequencing analysis reveals dynamic competitions among several MBA5SA1 variants in response to increasing selection pressure imposed during in vitro selection, with MBA5SA1 being the final winner of the competition. Additionally, MBA5SA1 was implemented into an enzyme-linked aptamer binding assay (ELABA), which was applied for detecting Omicron variants in the saliva of infected patients. The assay produced a sensitivity of 86.5 % and a specificity of 100 %, which were established with 83 clinical samples.

Serum assisted PD-L1 aptamer screening for improving its stability

Aptamers have shown potential for diagnosing clinical markers and targeted treatment of diseases. However, their limited stability and short half-life hinder their broader applications. Here, a real sample assisted capture-SELEX strategy is proposed to enhance the aptamer stability, using the selection of specific aptamer towards PD-L1 as an example. Through this developed selection strategy, the aptamer Apt-S1 with higher binding affinity and specificity towards PD-L1 was obtained as compared to the aptamer Apt-A2 which was screened by the traditional capture-SELEX strategy. Moreover, Apt-S1 exhibited a greater PD-L1 binding associated conformational change than Apt-A2, indicating its suitability as a biorecognition element. These findings highlight the potential of Apt-S1 in clinical applications requiring robust and specific targeting of PD-L1. Significantly, Apt-S1 exhibited a lower degradation rate in 10% diluted serum or pure human serum, under the physiological temperature and pH value, compared to Apt-A2. This observation suggested that Apt-S1 possesses higher stability and is more resistant to damage caused by the serum environmental factors, highlighting the superior stability of Apt-S1 over Apt-A2. Furthermore, defatted and deproteinized serum were used to investigate the potential reasons for the improved stability of Apt-S1. The results hinted that the pre-adaptation to nucleases present in serum during the selection process might have contributed to its higher stability. With its improved stability, higher affinity and specificity, Apt-S1 holds great potential for applications in PD-L1 assisted cancer diagnosis and treatment. Meanwhile, the results obtained in this work provide further evidence of the advantages of the real capture-SELEX strategy in improving aptamer stability compared to the traditional strategy.

Research Progress in Small-Molecule Detection Using Aptamer-Based SERS Techniques

Nucleic acid aptamers are single-stranded oligonucleotides that are selected through exponential enrichment (SELEX) technology from synthetic DNA/RNA libraries. These aptamers can specifically recognize and bind to target molecules, serving as specific recognition elements. Surface-enhanced Raman scattering (SERS) spectroscopy is an ultra-sensitive, non-destructive analytical technique that can rapidly acquire the "fingerprint information" of the measured molecules. It has been widely applied in qualitative and trace analysis across various fields, including food safety, environmental monitoring, and biomedical applications. Small molecules, such as toxins, antibiotics, and pesticides, have significant biological effects and are harmful to both human health and the environment. In this paper, we mainly introduced the application and the research progress of SERS detection with aptamers (aptamer-based SERS techniques) in the field of small-molecule detection, particularly in the analysis of pesticide (animal) residues, antibiotics, and toxins. And the progress and prospect of combining the two methods in detection were reviewed.

Dimeric DNA Aptamers for the Spike Protein of SARS-CoV-2 Derived from a Structured Library with Dual Random Domains

Multimeric aptamer strategies are often adopted to improve the binding affinity of an aptamer toward its target molecules. In most cases, multimeric aptamers are constructed by connecting pre-identified monomeric aptamers derived from in vitro selection. Although multimerization provides an added benefit of enhanced binding avidity, the characterization of different aptamer pairings adds more steps to an already lengthy procedure. Therefore, an aptamer engineering strategy that directly selects for multimeric aptamers is highly desirable. Here, an in vitro selection strategy is reported on using a pre-structured DNA library that forms dimeric aptamers. Rather than using a library containing a single random region, which is nearly ubiquitous in existing aptamer selections, the library contains two random regions separated by a flexible poly-thymidine linker. Following sixteen rounds of selection against the SARS-CoV-2 spike protein, a relevant model target protein due to the COVID-19 pandemic, the top aptamers displayed superb affinity with KD values as low as 150 pM. Further analysis reveals that each random region functions as a distinct binding moiety and works together to achieve higher affinity. The demonstrated strategy provides an accelerated method to obtain high-affinity aptamers, which may prove useful in future aptamer diagnostic and therapeutic applications.

High-throughput and computational techniques for aptamer design

INTRODUCTION

Aptamers refer to short ssDNA/RNA sequences that target small molecules, proteins, or cells. Aptamers have significantly advanced diagnostic applications, including biosensors for detecting specific biomarkers, state-of-the-art imaging, and point-of-care technology. Molecular computation helps identify aptamers with high-binding affinity, enabling high-throughput screening, predicting 3D structures, optimizing aptamers for improved stability, specificity, and complex target interactions.

AREA COVERED

Aptamers are versatile in the development of specific and sensitive diagnostics. However, there needs to be more understanding of the precise workflow that integrates sequence, structure, and interaction with the target. In this review, the author discusses how significant progress has been made in aptamer discovery using bioinformatics for sequence analysis, docking to model interactions, and MD simulations to account for dynamicity and predict free-energy. Furthermore, the author discusses how quantum chemical calculations are critical for modelling electronic structures and assignin spectroscopic signals.

EXPERT OPINION

Incorporating machine learning into the aptamer discovery brings a transformative advancement. With NGS datasets, SELEX, and experimental structures, the implementation of newer workflows yields aptamers with improved binding affinity. Leveraging transfer learning to models using experimental structures and aptamer sequences expands the aptamer design space significantly. As ML continues to evolve, it is poised to become central in accelerating aptamer discovery for biomedical applications in the next 5 years.

Isolation and characterization of ssDNA aptamers against BipD antigen of Burkholderia pseudomallei

BACKGROUND

Melioidosis is difficult to diagnose due to its wide range of clinical symptoms. The culture method is time-consuming and less sensitive, emphasizing the importance of rapid and accurate diagnostic tests for melioidosis. Burkholderia invasion protein D (BipD) of Burkholderia pseudomallei is a potential diagnostic biomarker. This study aimed to isolate and characterize single-stranded DNA aptamers that specifically target BipD.

METHODS

The recombinant BipD protein was produced, followed by isolation of BipD-specific aptamers using Systematic Evolution of Ligands by EXponential enrichment. The binding affinity and specificity of the selected aptamers were evaluated using Enzyme-Linked Oligonucleotide Assay.

RESULTS

The fifth SELEX cycle showed a notable enrichment of recombinant BipD protein-specific aptamers. Sequencing analysis identified two clusters with a total of seventeen distinct aptamers. AptBipD1, AptBipD13, and AptBipD50 were chosen based on their frequency. Among them, AptBipD1 exhibited the highest binding affinity with a Kd value of 1.0 μM for the recombinant BipD protein. Furthermore, AptBipD1 showed significant specificity for B. pseudomallei compared to other tested bacteria.

CONCLUSION

AptBipD1 is a promising candidate for further development of reliable, affordable, and efficient point-of-care diagnostic tests for melioidosis.

Selection of Plastic-Binding DNA Aptamers for Microplastics Detection

Plastics are critical materials for modern technological applications, yet environmental contamination by microplastics has become a growing concern. In this study, DNA aptamers were isolated for two of the most abundant plastic materials: polyvinylchloride (PVC) and polystyrene (PS). These aptamers contain approximately 90 % cytosine and thymine but only 10 % purine content. Among them, the PVC-1 aptamer binds to PVC with a six-fold higher capacity than a random sequenced DNA. Among the tested plastic materials, PVC and PS exhibited the highest specific binding capacity. Using fluorophore-labeled PVC-1 aptamer, PS/PVC microplastics as low as 1 mg were detected, and the aptamer was selective for microplastics over other environmentally relevant materials, such as silica. Molecular dynamics simulations indicated that the aptamer attempted to maximize contact with the plastic surface for adsorption. This plastic-binding aptamer is expected to find applications in environmental monitoring and has fundamental implications for surface-binding aptamers.

A high affinity and selective DNA aptamer for copper ions

Capture-SELEX was employed for the selection of DNA aptamers for Cu2+. The best aptamer named Cu-1 has a Kd of 14.2 nM as determined using the strand-displacement assay, representing an approximate 3000-fold improvement over a previously reported Cu2+ aptamer. The sensor achieved a limit of detection of 2.1 nM.

Recent Developments in Aptamer-Based Sensors for Diagnostics

Chronic and non-communicable diseases (NCDs) account for a large proportion of global disorders and mortality, posing significant burdens on healthcare systems. Early diagnosis and timely interference are critical for effective management and disease prevention. However, the traditional methods of diagnosis still suffer from high costs, time delays in processing, and infrastructure requirements that are usually unaffordable in resource-constrained settings. Aptamer-based biosensors have emerged as promising alternatives to offer enhanced specificity, stability, and cost-effectiveness for disease biomarker detection. The SELEX (Systematic Evolution of Ligands by Exponential Enrichment) methodology allows developing aptamers with high-affinity binding capabilities to a variety of targets, for instance proteins, cells, or even small molecules, hence rendering them suitable for NCD diagnosis. Aptasensors-recent developments in the electrochemical and optical dominion-offer much enhanced sensitivity, selectivity, and stability of detection across a diverse range of diseases from lung cancer and leukemia to diabetes and chronic respiratory disorders. This study provides a comprehensive review of progress in aptamer-based sensors, focusing on their role in point-of-care diagnostics and adaptability in a real-world environment with future directions in overcoming current limitations.

Higher Affinity Enables More Accurate Detection of SARS-CoV-2 in Human Saliva Using Aptamer-Based Litmus Test

Many aptamers have been generated by systematic evolution of ligands by exponential enrichment (SELEX) to recognize spike proteins of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2&ek), some of which have been engineered into dimeric and trimeric versions for enhanced affinity for diagnostic applications. However, no studies have been conducted to compare the utilities of monomeric, dimeric and trimeric aptamers in diagnostic assays with real clinical samples to answer the question of what levels of affinity an aptamer must have for accurate clinical diagnostics. Herein, we carried out a comparative study with two monomeric aptamers MSA1 and MSA5, one dimeric aptamer and two homotrimeric aptamers constructed with MSA1 and MSA5, with affinity varying by 1000-fold. Using a colorimetric sandwich assay to analyze 48 human saliva samples, we found that the trimeric aptamer assay (Kd≈10 pM) can identify the SARS-CoV-2 infection much more accurately than the dimeric aptamer assay (Kd≈100 pM) and monomeric aptamer assay (Kd≈10,000 pM). Based on the experimental data, we theoretically predict the levels of affinity an aptamer needs to possess to achieve 80-100 % sensitivity and 100 % specificity. The findings from this study highlight the need for deriving very high affinity aptamers to enable highly accurate detection of viral infection for future pandemics.

Phage LysSA163-CBD mediated specific recognition coupled with ATP bioluminescence for the sensitive detection of viable Staphylococcus aureus in food matrices

BACKGROUND

Staphylococcus aureus is a significant foodborne pathogen, commonly detected in milk and meat products. Conventional detection methods have limited sensitivity and specificity, which are time-consuming and susceptible to background interference from complex samples, and cannot effectively distinguish live and dead bacteria.

RESULTS

Herein, we developed a novel adenosine triphosphate (ATP) bioluminescence method coupled with magnetic separation, which is based on phage-encoded endolysin LysSA163-CBD (CBD 163) for rapid and specific detection of viable Staphylococcus aureus. The expressed protein (CBD 163) was derived from the phage LSA2301 and was successfully expressed in Escherichia coli BL21 following an induction period of 4 h at 37 °C, with a molecular weight approximating 40 kDa. The optimal conditions for CBD-magnetic beads (cMBs) to capture S. aureus cells were determined to be 100 μL/mL cMBs at 25 °C for 30 min. The viable S. aureus cells were disrupted by the Cetyl trimethyl ammonium bromide (CTAB) to release intracellular ATP. Then, the ATP reacted with the firefly luciferase and D-Luciferin-based bioluminescence (BL) reagents solution to generate intensive BL signal. The CBD-magnetic separation-ATP bioluminescence (cMS-BL) assay was able to quickly detect viable S. aureus via ATP bioluminescence in 45 min, with a detection range from 5 × 103 to 5 × 107 CFU/mL and limit of detection (LOD) of 190 CFU/mL. Additionally, the cMS-BL method exhibited high specificity and anti-interference ability, which has been successfully applied to quantify S. aureus cells in crayfish-tail, chicken, and skim milk.

SIGNIFICANCE AND NOVELTY

These results demonstrate the potential of CBD 163 as a versatile and robust biorecognition element for rapid and specific detection of viable S. aureus in food matrices. The proposed phage-derived bacteria-binding proteins-based protocol for BL detection shows various advantages, including high sensitivity, simple operation, and the capability to distinguish live bacteria, providing a strategy for designing high-quality biorecognition element toward foodborne pathogens.

The Emerging Era of Molecular Medicine

The era of molecular medicine arose as we began to diagnose and treat diseases based on understanding how genes, proteins, and cells work, providing optimal therapeutic care through molecular profiling. Central to molecular medicine is molecular recognition, which is underpinned by techniques involving omics analysis, gene editing, and targeted agents. Recent advancements in these tools not only expand our understanding of biological processes but also aid in the development of diagnostic and treatment modalities at the molecular level, thus bridging the gap between medical research and clinical applications. This perspective traces the development of molecular tools, highlighting, along the way, their pivotal role in advancing molecular medicine for the global health of people.

Spatial Engineering of Heterotypic Antigens on a DNA Framework for the Preparation of Mosaic Nanoparticle Vaccines with Enhanced Immune Activation against SARS-CoV-2 Variants

Mosaic nanoparticle vaccines with heterotypic antigens exhibit broad-spectrum antiviral capabilities, but the impact of antigen proportions and distribution patterns on vaccine-induced immunity remains largely unexplored. Here, we present a DNA nanotechnology-based strategy for spatially assembling heterotypic antigens to guide the rational design of mosaic nanoparticle vaccines. By utilizing two aptamers with orthogonal selectivity for the original SARS-CoV-2 spike trimer and Omicron receptor-binding domain (RBD), along with a DNA soccer-ball framework, we precisely manipulate the spacing, stoichiometry, and overall distribution of heterotypic antigens to create mosaic nanoparticles with average, bipolar, and unipolar antigen distributions. Systematic in vitro and in vivo immunological investigations demonstrate that 30 heterotypic antigens in equivalent proportions, with an average distribution, lead to higher production of broad-spectrum neutralizing antibodies compared to the bipolar and unipolar distributions. Furthermore, the precise assembly utilizing our developed methodology reveals that a mere increment of five Omicron RBD antigens on a nanoparticle (from 15 to 20) not only diminishes neutralization against the Omicron variant but also triggers excessive inflammation. This work provides a unique perspective on the rational design of mosaic vaccines by highlighting the significance of the spatial placement and proportion of heterotypic antigens in their structure-activity mechanisms.

Monitoring of trace oxytetracycline using a porphyrin-MOF layer-based electrochemical aptasensor

A two-dimensional porphyrin-MOF nanolayer was developed to construct an electrochemical aptasensor for monitoring oxytetracycline from 0.01 pg mL-1 to 0.1 ng mL-1. This aptasensor exhibited high sensitivity, outstanding selectivity, good stability, fine reproducibility, and quantitative detection ability in real samples.

Cost-effective evaluation of Aptamer candidates in SELEX-based Aptamer isolation

Aptamers are short, single-stranded nucleic acids with high affinity and specificity for various targets, making them valuable in diagnostics and therapeutics. Their isolation traditionally involves a time-consuming and costly process called SELEX. While SELEX methods have evolved to improve binding and amplification, the crucial step of aptamer identification from sequencing data remains expensive and often overlooked. Common identification methods require modification of aptamer candidates with labels like biotin or fluorescent dyes, which becomes costly and cumbersome for high-throughput sequencing data. This paper presents an efficient and cost-effective approach to streamline aptamer identification. It employs asymmetric polymerase chain reaction (PCR) to generate modified single-stranded DNA copies of aptamer candidates, simplifying the modification process. By using excess modified forward primers and limited reverse primers, this method reduces costs since only unmodified candidates need to be synthesized initially. The approach was demonstrated with an IgE protein aptamer and successfully applied to identify aptamers from a pool of 12 candidates against a monoclonal antibody. The validity of the results was further confirmed through the direct synthesis of fluorophore-conjugated aptamer candidates, yielding consistent outcomes while reducing the cost by threefold. This approach addresses a critical bottleneck in aptamer discovery by significantly reducing the time and cost associated with aptamer identification, facilitating aptamer-based research and making aptamers more accessible for various applications in diagnostics and therapeutics.

Selection of structure-induced aptamer targeting small molecule based on capillary sieving electrophoresis

In this study, a structure-induced aptamer targeting small molecules was selected using capillary sieving electrophoresis (CSE). CSE was conducted using a capillary filled with a background solution containing hydroxypropyl cellulose as a sieving matrix to separate the aptamer candidates by changing their structures via complexation. Before aptamer selection, the original random-sequence DNA library was used to create structure-not-preorganized DNA sub-library containing straight-chain-like structures using CSE. Next, a structure-induced aptamer targeting L-tyrosinamide was selected from the prepared sub-library. Six aptamer candidates were selected, one of which showed a binding ability comparable to that of the reported L-tyrosinamide aptamer and selectivity toward the analogs. These results indicated that the proposed method can be applied to select structure-induced aptamers that target small molecules.

Graphene Multiplexed Sensor for Point-of-Need Viral Wastewater-Based Epidemiology

Wastewater-based epidemiology (WBE) can help mitigate the spread of respiratory infections through the early detection of viruses, pathogens, and other biomarkers in human waste. The need for sample collection, shipping, and testing facilities drives up the cost of WBE and hinders its use for rapid detection and isolation in environments with small populations and in low-resource settings. Given the ubiquitousness and regular outbreaks of respiratory syncytial virus, SARS-CoV-2, and various influenza strains, there is a rising need for a low-cost and easy-to-use biosensing platform to detect these viruses locally before outbreaks can occur and monitor their progression. To this end, we have developed an easy-to-use, cost-effective, multiplexed platform able to detect viral loads in wastewater with several orders of magnitude lower limit of detection than that of mass spectrometry. This is enabled by wafer-scale production and aptamers preattached with linker molecules, producing 44 chips at once. Each chip can simultaneously detect four target analytes using 20 transistors segregated into four sets of five for each analyte to allow for immediate statistical analysis. We show our platform's ability to rapidly detect three virus proteins (SARS-CoV-2, RSV, and Influenza A) and a population normalization molecule (caffeine) in wastewater. Going forward, turning these devices into hand-held systems would enable wastewater epidemiology in low-resource settings and be instrumental for rapid, local outbreak prevention.

Nanostructured transition metal dichalcogenides-based colorimetric sensors: Synthesis, characterization, and emerging applications

Nanostructured transition metal dichalcogenides (TMDCs) have garnered significant attention as prospective materials for the development of highly sensitive and versatile colorimetric sensors. This work explores the synthesis, characterization, and emerging applications of TMDC-based sensors, focusing on their unique structural aspects and inherent properties. The synthesis methods involve tailored fabrication techniques, such as chemical vapor deposition and hydrothermal processes, aimed at producing well-defined nanostructures that enhance sensor performance. Characterization techniques, including microscopy, spectroscopy, and surface analysis, are employed to elucidate the structural and chemical features of the nanostructured TMDCs. These analyses provide insights into the correlation between the material's morphology and its sensing capabilities. The colorimetric sensing mechanism relies on the modulation of optical properties in response to specific analytes, enabling rapid and visual detection. The emerging applications of TMDC-based colorimetric sensors span diverse fields, including environmental monitoring, healthcare, and industrial processes. The sensors exhibit high sensitivity, selectivity, and real-time response, making them ideal candidates for detecting various target analytes. Furthermore, their integration with complementary technologies such as microfluidics, can facilitate the development of on-site and point-of-care applications. This work highlights the interdisciplinary significance of nanostructured TMDC-based colorimetric sensors and underscores their potential contributions to addressing contemporary challenges in sensing technology.

Artificial Intelligence in Point-of-Care Biosensing: Challenges and Opportunities

The integration of artificial intelligence (AI) into point-of-care (POC) biosensing has the potential to revolutionize diagnostic methodologies by offering rapid, accurate, and accessible health assessment directly at the patient level. This review paper explores the transformative impact of AI technologies on POC biosensing, emphasizing recent computational advancements, ongoing challenges, and future prospects in the field. We provide an overview of core biosensing technologies and their use at the POC, highlighting ongoing issues and challenges that may be solved with AI. We follow with an overview of AI methodologies that can be applied to biosensing, including machine learning algorithms, neural networks, and data processing frameworks that facilitate real-time analytical decision-making. We explore the applications of AI at each stage of the biosensor development process, highlighting the diverse opportunities beyond simple data analysis procedures. We include a thorough analysis of outstanding challenges in the field of AI-assisted biosensing, focusing on the technical and ethical challenges regarding the widespread adoption of these technologies, such as data security, algorithmic bias, and regulatory compliance. Through this review, we aim to emphasize the role of AI in advancing POC biosensing and inform researchers, clinicians, and policymakers about the potential of these technologies in reshaping global healthcare landscapes.

A FRET based ultrasensitive fluorescent aptasensor for 6'-sialyllactose detection

As a kind of human milk oligosaccharide, 6'-sialyllactose (6'-SL) plays an important role in promoting infant brain development and improving infant immunity. The content of 6'-SL in infant formula milk powder is thus one of the important nutritional indexes. Since the lacking of efficient and rapid detection methods for 6'-SL, it is of great significance to develop specific recognition elements and establish fast and sensitive detection methods for 6'-SL. Herein, using 6'-SL specific aptamer as the recognition element, catalytic hairpin assembly as the signal amplification technology and quantum dots as the signal label, a fluorescence biosensor based on fluorescence resonance energy transfer (FRET) was constructed for ultra-sensitive detection of 6'-SL. The detection limit of this FRET-based fluorescent biosensor is 0.3 nM, and it has some outstanding characteristics such as high signal-to-noise ratio, low time-consuming, simplicity and high efficiency in the actual sample detection. Therefore, it has broad application prospect in 6'-SL detection.

CRISPR/Cas12a-Amplified Aptamer Switch Microplate Assay for Small Molecules

The presence of small molecule contaminants such as mycotoxins and heavy metals in foods and the environment causes a serious threat to human health and huge economic losses. The development of simple, rapid, sensitive, and on-site methods for small molecule pollutant detection is highly demanded. Here, combining the advantages of structure-switchable aptamer-mediated signal conversion and CRISPR/Cas12a-based signal amplification, we developed a CRISPR/Cas12a-amplified aptamer switch assay on a microplate for sensitive small molecule detection. In this assay, a short DNA strand complementary to the aptamer (cDNA) is immobilized on a microplate, which can capture the aptamer-linked active DNA probe (Apt-acDNA) in the sample solution when the target is absent. With the addition of the Cas12a reporter system, the captured Apt-acDNA probes activate Cas12a to indiscriminately cleave fluorescent DNA substrates, producing a high fluorescence signal. When the target is present, the Apt-acDNA probe specifically binds to the target rather than hybridizing with cDNA on the microplate, and the fluorescence signal is reduced. The analytical performance of our method was demonstrated by the detection of two highly toxic pollutants, aflatoxin B1 (AFB1) and cadmium ion (Cd2+), as examples. The assay exhibited good selectivity and high sensitivity, with detection limits of 31 pM AFB1 and 3.9 nM Cd2+. It also allowed the detection of targets in the actual sample matrix. With the general signal conversion strategy, this method can be used to detect other targets by simply changing the aptamer and cDNA, showing potential practical applications in broad fields.

Development of Better Aptamers: Structured Library Approaches, Selection Methods, and Chemical Modifications

Systematic evolution of ligands by exponential enrichment (SELEX) has been used to discover thousands of aptamers since its development in 1990. Aptamers are short single-stranded oligonucleotides capable of binding to targets with high specificity and selectivity through structural recognition. While aptamers offer advantages over other molecular recognition elements such as their ease of production, smaller size, extended shelf-life, and lower immunogenicity, they have yet to show significant success in real-world applications. By analyzing the importance of structured library designs, reviewing different SELEX methodologies, and the effects of chemical modifications, we provide a comprehensive overview on the production of aptamers for applications in drug delivery systems, therapeutics, diagnostics, and molecular imaging.

State-of-the-art electrochemical biosensors based on covalent organic frameworks and their hybrid materials

As the development of global population and industry civilization, the accurate and sensitive detection of intended analytes is becoming an important and great challenge in the field of environmental, medical, and public safety. Recently, electrochemical biosensors have been constructed and used in sensing fields, such as antibiotics, pesticides, specific markers of cancer, and so on. Functional materials have been designed and prepared to enhance detection performance. Among all reported materials, covalent organic frameworks (COFs) are emerging as porous crystalline materials to construct electrochemical biosensors, because COFs have many unique advantages, including large surface area, high stability, atom-level designability, and diversity, to achieve a far better sensing performance. In this comprehensive review, we not only summarize state-of-the-art electrochemical biosensors based on COFs and their hybrid materials but also highlight and discuss some typical examples in detail. We finally provide the challenge and future perspective of COFs-based electrochemical biosensors.

Dynamic selection of high-affinity aptamers using a magnetically activated continuous deflection microfluidic chip

To accelerate the discovery of high-affinity aptamers, a magnetically activated continuous deflection (MACD) chip was designed. The MACD chip could achieve dynamic selection in a continuous flow, which meant that the binding and separation were carried out consecutively. Dynamic selection could make selection efficient. Low-affinity sequences could be eluted in time and high-affinity sequences could be enriched via dynamic selection. The stringency of the conditions could be further increased by lowering the target concentration in the dynamic selection. Finally, a C.al3 aptamer with high-affinity and high-specificity for Candida albicans (C. albicans) was obtained through six rounds of selection. Its dissociation constant (Kd) was 7.9 nM. This demonstrated that dynamic selection using a MACD chip was an effective method for high-affinity aptamer selection.

Fluorometric and Colorimetric Method for SARS-CoV-2 Detection Using Designed Aptamer Display Particles

SARS-CoV-2, the virus responsible for the COVID-19 pandemic, has spurred the urgent need for practical diagnostics with high sensitivity and selectivity. Although advanced diagnostic tools have emerged to efficiently control pandemics, they still have costly limitations owing to their reliance on antibodies or enzymes and require high-tech equipment. Therefore, there is still a need to develop rapid and low-cost diagnostics with high sensitivity and selectivity. In this study, we generated aptamer display particles (AdP), enabling easy fabrication of a SARS-CoV-2 detection matrix through particle PCR, and applied it to diagnosis using fluorometric and colorimetric assays. We designed two AdPs, C1-AdP and C4-AdP, displayed with SpS1-C1 and SpS1-C4 aptamers, respectively, and showed their high binding ability against SARS-CoV-2 spike protein with a concentration-dependent fluorescence increase. This enabled detection even at low concentrations (0.5 nM). To validate its use as a diagnostic tool for SARS-CoV-2, we designed a sandwich-type assay using two AdPs and high-quality aptamers targeting SARS-CoV-2 pseudoviruses. The fluorometric assay achieved a detection limit of 3.9 × 103 pseudoviruses/mL. The colorimetric assay using an amplification approach exhibited higher sensitivity, with a detection limit of 1 × 101 pseudoviruses/mL, and a broad range of over four orders of magnitude was observed.

A Colorimetric Biosensing Platform with Aptamers, Rolling Circle Amplification and Urease-Mediated Litmus Test

Here we report on an ultra-sensitive colorimetric sensing platform that takes advantage of both the strong amplification power of rolling circle amplification (RCA) and the high efficiency of a simple urease-mediated litmus test. The presence of a target triggers the RCA reaction, and urease-labelled DNA can hybridize to the biotinylated RCA products and be immobilized onto streptavidin-coated magnetic beads. The urease-laden beads are then used to hydrolyze urea, leading to an increase in pH that can be detected by a simple litmus test. We show this sensing platform can be easily integrated with aptamers for sensing diverse targets via the detection of human thrombin and platelet-derived growth factor (PDGF) utilizing structure-switching aptamers as well as SARS-CoV-2 in human saliva using a spike-binding trimeric DNA aptamer. Furthermore, we demonstrate that this colorimetric sensing platform can be integrated into a simple paper-based device for sensing applications.

Apta FastZ: An Algorithm for the Rapid Identification of Aptamers with Defined Binding Affinities

Real-time biomolecular monitoring requires biosensors based on affinity reagents, such as aptamers, with moderate to low affinities for the best binding dynamics and signal gain. We recently reported Pro-SELEX, an approach that utilizes parallelized SELEX and high-content bioinformatics for the selection of aptamers with predefined binding affinities. The Pro-SELEX pipeline relies on an algorithm, termed AptaZ, that can predict the binding affinities of selected aptamers. The original AptaZ algorithm is computationally complex and slows the overall throughput of Pro-SELEX. Here, we present Apta FastZ, a rapid equivalent of AptaZ. The Apta FastZ algorithm considers the spare nature of the sequences from SELEX and is coded to avoid unnecessary comparison between sequences. As a result, Apta FastZ achieved a 10 to 40-fold faster computing speed compared to the original AptaZ algorithm while maintaining identical outcomes, allowing the bioinformatics to be completed within 1-10 h for large-scale data sets. We further validated the affinity of myeloperoxidase aptamers predicted by Apta FastZ by experiments and observed a high level of linear correlation between predicted scores and measured affinities. Taken together, the implementation of Apta FastZ could greatly accelerate the current Pro-SELEX workflow, allowing customized aptamers to be discovered within 3 days using preselected DNA libraries.

Fabrication of a disposable aptasensing chip for simultaneous label-free detection of four common coexisting mycotoxins

BACKGROUND

Coexisting multiple mycotoxins in food poses severe health risks on humans due to the augmented toxicity. Current multiplex detection methods for mycotoxins have evolved from instrumental analyses to rapid methods based on the specific recognition of antibody/aptamer using different signal transducers. However, nearly all of the reported aptasensors for multiple mycotoxins detection require external labels and can only simultaneous detection of two mycotoxins due to the limitation of distinguishable labels. The tedious labeling process definitely increases the operation complexity and the detection cost. Therefore, rapid method for simultaneous label-free detection of multiple mycotoxins in cereals is urgently needed.

RESULTS

A disposable aptasensing chip was designed for simultaneous label-free detection of fumonisin B1 (FB1), aflatoxin B1 (AFB1), zearalenone (ZEN), and ochratoxin A (OTA) in one sample. Specifically, ITO conductive glass was divided into a rectangle (35 × 25 mm) and then etched by laser to set aside the required four ITO working electrodes (6 mm in diameter) with respective conductive channels. Gold nanoparticles were electrodeposited on the working electrodes to provide abundant anchoring sites for thiolated aptamers immobilization. On this basis, a disposable aptasensing chip for simultaneous label-free detection of four common coexisting mycotoxins has been developed, which used electrochemical impedance spectroscopy as transducer to measure direct biorecognition of the aptamer and corresponding target. This aptasensing chip provided wide linear ranges of 5-1000, 10-250, 10-1250, 10-1500 ng/mL for FB1, AFB1, ZEN, OTA, respectively, with the respective detection limit of 2.47, 3.19, 5.38, 4.87 ng/mL (S/N = 3).

SIGNIFICANCE AND NOVELTY

This aptasensing chip shows fantastic characteristics of great simplicity and portability, easy operation, and multiple mycotoxins recognition. They are easy to produce on a large scale at low cost and the design concept can be easily expanded to screen a large panel of coexisting targets. This work provides a new avenue for multi-target detection and represents a substantial advance toward food quality and safety monitoring or other fields.

Profiling Additional Effects of Aptamer Fluorophore Modification on Microscale Thermophoresis Characterization of Aptamer-Target Binding

Aptamers are promising affinity ligands with considerable applications, such as biosensors, disease diagnosis, therapy, etc. Characterization of aptamer-target binding is important in aptamer selection and aptamer applications. Microscale thermophoresis (MST) is an emerging optical technique for molecular interactions, which monitors fluorescence responses of fluorescent molecules in a microscopic temperature gradient. Harnessing merits in trace sample consumption, high speed, free separation, free immobilization, and ratiometric analysis, MST draws intense wide attention. MST is often applied for aptamer-target binding studies using fluorescently labeled aptamers. However, the MST signal is strongly dependent on fluorophore modifications at aptamers, which brings additional challenges and effects for MST analyzing aptamer affinity. Here, we systematically explored effects of fluorophore modifications (e.g., fluorophore types, fluorophore positions, etc.) of aptamer probes on MST characterizing aptamer-target interactions and identified gaps of MST analysis in aptamer affinity determination, taking aptamers against cadmium ions and aflatoxin B1 as two representatives. The same aptamers with different fluorophore modifications showed distinct MST signals in response magnitudes and signs as well as determined affinities, and some of them failed to respond to target binding and gave false affinity information in MST. A competitive MST method can be used to extract the affinity of unmodified aptamers, excluding effects of fluorophore modification. This work highlights that appropriate fluorophore modification is crucial in MST analysis of aptamer affinity, and caution is needed in MST applications, providing a basis for rational design of the MST method for the reliable molecular interaction study.

Selection of aptamers using β-1,3-glucan recognition protein-tagged proteins and curdlan beads

RNA aptamersare nucleic acids that are obtained using the systematic evolution of ligands by exponential enrichment (SELEX) method. When using conventional selection methods to immobilize target proteins on matrix beads using protein tags, sequences are obtained that bind not only to the target proteins but also to the protein tags and matrix beads. In this study, we performed SELEX using β-1,3-glucan recognition protein (GRP)-tags and curdlan beads to immobilize the acute myeloid leukaemia 1 (AML1) Runt domain (RD) and analysed the enrichment of aptamers using high-throughput sequencing. Comparison of aptamer enrichment using the GRP-tag and His-tag suggested that aptamers were enriched using the GRP-tag as well as using the His-tag. Furthermore, surface plasmon resonance analysis revealed that the aptamer did not bind to the GRP-tag and that the conjugation of the GRP-tag to RD weakened the interaction between the aptamer and RD. The GRP-tag could have acted as a competitor to reduce weakly bound RNAs. Therefore, the affinity system of the GRP-tagged proteins and curdlan beads is suitable for obtaining specific aptamers using SELEX.

Strict Interactions of Fifth Letters, Hydrophobic Unnatural Bases, in XenoAptamers with Target Proteins

XenoAptamers are DNA fragments containing additional letters (unnatural bases, UBs) that bind specifically to their target proteins with high affinities (sub-nanomolar KD values). One of the UBs is the highly hydrophobic 7-(2-thienyl)imidazo[4,5-b]pyridine (Ds), which significantly increases XenoAptamers' affinities to targets. Originally, Ds was developed as a third base pair with a complementary UB, 2-nitro-4-propynylpyrrole (Px), for replication, and thus it can be used for aptamer generation by an evolutional engineering method involving PCR amplification. However, it is unclear whether the Ds base is the best component as the hydrophobic fifth-letter ligand for interactions with target proteins. To optimize the ligand structure of the fifth letter, we prepared 13 Ds variants and examined the affinities of XenoAptamers containing these variants to target proteins. The results obtained using four XenoAptamers prepared by the replacement of Ds bases with variants indicated that subtle changes in the chemical structure of Ds significantly affect the XenoAptamer affinities. Among the variants, placing either 4-(2-thienyl)pyrrolo[2,3-b]pyridine (Ys) or 4-(2-thienyl)benzimidazole (Bs) at specific Ds positions in each original XenoAptamer greatly improved their affinities to targets. The Ys and Bs bases are variants derived by replacing only one nitrogen with a carbon in the Ds base. These results demonstrate the strict intramolecular interactions, which are not simple hydrophobic contacts between UBs and targets, thus providing a method to mature XenoAptamers' affinities to targets.

Selection of optimised ligands by fluorescence-activated bead sorting

The chemistry of aptamers is largely limited to natural nucleotides, and although modifications of nucleic acids can enhance target aptamer affinity, there has not yet been a technology for selecting the right modifications in the right locations out of the vast number of possibilities, because enzymatic amplification does not transmit sequence-specific modification information. Here we show the first method for the selection of specific nucleoside modifications that increase aptamer binding efficacy, using the oncoprotein EGFR as a model target. Using fluorescence-activated bead sorting (FABS), we have successfully selected optimized aptamers from a library of >65 000 variations. Hits were identified by tandem mass spectrometry and validated by using an EGFR binding assay and computational docking studies. Our results provide proof of concept for this novel strategy for the selection of chemically optimised aptamers and offer a new method for rapidly synthesising and screening large aptamer libraries to accelerate diagnostic and drug discovery.

Structural basis for high-affinity recognition of aflatoxin B1 by a DNA aptamer

The 26-mer DNA aptamer (AF26) that specifically binds aflatoxin B1 (AFB1) with nM-level high affinity is rare among hundreds of aptamers for small molecules. Despite its predicted stem-loop structure, the molecular basis of its high-affinity recognition of AFB1 remains unknown. Here, we present the first high-resolution nuclear magnetic resonance structure of AFB1-AF26 aptamer complex in solution. AFB1 binds to the 16-residue loop region of the aptamer, inducing it to fold into a compact structure through the assembly of two bulges and one hairpin structure. AFB1 is tightly enclosed within a cavity formed by the bulges and hairpin, held in a place between the G·C base pair, G·G·C triple and multiple T bases, mainly through strong π-π stacking, hydrophobic and donor atom-π interactions, respectively. We further revealed the mechanism of the aptamer in recognizing AFB1 and its analogue AFG1 with only one-atom difference and introduced a single base mutation at the binding site of the aptamer to increase the discrimination between AFB1 and AFG1 based on the structural insights. This research provides an important structural basis for understanding high-affinity recognition of the aptamer, and for further aptamer engineering, modification and applications.

Sensitive microscale thermophoresis assay for rapid ochratoxin A detection with fluorescently labeled engineered aptamer

Ochratoxin A (OTA) is a widespread mycotoxin that causes contamination in a variety of foodstuffs and environments, inducing great health risks to humans and animals. Rapid and sensitive detection of OTA is necessary for food safety, environmental health, and risk assessment. Herein, we report an aptamer microscale thermophoresis (MST) assay for OTA, with the unique merits of ratiometric analysis, rapid measurement, simple operation, high sensitivity, low sample consumption, and high throughput. A fluorescein (FAM)-labeled high-affinity DNA aptamer with a G-quadruplex and duplex structure was used as the recognition element for OTA, and MST, which measures the fluorescence responses of the sample solution inside capillaries to a mild temperature increase generated by infrared laser heating, was employed for signal generation. Upon OTA binding, the FAM-labeled aptamer probe underwent changes in conformation and stability, and the bound and unbound aptamer probes showed significant differences in their MST signals. To achieve sensitive detection of OTA with a large signal change, we systematically characterized aptamers with different stem lengths, which had large effects on the MST responses of the aptamer probes to OTA. We found that a 32-mer aptamer with FAM label at the 3' end gave a sensitive MST response to OTA, allowing OTA detection within seconds with a detection limit of 0.98 nM under optimal experimental conditions. This aptamer MST assay shows potential in real sample analysis and broad applications.

A high-dimensional microfluidic approach for selection of aptamers with programmable binding affinities

Aptamers are being applied as affinity reagents in analytical applications owing to their high stability, compact size and amenability to chemical modification. Generating aptamers with different binding affinities is desirable, but systematic evolution of ligands by exponential enrichment (SELEX), the standard for aptamer generation, is unable to quantitatively produce aptamers with desired binding affinities and requires multiple rounds of selection to eliminate false-positive hits. Here we introduce Pro-SELEX, an approach for the rapid discovery of aptamers with precisely defined binding affinities that combines efficient particle display, high-performance microfluidic sorting and high-content bioinformatics. Using the Pro-SELEX workflow, we were able to investigate the binding performance of individual aptamer candidates under different selective pressures in a single round of selection. Using human myeloperoxidase as a target, we demonstrate that aptamers with dissociation constants spanning a 20-fold range of affinities can be identified within one round of Pro-SELEX.

Biomolecular sensors for advanced physiological monitoring

Body-based biomolecular sensing systems, including wearable, implantable and consumable sensors allow comprehensive health-related monitoring. Glucose sensors have long dominated wearable bioanalysis applications owing to their robust continuous detection of glucose, which has not yet been achieved for other biomarkers. However, access to diverse biological fluids and the development of reagentless sensing approaches may enable the design of body-based sensing systems for various analytes. Importantly, enhancing the selectivity and sensitivity of biomolecular sensors is essential for biomarker detection in complex physiological conditions. In this Review, we discuss approaches for the signal amplification of biomolecular sensors, including techniques to overcome Debye and mass transport limitations, and selectivity improvement, such as the integration of artificial affinity recognition elements. We highlight reagentless sensing approaches that can enable sequential real-time measurements, for example, the implementation of thin-film transistors in wearable devices. In addition to sensor construction, careful consideration of physical, psychological and security concerns related to body-based sensor integration is required to ensure that the transition from the laboratory to the human body is as seamless as possible.

A fluorescence aptasensor based on hybridization chain reaction for simultaneous detection of T-2 toxins and zearalenone1

It is extremely necessary to establish a rapid and high-throughput method to detect mycotoxins in food, because grains and cereals are greatly vulnerable to mycotoxins before and after harvest. In this study, we developed a portable aptasensor based on streptavidin magnetic microspheres (MMPs) and hybridization chain reaction (HCR) to simultaneously detect T-2 toxin and zearalenone (ZEN) in corn and oat flour. The MMPs compete with the aptamer for binding, which releases more H0 and triggers HCR with the H1 intermediate modified using 6-FAM and BHQ-1 and the unmodified H2. Subsequently, placing the HCR system corresponding to T-2 and ZEN in a constant-temperature fluorescence detector resulted in well-recovered fluorescence of the HCR products. T-2 and ZEN exhibited good fluorescence response in the dynamic range of 0.001-10 ng mL^-1 and 0.01-100 ng mL^-1 with detection limits of 0.1 pg mL^-1 and 1.2 pg mL^-1, respectively. In addition, this strategy achieved the selective detection of T-2 and ZEN in the spiked corn and oat flour samples. The results are also in good agreement with those obtained using commercial ELISA kits. This developed aptasensor with the characteristics of simple operation and portability has the application potential of establishing sensitive and portable field detection of various mycotoxins.

Recent Progress in Functional-Nucleic-Acid-Based Fluorescent Fiber-Optic Evanescent Wave Biosensors

Biosensors capable of onsite and continuous detection of environmental and food pollutants and biomarkers are highly desired, but only a few sensing platforms meet the "2-SAR" requirements (sensitivity, specificity, affordability, automation, rapidity, and reusability). A fiber optic evanescent wave (FOEW) sensor is an attractive type of portable device that has the advantages of high sensitivity, low cost, good reusability, and long-term stability. By utilizing functional nucleic acids (FNAs) such as aptamers, DNAzymes, and rational designed nucleic acid probes as specific recognition ligands, the FOEW sensor has been demonstrated to be a general sensing platform for the onsite and continuous detection of various targets ranging from small molecules and heavy metal ions to proteins, nucleic acids, and pathogens. In this review, we cover the progress of the fluorescent FNA-based FOEW biosensor since its first report in 1995. We focus on the chemical modification of the optical fiber and the sensing mechanisms for the five above-mentioned types of targets. The challenges and prospects on the isolation of high-quality aptamers, reagent-free detection, long-term stability under application conditions, and high throughput are also included in this review to highlight the future trends for the development of FOEW biosensors capable of onsite and continuous detection.

Success probability of high-affinity DNA aptamer generation by genetic alphabet expansion

Nucleic acid aptamers as antibody alternatives bind specifically to target molecules. These aptamers are generated by isolating candidates from libraries with random sequence fragments, through an evolutionary engineering system. We recently reported a high-affinity DNA aptamer generation method that introduces unnatural bases (UBs) as a fifth letter into the library, by genetic alphabet expansion. By incorporating hydrophobic UBs, the affinities of DNA aptamers to target proteins are increased over 100-fold, as compared with those of conventional aptamers with only the natural four letters. However, there is still plenty of room for improvement of the methods for routinely generating high-affinity UB-containing DNA (UB-DNA) aptamers. The success probabilities of the high-affinity aptamer generation depend on the existence of the aptamer candidate sequences in the initial library. We estimated the success probabilities by analysing several UB-DNA aptamers that we generated, as examples. In addition, we investigated the possible improvement of conventional aptamer affinities by introducing one UB at specific positions. Our data revealed that UB-DNA aptamers adopt specific tertiary structures, in which many bases including UBs interact with target proteins for high affinity, suggesting the importance of the UB-DNA library design. This article is part of the theme issue 'Reactivity and mechanism in chemical and synthetic biology'.