High affinity truncated DNA aptamers for the development of fluorescence based progesterone biosensors

Aptamer-based biosensors for the detection of neonicotinoid insecticides in environmental samples: A systematic review

Neonicotinoids, sometimes abbreviated as neonics, represent a class of neuro-active insecticides with chemical similarities to nicotine. Neonicotinoids are the most widely adopted group of insecticides globally since their discovery in the late 1980s. Their physiochemical properties surpass those of previously established insecticides, contributing to their popularity in various sectors such as agriculture and wood treatment. The environmental impact of neonicotinoids, often overlooked, underscores the urgency to develop tools for their detection and understanding of their behavior. Conventional methods for pesticide detection have limitations. Chromatographic techniques are sensitive but expensive, generate waste, and require complex sample preparation. Bioassays lack specificity and accuracy, making them suitable as preliminary tests in conjunction with instrumental methods. Aptamer-based biosensor is recognized as an advantageous tool for neonicotinoids detection due to its rapid response, user-friendly nature, cost-effectiveness, and suitability for on-site detection. This comprehensive review represents the inaugural in-depth analysis of advancements in aptamer-based biosensors targeting neonicotinoids such as imidacloprid, thiamethoxam, clothianidin, acetamiprid, thiacloprid, nitenpyram, and dinotefuran. Additionally, the review offers valuable insights into the critical challenges requiring prompt attention for the successful transition from research to practical field applications.

A nitrogen-doped hollow carbon nanospheres-based aptasensor for non-invasive salivary detection of progesterone

Developing an easy-to-use and non-invasive sensor for monitoring progesterone (P4) as a multi-functional hormone is highly demanded for point-of-care testing. In this study, an ultrasensitive electrochemical aptasensor is fabricated for monitoring P4 in human biofluids. The sensing interface was designed based on the porous nitrogen-doped hollow carbon spheres (N-HCSs). The N-HCSs covalently immobilized high-dense aptamer (Apt) sequences as the bioreceptor of P4. The electron transfer of the redox probe was hindered by incubating P4 on the aptasensor surface and forming the P4-Apt complexes. Meanwhile, the signaling was decreased under two wide linear dynamic ranges (LDRs) from 10 fM to 5.6 μM with a limit of detection (LOD) value of 3.33 fM. The aptasensor presented satisfactory selectivity in the presence of different off-target species with successful feasibility for P4 detection in some human urine and saliva samples. The aptasensor with high sensitivity, as an advantage for on-site and sensitive measurement of P4, can be considered a non-invasive tool for routine analysis of real-world clinical samples method.

Advances of aptamer-based small-molecules sensors in body fluids detection

The field of aptamer-based sensing has evolved considerably over the past three decades. The aptamer sensor-based detection of small-molecule targets in body fluids is designed for real-time or rapid, low-cost, non- or minimally invasive tracking and diagnosis of human health status. It can be achieved by specifically monitoring biomarkers or metabolites excreted from various body fluids, including blood, urine, cerebrospinal fluid, saliva, ect. This article reviews a comprehensive collection of aptamer-based sensors for detecting small-molecule in various body fluids. A comparative analysis of aptamer features, emerging chemistry, advanced sensing materials, transduction techniques, and detection performance is conducted, and the strengths and pitfalls of each approach are discussed. Finally, the development process and application challenges of aptamer-based sensors in the detection of small-molecule in body fluids are presented and discussed.

Design and Validation of a Short Novel Estradiol Aptamer and Exploration of Its Application in Sensor Technology

The specific and sensitive detection of 17β-estradiol (E2) is critical for diagnosing and treating numerous diseases, and aptamers have emerged as promising recognition probes for developing detection platforms. However, traditional long-sequence E2 aptamers have demonstrated limited clinical performance due to redundant structures that can affect their stability and recognition ability. There is thus an urgent need to further optimize the structure of the aptamer to build an effective detection platform for E2. In this work, we have designed a novel short aptamer that retains the key binding structure of traditional aptamers to E2 while eliminating the redundant structures. The proposed aptamer was evaluated for its binding properties using microscale thermophoresis, a gold nanoparticle-based colorimetric method, and electrochemical assays. Our results demonstrate that the proposed aptamer has excellent specific recognition ability for E2 and a high affinity with a dissociation constant of 92 nM. Moreover, the aptamer shows great potential as a recognition probe for constructing a highly specific and sensitive clinical estradiol detection platform. The aptamer-based electrochemical sensor enabled the detection of E2 with a linear range between 5 pg mL-1 and 10 ng mL-1 (R2 = 0.973), and the detection capability of a definite low concentration level was 5 pg mL-1 (S/N = 3). Overall, this novel aptamer holds great promise as a valuable tool for future studies on the role of E2 in various physiological and pathological processes and for developing sensitive and specific diagnostic assays for E2 detection in clinical applications.

A homogeneous label-free electrochemical aptasensor based on an omega-like DNA nanostructure for progesterone detection

A novel homogeneous label-free electrochemical aptamer sensor for the detection of progesterone was prepared by combining a well-designed omega (Ω)-like DNA (Ω-DNA) nanostructure, with an isothermal cycling amplification strategy based on the highly efficient exonuclease III (Exo III). The omega-like (Ω) DNA is composed of two oligonucleotide strands: DNA1 and DNA2. The Pro aptamer triggers a chain displacement reaction of Ω-DNA nanostructures, forms a new double-stranded DNA structure (aptamer precursor-DNA2), and releases DNA1. Then, Exo III selectively cleaves the DNA duplex and releases the Pro aptamer to participate in a new displacement reaction. Meanwhile, the released DNA1 strands gain access to the strongly bound hemin, forming a hemin/G-quadruplex (DNAzyme). In the presence of hydrogen peroxide (H2O2), differential pulse voltammetry (DPV) was used to detect the current signal from the oxidation of o-phenylenediamine (OPD) to aminoazobenzene (DAP) catalyzed by DNAzyme. However, the amount of released DNA1 from the Ω-DNA nanostructures is reduced in the presence of the target Pro, and the DPV signal declines because of the small amount of DNAzyme formed. The developed electrochemical aptasensor has a wide dynamic linear relationship in the range of 1 pg mL-1 to 10 ng mL-1 under optimal conditions. Its detection limit is down to 0.3 pg mL-1, providing a potential platform for a sensitive Pro assay among electrochemical assays.

Recent advances in proteomic-based diagnostics of cystic fibrosis

INTRODUCTION

Cystic fibrosis (CF) is a genetic disease characterized by thick and sticky mucus accumulation, which may harm numerous internal organs. Various variables such as gene modifiers, environmental factors, age of diagnosis, and CF transmembrane conductance regulator (CFTR) gene mutations influence phenotypic disease diversity. Biomarkers that are based on genomic information may not accurately represent the underlying mechanism of the disease as well as its lethal complications. Therefore, recent advancements in mass spectrometry (MS)-based proteomics may provide deep insights into CF mechanisms and cellular functions by examining alterations in the protein expression patterns from various samples of individuals with CF.

AREAS COVERED

We present current developments in MS-based proteomics, its application, and findings in CF. In addition, the future roles of proteomics in finding diagnostic and prognostic novel biomarkers.

EXPERT OPINION

Despite significant advances in MS-based proteomics, extensive research in a large cohort for identifying and validating diagnostic, prognostic, predictive, and therapeutic biomarkers for CF disease is highly needed.

Nucleic acid aptamer-based biosensors and their application in thrombin analysis

Thrombin is a multifunctional serine protease that plays an important role in coagulation and anticoagulation processes. Aptamers have been widely applied in biosensors due to their high specificity, low cost and good biocompatibility. This review summarizes recent advances in thrombin quantification using aptamer-based biosensors. The primary focus is optical sensors and electrochemical sensors, along with their applications in thrombin analysis and disease diagnosis.

Simple and cheap CRISPR/Cas12a biosensor based on plug-and-play of DNA aptamers for the detection of endocrine-disrupting compounds

Endocrine-disrupting compounds (EDCs) are widely distributed in the environment. Here, we present a CRISPR/Cas12a (CAS) biosensor based on DNA aptamers for point-of-care detection of EDCs. Two typical EDCs, 17β-estradiol (E2) and bisphenol A (BPA), were selected to be detected by the CAS biosensors via the plug-and-play of their DNA aptamers. The results indicated that the performance of the CAS biosensors can be well regulated by controlling the trans-cleavage activity of Cas12a on a single-stranded DNA reporter and optimizing the sequence and ratio of DNA aptamer and activator DNA. Ultimately, two reliable and specific biosensors were developed, with the linear range and limit of detection of 0.2-25 nM and 0.08 nM for E2 and of 0.1-250 nM and 0.06 nM for BPA, respectively. Compared to the existing detection methods, the CAS biosensors showed higher reliability and sensitivity with simple operation, short detection time, and no costly equipment.

Optimization of an aptamer against Prorocentrum minimum - A common harmful algae by truncation and G-quadruplex-forming mutation

Harmful algal blooms (HABs) caused by Prorocentrum minimum have seriously posed economic losses and ecological disasters. To reduce these losses, aptamers are used as a new molecular probe to establish rapid methods. Herein, to improve the affinity and application of aptamers in the detection of harmful algae, the optimization was performed on the previously reported aptamers against P. minimum. First, a total of seven candidate aptamers, including three truncated aptamers (TA1, TA2 and TA3) and four mutant aptamers (MA1, MA2, MA3 and MA4), were obtained by truncation and G-quadruplex (GQ)-forming mutation. Next, the specificity and affinity test by flow cytometry revealed that except for TA1 and TA2, all of the candidate aptamers are specific with the equilibrium dissociation constant of (40.4 ± 5.5) nM for TA3, (63.3 ± 24.0) nM for MA1, (71.7 ± 14.6) nM for MA2, (365.9 ± 74.4) nM for MA3, and (21.1 ± 0.5) nM for MA4, respectively. The circular dichroism analysis of the mutant aptamers demonstrated that the GQ structures formed by MA1/MA2, MA3 and MA4 were antiparallel, mixed parallel and parallel, respectively. The affinity of aptamers with various GQ is in the order of parallel structure > antiparallel structure > mixed parallel structure. In addition, to further improve binding ability, the binding conditions of MA4 were optimized as follows: binding time, 60 min; binding temperature, 37 °C; pH of the binding buffer, 7.5; and Na⁺/Mg²⁺ concentration in the binding buffer, 100 mM/0.5 mM. The binding examination by fluorescence microscopy showed that MA4 had a stronger binding ability to P. minimum than the original aptamer. Taken together, this study not only obtained an aptamer with higher affinity than the original aptamer, which laid a good foundation for subsequent application, but also may provide a feasible reference method for aptamer optimization.

Development of an Impedimetric Aptasensor for Detection of Progesterone in Undiluted Biological Fluids

A cost-effective, deployable, and quantitative progesterone biosensor is desirable for regular progesterone sensing in biological and environmental samples to safeguard public health. Aptasensors have been shown to be affordable as compared to antibody-based sensors, but so far, none of the progesterone aptamers could detect it in undiluted and unprocessed biological samples. Thus, to select an aptamer suitable for biosensing in unprocessed biological samples, a modified magnetic bead-based approach with counter-selection in milk and serum was performed. G-quadruplex forming progesterone aptamers were preferentially screened through in silico, gold nanoparticle-based adsorption-desorption assay and circular dichroism spectroscopy. GQ5 aptamer showed extended stability and a high progesterone binding affinity (K D 5.29 ± 2.9 nM) as compared to any other reported progesterone aptamers (P4G11 and P4G13). Under optimized conditions, GQ5 aptamer was coated on the gold electrode to develop an impedimetric aptasensor (limit of detection: 0.53, 0.91, and 1.9 ng/mL in spiked buffer, undiluted milk, and serum, respectively, with the dynamic range of detection from 0.1 to 50 ng/mL in buffer and 0.1 to 30 ng/mL in both milk and serum). The aptasensor exhibited a very high level of κ value (>0.9) with ELISA to detect progesterone in milk and serum. The aptasensor could be regenerated three times and can be stored for up to 10 days at 4 °C. Therefore, GQ5 may be used to develop a portable impedimetric aptasensor for clinical and on-site progesterone sensing in various biological and environmental samples.

Virtual screening of truncated single stranded DNA aptamers for Staphylococcal enterotoxin type A

Single stranded DNA (ssDNA)/RNA aptamers, are screened through the labor intensive, iterative Systematic Evolution of Ligand by Exponential Enrichment process (SELEX) method. Complete sequence of screened aptamers never interacts with target or participates in final structure. Hence, in silico tools can be used to redesign a short length aptamer from previously reported aptamers which can have high affinity and specificity to the target. This approach is fast, cost effective, and less laborious than in vitro SELEX towards finding an aptamer sequence with better affinity with the target. Here, Staphylococcal enterotoxin type A (SEA) was used as target. A total of nine aptamers reported for different Staphylococcal food poisoning (SFP) enterotoxins were used as a starting pool. The aptamers were variously truncations and thoroughly analyzed through in silico methods. Three truncated aptamers namely AptSEA1.4, AptSEA2.4 and AptSEA8.4 were found to show higher affinity with target SEA. The computational data was also validated with DOT BLOT assay complemented with image analysis. These results also confirmed that the % specific binding and the dissociation constant (Kd) of truncated aptamers AptSEA1.4, AptSEA2.4 and AptSEA8.4 was better than their original counterparts. The truncated aptamers showed great promise to be used as a capture reagent in developing a sensitive assay for detection of SEA.Communicated by Ramaswamy H. Sarma.

Nanomaterial-Based Fluorescent Biosensor for Food Safety Analysis

Food safety issues have become a major threat to public health and have garnered considerable attention. Rapid and effective detection methods are crucial for ensuring food safety. Recently, nanostructured fluorescent materials have shown considerable potential for monitoring the quality and safety of food because of their fascinating optical characteristics at the nanoscale. In this review, we first introduce biomaterials and nanomaterials for food safety analysis. Subsequently, we perform a comprehensive analysis of food safety using fluorescent biosensors based on nanomaterials, including mycotoxins, heavy metals, antibiotics, pesticide residues, foodborne pathogens, and illegal additives. Finally, we provide new insights and discuss future approaches for the development of food safety detection, with the aim of improving fluorescence detection methods for the practical application of nanomaterials to ensure food safety and protect human health.

Carbon Dots Conjugated Antibody as an Effective FRET-Based Biosensor for Progesterone Hormone Screening

In this work, carbon dots (CDs) were synthesized by a one-step hydrothermal method using citric acid and ethylene diamine, and covalently functionalized with antibodies for the sensing of progesterone hormone. The structural and morphological analysis reveals that the synthesized CDs are of average size (diameter 8-10 nm) and the surface functionalities are confirmed by XPS, XRD and FT-IR. Further graphene oxide (GO) is used as a quencher due to the fluorescence resonance energy transfer (FRET) mechanism, whereas the presence of the analyte progesterone turns on the fluorescence because of displacement of GO from the surface of CDs effectively inhibiting FRET efficiency due to the increased distance between donor and acceptor moieties. The linear curve is obtained with different progesterone concentrations with 13.8 nM detection limits (R2 = 0.974). The proposed optical method demonstrated high selectivity performance in the presence of structurally resembling interfering compounds. The PL intensity increased linearly with the increased progesterone concentration range (10-900 nM) under the optimal experimental parameters. The developed level-free immunosensor has emerged as a potential platform for simplified progesterone analysis due to the high selectivity performance and good recovery in different samples of spiked water.

Systematic bio-fabrication of aptamers and their applications in engineering biology

Aptamers are single-stranded DNA or RNA molecules that have high affinity and selectivity to bind to specific targets. Compared to antibodies, aptamers are easy to in vitro synthesize with low cost, and exhibit excellent thermal stability and programmability. With these features, aptamers have been widely used in biology and medicine-related fields. In the meantime, a variety of systematic evolution of ligands by exponential enrichment (SELEX) technologies have been developed to screen aptamers for various targets. According to the characteristics of targets, customizing appropriate SELEX technology and post-SELEX optimization helps to obtain ideal aptamers with high affinity and specificity. In this review, we first summarize the latest research on the systematic bio-fabrication of aptamers, including various SELEX technologies, post-SELEX optimization, and aptamer modification technology. These procedures not only help to gain the aptamer sequences but also provide insights into the relationship between structure and function of the aptamers. The latter provides a new perspective for the systems bio-fabrication of aptamers. Furthermore, on this basis, we review the applications of aptamers, particularly in the fields of engineering biology, including industrial biotechnology, medical and health engineering, and environmental and food safety monitoring. And the encountered challenges and prospects are discussed, providing an outlook for the future development of aptamers.

An Allosteric Transcription Factor DNA-Binding Electrochemical Biosensor for Progesterone

We describe an electrochemical strategy to transduce allosteric transcription factor (aTF) binding affinity to sense steroid hormones. Our approach utilizes square wave voltammetry to monitor changes in current output as a progesterone (PRG)-specific aTF (SRTF1) unbinds from the cognate DNA sequence in the presence of PRG. The sensor detects PRG in artificial urine samples with sufficient sensitivity suitable for clinical applications. Our results highlight the capability of using aTFs as the biorecognition elements to develop electrochemical point-of-care biosensors for the detection of small-molecule biomarkers and analytes.

Three-dimensional modeling of streptomycin binding single-stranded DNA for aptamer-based biosensors, a molecular dynamics simulation approach

Streptomycin (STR) an aminoglycoside antibiotic which is used against bacteria in human and animal infection, have serious side effects on different parts of human body. Therefore, there is a crucial need to detect trace amount of it in serum and food products. Aptamers are oligonucleotides or peptides, which bind their targets with high affinity and specificity. These properties make aptamers as suitable candidates for biosensing applications. A 79-mer ss-DNA aptamer was applied for the detection of small amount of STR in various aptasensors. But there is no structural information on the STR-binding aptamer and molecular details underlying the aptamer-STR binding remain unexplored. In this study we provided a 3D-structural model for 79-mer ss-DNA aptamer from the sequence. Using docking program and molecular dynamics (MD) simulation we predicted the binding pocket of ss-DNA aptamer. Our results show STR streptose ring is buried within the groove of DNA model and capped by non Watson-Crick bases. STR interacts with aptamer through forming stable hydrogen bonds. Our computational findings are in fair agreement with experimental results. With the atomic structural details, we gained new insight into the Apt-STR binding interaction that can help to further optimize aptamer efficiency in biosensing applications.Communicated by Ramaswamy H. Sarma.

Improving Biosensors by the Use of Different Nanomaterials: Case Study with Microcystins as Target Analytes

The eutrophication of lakes and rivers without adequate rainfall leads to excessive growth of cyanobacterial harmful algal blooms (CyanoHABs) that produce toxicants, green tides, and unpleasant odors. The rapid growth of CyanoHABs owing to global warming, climate change, and the development of rainforests and dams without considering the environmental concern towards lakes and rivers is a serious issue. Humans and livestock consuming the toxicant-contaminated water that originated from CyanoHABs suffer severe health problems. Among the various toxicants produced by CyanoHABs, microcystins (MCs) are the most harmful. Excess accumulation of MC within living organisms can result in liver failure and hepatocirrhosis, eventually leading to death. Therefore, it is essential to precisely detect MCs in water samples. To date, the liquid chromatography-mass spectrometry (LC-MS) and enzyme-linked immunosorbent assay (ELISA) have been the standard methods for the detection of MC and provide precise results with high reliability. However, these methods require heavy instruments and complicated operation steps that could hamper the portability and field-readiness of the detection system. Therefore, in order for this goal to be achieved, the biosensor has been attracted to a powerful alternative for MC detection. Thus far, several types of MC biosensor have been proposed to detect MC in freshwater sample. The introduction of material is a useful option in order to improve the biosensor performance and construct new types of biosensors. Introducing nanomaterials to the biosensor interface provides new phenomena or enhances the sensitivity. In recent times, different types of nanomaterials, such as metallic, carbon-based, and transition metal dichalcogenide-based nanomaterials, have been developed and used to fabricate biosensors for MC detection. This study reviews the recent advancements in different nanomaterial-based MC biosensors.

Emerging trends in developing biosensor techniques to undertake plant phosphoproteomic analysis

Protein modifications particularly phosphorylation is governed by a complex array of mechanisms to attain a functional conformation and regulate important biological processes in organisms during external environmental stimuli and hormone signaling. Phosphoproteomics is a promising field of proteomics for identification of proteins with phosphate groups and their impact on structure, function and localization of proteins. Techniques that allow quantitative detection of proteins and their post-translational modifications (PTMs) have immensely led to understand the structural and functional dynamics of proteins. Biosensor systems are a relatively new biotechnological approach that works on the principle of transforming the interactions of different biological samples viz proteins, enzymes, aptamers, nucleic acids and so on into the signals such as electrochemical, colorimetric, optical or magnetic which have been effectively useful in the detection and characterization of phosphoproteins. The focus of our review is to provide a comprehensive account of the critical role and utility of novel biosensors such as, fluorescence based, enrichment based, nanobody based biosensors, as promising technical intercessions to identify phosphoproteins and their influence on structural dynamics of proteins. Furthermore, by studying the innovative phosphoprotein biosensors we will be able to identify the aberrant phosphorylation patterns to precisely diagnose diseases.

Aptamer-Based Fluorescent Biosensor for the Rapid and Sensitive Detection of Allergens in Food Matrices

Food allergies have seriously affected the life quality of some people and even endangered their lives. At present, there is still no effective cure for food allergies. Avoiding the intake of allergenic food is still the most effective way to prevent allergic diseases. Therefore, it is necessary to develop rapid, accurate, sensitive, and reliable analysis methods to detect food allergens from different sources. Aptamers are oligonucleotide sequences that can bind to a variety of targets with high specificity and selectivity, and they are often combined with different transduction technologies, thereby constructing various types of aptamer sensors. In recent years, with the development of technology and the application of new materials, the sensitivity, portability, and cost of fluorescence sensing technology have been greatly improved. Therefore, aptamer-based fluorescence sensing technology has been widely developed and applied in the specific recognition of food allergens. In this paper, the classification of major allergens and their characteristics in animal and plant foods were comprehensively reviewed, and the preparation principles and practical applications of aptamer-based fluorescence biosensors are summarized. In addition, we hope that this article can provide some strategies for the rapid and sensitive detection of allergens in food matrices.

A highly sensitive and group-targeting aptasensor for total phthalate determination in the environment

As the most widely used and typical kind of plasticizers, phthalate esters (PAEs) have become one of the most common environmental pollutants in the world. Therefore, it is necessary to develop a rapid and convenient method for determining the total amount of PAEs. Herein, a molecularly tailored broad-spectrum aptamer that can recognize multiple similarly structured total amounts of PAEs (TP) and bind them with high affinity has been successfully fabricated. Mfold (multiple folding) secondary structure simulation and molecular truncation were both utilized to obtain the most effective binding region from the parental full-length (39-mer) aptamer. The results show that the PAE-binding affinity of the truncated 24-mer aptamer produced by removing nonessential flanking nucleotides was improved by 1.5-fold. The linear range of TP detection is 0.003-10 μg/L, and the limit of detection is 1 ng/L. Notably, our study provides new insights into the group-targeting identification of certain pollutants and determination of their total amounts, exhibiting great potential for practical applications.

Determination of minimal sequence for zearalenone aptamer by computational docking and application on an indirect competitive electrochemical aptasensor

Aptamers are short single-stranded oligonucleotides (either DNA or RNA) that can fold into well-defined three-dimensional (3D) spatial structures which enable them to capture their specific target by complementary shape interactions. Aptamers are selected from large random libraries through the SELEX process and only a small fraction of the sequence is involved in direct docking with the target. In this paper, we describe the possible truncation variants of zearalenone (ZEA) aptamer which might be an effective binding region for the target. The originally selected zearalenone (ZEA) aptamer was 80-mer in length and shown to bind the target with a high affinity (K_d = 41 ± 5 nM). Herein, computational docking simulation was performed with 15 truncated variants to determine the predicted binding energy and responsible binding site of the aptamer-analyte complex. The results revealed that 5 truncated variants had binding energy lower than - 7.0 kcal/mol. Circular dichroism analysis was performed on the shortlisted aptamer and the conformational change of aptamers was observed with the presence of an analyte. Aptamer Z3IN (29-mer) was chosen as the most enhanced affinity for its target with a dissociation constant of 11.77 ± 1.44 nM. The aptamer was further applied in the electrochemical aptasensor of ZEA based on an indirect competitive format. The results demonstrated that the truncated aptamer leads to an enhancement of the sensitivity of the biosensor.

Bimodular thrombin aptamers with two types of non-covalent locks

Aptamers are structured oligonucleotides that specifically bind their targets. Oligonucleotides can be assembled in large nanostructures via intermolecular duplexes or G-quadruplexes. Addition of aptamers can be used to create nanostructures that bind specifically certain targets. Here two types of self-assembling locks were used to create bimodular aptamer constructions. Well-known aptamer to thrombin was chosen as a model object. The assembly of duplex locks was more efficient at low concentrations. The functional activity of aptamer modules was nearly the same as in HD1. However, the affinity of bimodular aptamers with G-quadruplex locks to immobilized thrombin was 5-10 times higher.

Colorimetric aptasensor for on-site detection of oxytetracycline antibiotic in milk

Oxytetracycline (OTC), one of the largely used antibiotic in veterinary practice has been banned due to its potential side effects. Development of a field applicable and affordable kit to detect OTC will help to eliminate such milk from human consumption. An aptamer has been designed (27 nt; K_d = 29.2 ± 19.4 nM) through rational truncation. OTC interacts with this aptamer in G rich regions as confirmed by molecular modelling and circular dichroism spectroscopy. To develop a lateral flow based aptasensor, OTC was conjugated with a 7 kDa carrier protein to immobilize onto the nitrocellulose membrane. Using 0.125 µM aptamer-gold conjugate, assay could visually detects upto 5 ng/mL of OTC in spiked milk within 10 mins [Limit of quantitation (LOQ)-0.254 ± 1.62 ng/mL; permissible limit 100 ng/mL]. It showed no cross reactivity with components of milk and data correlated with analysis done through HPLC.

Translational control of enzyme scavenger expression with toxin-induced micro RNA switches

Biological computation requires in vivo control of molecular behavior to progress development of autonomous devices. miRNA switches represent excellent, easily engineerable synthetic biology tools to achieve user-defined gene regulation. Here we present the construction of a synthetic network to implement detoxification functionality. We employed a modular design strategy by engineering toxin-induced control of an enzyme scavenger. Our miRNA switch results show moderate synthetic expression control over a biologically active detoxification enzyme molecule, using an established design protocol. However, following a new design approach, we demonstrated an evolutionarily designed miRNA switch to more effectively activate enzyme activity than synthetically designed versions, allowing markedly improved extrinsic user-defined control with a toxin as inducer. Our straightforward new design approach is simple to implement and uses easily accessible web-based databases and prediction tools. The ability to exert control of toxicity demonstrates potential for modular detoxification systems that provide a pathway to new therapeutic and biocomputing applications.

Truncated affinity-improved aptamers for 17β-estradiol determination by AuNPs-based colorimetric aptasensor

17β-estradiol (E2) residues could enrich in organisms via food chain and lead to harmful biological effects for human body. To ascertain the binding domain of original E2 aptamer (E00) with long-sequence (76-mer), we developed novel truncated aptamers from E00, through rationally designed truncation by intercepting a single ring or a combination of rings (containing hairpin loop, interior loop or multiloop) at different sites and retaining appropriate double helix regions. Through comparison, 15-mer E09 presented improved affinity and higher specificity, indicating the hairpin loop near to 3' end of E00 served on the binding domain to E2. E09 was used for gold nanoparticles (AuNPs)-based colorimetric determination of E2, achieved the detection limit of 0.02 μg/mL. The truncated aptamer (only 15-mer) first proposed in this study has great application potential in E2 determination, and this work provides proof-of-concept study for truncation of other long-sequence aptamers.

Chemical Modification of Aptamers for Increased Binding Affinity in Diagnostic Applications: Current Status and Future Prospects

Aptamers are short single stranded DNA or RNA oligonucleotides that can recognize analytes with extraordinary target selectivity and affinity. Despite their promising properties and diagnostic potential, the number of commercial applications remains scarce. In order to endow them with novel recognition motifs and enhanced properties, chemical modification of aptamers has been pursued. This review focuses on chemical modifications, aimed at increasing the binding affinity for the aptamer's target either in a non-covalent or covalent fashion, hereby improving their application potential in a diagnostic context. An overview of current methodologies will be given, thereby distinguishing between pre- and post-SELEX (Systematic Evolution of Ligands by Exponential Enrichment) modifications.

Probing high-affinity aptamer binding region and development of aptasensor platform for the detection of cylindrospermopsin

Cylindrospermopsin (CYN) is one of the most concerning cyanotoxins due to its potential toxicity and spreading to various environments including drinking water. CYN has potential interferences with human and animal metabolic pathways, which influence the functions of organs including liver, kidneys, lungs, etc. CYN is involved in the inhibition of protein synthesis and detachment of ribosomes from the endoplasmic reticulum membrane. It also interacts with soluble proteins, which are associated with protein translations. It is believed that cytochrome 450 is responsible for the rapid toxicity of CYN. Researchers are urged to develop a high-throughput screening method for the detection of CYN in water. Construction of low cost, rapid, and sensitive analytical methods for the detection of CYN is challenging. Here, we used graphene oxide (GO) as the fluorescence sensing platform for probing the high affinity of the short aptamer derived from the wild-type long aptamer-CYN sensing. The biosensor construction involved two steps: first, quenching the fluorescence of fluorescent-labelled truncated aptamer using GO as a quencher and, second, fluorescence recovery in the presence of CYN by competitive binding between the target and GO. One of the truncate aptamers has a 12-fold higher affinity and enhances sensitivity compared to the long aptamer sequence. The limit of detection of the high affinity truncated aptamer is 17 pM which is 6-fold lower than the long aptamer (100 pM). The sensor specifically detects CYN in the presence of other potential interfering toxins. The performance of the sensor was validated using CYN spiked tap water with very good recovery percentage. A rapid and highly sensitive detection of CYN from water resources has been achieved using this method.

An antibody-aptamer sandwich cathodic photoelectrochemical biosensor for the detection of progesterone

The progesterone (P4) level in body fluids can act as an indicator for early pregnancy diagnosis and offers insight into mammalian somatic function. In this work, we designed an antibody-aptamer based sandwich assay as a cathodic photoelectrochemical (PEC) biosensor for P4 detection. The composites of carbon dots and graphene oxide (CDs-GO) with favorable cathodic photocurrent response were used as photoactive materials on which the antibody (Ab) of P4 was immobilized. Meanwhile, high affinity truncated P4 aptamer was immobilized on Au-CuO-Cu₂O to act as a bioconjugate. When P4 was present, the aptamer-Au-CuO-Cu₂O bioconjugate could amplify the cathodic photocurrent of CDs-GO modified electrode through Ab-P4-aptamer interactions. Under optimum conditions, the cathodic photocurrent of the constructed PEC biosensor was found to increase linearly with P4 in a wide concentration range from 0.5 nM to 180 nM, with a low detection limit (3S/N) of 0.17 nΜ. The proposed cathodic PEC sensing platform demonstrated high selectivity, satisfying reproducibility, good stability. The sensor was successfully applied in the determination of P4 in human serum samples.

Label-free electrochemical aptasensor for progesterone detection in biological fluids

A label-free electrochemical progesterone (P4) aptasensor was successfully developed by covalently immobilizing NH₂-functionalized P4-specific aptamer on the electrode surface. The NiO-Au hybrid nanofibers were synthesized by the electrospinning technique. GQDs-NiO-AuNFs nanocomposite was prepared by dispersing of electrospun NiO-AuNFs in the as-synthesized graphene quantum dots (GQDs) solution and stirring for 24 h. Novel GQDs-NiO-AuNFs nano-architecture in combination with functionalized multiwalled carbon nanotubes (f-MWCNTs) were further utilized to modify screen printed carbon electrode (SPCE) in order to construct an effective immobilization matrix with plenty of carboxylic functional groups. The stepwise assembly process of the designed aptasensor was characterized by cyclic voltammetry (CV) and electrochemical impedance spectroscopy (EIS). The aptamer-progesterone complex formation led to a hindered electron transfer reaction on the sensing interface, which decreased the redox probe peak current. Based on of this, progesterone could be quantitatively detected by monitoring the decrease of differential pulse voltammetric (DPV) responses of [Fe(CN)₆]^3-/4- peak current with increasing the progesterone concentration. Under optimized experimental parameters, the aptasensor exhibited a dynamic concentration range from 0.01 to 1000 nM and a detection limit of 1.86 pM. The proposed aptasensor was successfully employed for the determination of progesterone in human serum samples and pharmaceutical formulations.

Isolation ssDNA aptamers specific for both live and viable but nonculturable stateVibrio vulnificususing whole bacteria-SEILEX technology

Vibrio vulnificus is a ubiquitous marine bacterium that may cause rapid and deadly infection, threatening lives of people living around natural bodies of water, especially in coastal regions. However, traditional culture-based methods are time-consuming and unable to detect Viable But Non-Culturable (VBNC) V. vulnificus cells. In this work, we isolated a batch of detection aptamers specifically binding to V. vulnificus in all culture status. With traditional whole bacteria-SELEX (Systematic Evolution of Ligands by EXponential enrichment), flow cytometer analysis and imaging, we identify 18 candidates and validated two of them (V8 and V13) as applicable aptamers. Their truncated sequences also showed comparable performance. The dissociation constant (KD) value of V8 is shown to be as low as 11.22 ± 1.32 nM. Optimal aptamers V8 and V13 are also validated to be effective to detect different Vibrio vulnificus strains under different binding environments using flow cytometry. As for detection parameters, the LOD of the V8 from cytometry is 29.96 CFU mL⁻¹, and the linear range is 10²–5 × 10⁵ CFU mL⁻¹. This is the first case demonstrating that aptamers can detect the existence of VBNC bacteria as well as live bacteria.

With whole-bacteria SELEX, we got aptamers that can bind to V. vulnificus in VBNC Status for the first time.

Aptameric biosensor for the sensitive detection of major shrimp allergen, tropomyosin

The development of a sensitive and rapid detection approach for allergens in various food matrices is essential to assist patients in managing their allergies. The most common methods used for allergen detection are based on immunoassays, PCR and mass spectrometry. However, all of them are very complex and time-consuming. Herein, an aptamer biosensor for the detection of the major shrimp allergen tropomyosin (TM) was developed. Graphene oxide (GO) was used as a platform for screening of the minimal-length aptamer sequence required for high-affinity target binding. A fluorescein dye labeled GO quenches the truncated aptamer by π-stacking interactions. After the addition of TM, the fluorescence was restored due to the competitive binding of the aptamer to GO. One of the truncated aptamers was found to bind to TM with four-fold higher affinity (30 nM) compared to the full-length aptamer (124 nM), with a limit of detection (LOD) of 2 nM. The aptamer-based sensor demonstrates the sensitive, selective, and specific detection of TM in 30 min. The performance of the sensor was confirmed using TM spiked chicken soup, resulting in a high percentage recovery (~97 ± 10%). The association of GO and labelled aptamer sensor platform has shown the rapid detection of TM in food, which is compared to other methods very sensitive, specific and performs in high throughput application.

One-Pot SELEX: Identification of Specific Aptamers against Diverse Steroid Targets in One Selection

Aptamers are well-established biorecognition molecules used in a wide variety of applications for the detection of their respective targets. However, individual SELEX processes typically performed for the identification of aptamers for each target can be quite time-consuming, labor-intensive, and costly. An alternative strategy is proposed herein for the simultaneous identification of different aptamers binding distinct but structurally similar targets in one single selection. This one-pot SELEX approach, using the steroids estradiol, progesterone, and testosterone as model targets, was achieved by combining the benefits of counter-SELEX with the power of next-generation sequencing and bioinformatics analysis. The pools from the last stage of the selection were compared in order to discover sequences with preferential abundance in only one of the pools. This led to the identification of aptamer candidates with potential specificity to a single steroid target. Binding studies demonstrated the high affinity of each selected aptamer for its respective target, and low nanomolar range dissociation constants calculated were similar to those previously reported for steroid-binding aptamers selected using traditional SELEX approaches. Finally, the selected aptamers were exploited in microtiter plate assays, achieving nanomolar limits of detection, while the specificity of these aptamers was also demonstrated. Overall, the one-pot SELEX strategy led to the discovery of aptamers for three different steroid targets in one single selection without compromising their affinity or specificity, demonstrating the power of this approach of aptamer discovery for the simultaneous selection of aptamers against multiple targets.

A Bottom-Up Approach for Developing Aptasensors for Abused Drugs: Biosensors in Forensics

Aptamer-based point-of-care (POC) diagnostics platforms may be of substantial benefit in forensic analysis as they provide rapid, sensitive, user-friendly, and selective analysis tools for detection. Aptasensors have not yet been adapted commercially. However, the significance of the applications of aptasensors in the literature exceeded their potential. Herein, in this review, a bottom-up approach is followed to describe the aptasensor development and application procedure, starting from the synthesis of the corresponding aptamer sequence for the selected analyte to creating a smart surface for the sensitive detection of the molecule of interest. Optical and electrochemical biosensing platforms, which are designed with aptamers as recognition molecules, detecting abused drugs are critically reviewed, and existing and possible applications of different designs are discussed. Several potential disciplines in which aptamer-based biosensing technology can be of greatest value, including forensic drug analysis and biological evidence, are then highlighted to encourage researchers to focus on developing aptasensors in these specific areas.

Lateral flow aptasensor for progesterone: Competitive target recognition and displacement of short complementary sequences

There is a pressing need for simple and accurate analytical tools to assess the level of EDCs in environmental samples. In this work, a simple and highly sensitive competitive lateral flow assay (LFA) was developed for progesterone (P4). Gold nanoparticles (AuNPs) were functionalized with a previously isolated 60-mer aptamer for P4 and further hybridized with 8-mer complementary sequence modified with biotin. In the absence of P4, AuNP-duplexed aptamer conjugates are capture by a test line made with streptavidin. Conformational change within aptamer sequence upon target recognition causes the release of the biotinylated complementary sequence and disappearance of the colored test line. By optimizing the hybridization location of the 8-mer biotinylated sequences, the sensitivity of sensor was improved by 20-folds to achieve 5 nM detection level of P4 in buffer and spiked tap water samples. The simply fabricated sensor demonstrated a dynamic range in the lower nanomolar range and excellent selectivity against potential interfering molecules including the closely similar 17β-estradiol (E2). The sensor can be used as a fast screening tool to assess the level of P4 in water. Implementing the developed assay avoids applying laborious extraction procedures and lengthily analysis by conventional chromatography based instruments.

Label-Free Fluorescent Aptasensor for Small Targets via Displacement of Groove Bound Curcumin Molecules

Signal transduction based on fluorescence is one of the most common optical aptasensors for small molecules. Sensors with a number of unique features including high sensitivity, low cost, and simple operation can be constructed easily. However, the label-free fluorescent approach is limited to synthetic dyes that bind strongly to the aptamer sequence and result in a diminished sensor operation with high detection limits. In this study, we report the use of curcumin as a fluorescent probe to signal aptamer/small target binding events. A substantial enhancement in curcumin's fluorescent emission was observed when bound into the grooves of vitamin D₃ (VTD3) binding aptamer, as an example. However, the introduction of the target molecule causes the aptamer to undergo a conformational change that favors complexing the target molecule over binding the curcumin dye. The sensor was able to detect VTD3 down to 1 fM concentration in buffer solutions and extracted blood samples, operate at a wide dynamic range, and discriminate against potential biological interfering molecules including VTD2. The operation of the curcumin based fluorescent sensor is at least six orders of magnitude more sensitive than a VTD3 sensor constructed with the synthetic dye SYBR Green I. The generality of the reported label-free approach was applied with a previously isolated 75-mer bisphenol-A (BPA) aptamer, confirming that the reported sensing strategy is not confined on a particular aptamer sequence. Our work not only reports a novel sensor format for the detection of small molecules, but also serves fluorescent sensor's most pressing need being novel fluorophores for multiplex targets detection.

Preparation of DNA-functionalized surfaces for simultaneous homeotropic orientation of liquid crystals and optical recognition of analytes: application to the determination of progesterone

The work describes a simplified method for the preparation of liquid crystal (LC) bioassay using DNA-based capture molecules and having lower detection limits. The capture DNA probes of the stem-loop structure were immobilized on the surface of a glass slide. A homeotropic orientation of LC molecules can be obtained with the proper surface coverage of capture DNA probes. In the presence of analytes (specifically shown here for the progesterone as a model analyte), the molecular binding between capture DNA probes and progesterone opens the loop of the capture DNA probes. The opened sequence is then amenable to hybridization with a reporter DNA probe that is immobilized on gold nanoparticles. This changes the surface microstructure, disrupts the orientation of LC molecules, and results in an enhanced optical response, expressed as the average grey value of the images. This new kind of surface treatment for simultaneous recognition of target molecules and homeotropic anchoring of LCs reduces the number of preparation steps and makes the process of LC bioassay easier. This method has a detection limit as low as 0.1 pmol·L^-1 of progesterone. Graphical abstract Schematic presentation of the liquid crystal-based DNA assay. DMOAP: Dimethyloctadecyl[3-(trimethoxysilyl)propyl]ammonium chloride; TEA: Triethoxsilylbutyraldehyde; 5CB: 4-cyano-4'-pentylbiphenyl; P4: progesterone.

An aptamer based fluorometric microcystin-LR assay using DNA strand-based competitive displacement

The high-affinity region of a truncated aptamer was applied to the development of a sensitive method for the determination of microcystin-LR (MC-LR) using competitive displacement and molecular beacons. In this assay, the fluorophore and quencher labelled complementary sequences of the aptamer are hybridized with the truncated aptamer to form a fluorophore-quencher pair. In the presence of MC-LR, the aptamer duplex dissociates, and the fluorophore-quencher pair is separated. This turn leads to an increase in the yellow fluorescence which is best measured at excitation/emission wavelengths of 555/580 nm. One of the truncated aptamers showed a 50-fold increase in the affinity (0.93 nM) compared to the wild type aptamer (50 nM). The truncated sequence shows considerable cross-reactivity with L congeners but none with other congeners. The assay works in 0.5 to 200 nM MC-LR concentration range. It was applied to spiked tap water samples and gave recoveries around 95 ± 5%. Graphical abstract Schematic representation of a method for determination of microcystin-LR via fluorescence that is induced by competitive displacement of complementary DNA strands in a truncated dsDNA aptamer.

Computational analysis and optimization of carcinoembryonic antigen aptamers and experimental evaluation

Carcinoembryonic antigen (CEA), a highly glycosylated protein, overexpresses in many cancers. In this study, computational methods were used to optimize CEA aptamers. Experimental evaluvation of selected aptamers were conducted through electrochemical impedance spectroscopy. After two and three-dimensional structure modeling, the complexes of twelve reported aptamers against CEA were simulated using the ZDOCK server. Based on docking scores, two aptamer sequences (CSR59 and CSR57.1) were selected and used to create a new library. This ssDNA aptamer library consisting of 91 sequences was created using diverse in silico mutational methods. We obtained seventeen sequences having higher binding scores than reported sequences. Based on ZDOCK scores, the interaction domain of CEA, and steric hindrance due to glycosylation, two aptamer sequences (G3S1.5 and G2S2.2) were selected. An impedimetric aptasensor was designed, and selected aptamers were used as biorecognition elements. Resistance to charge transfer (Rct) quantities confirmed the bioinformatic approach and molecular docking scores. The result showed that the interaction ability of selected aptamers was about 13.5 fold higher than the control. It can be concluded that the selected aptamers have good potential for detection of carcinoembryonic antigen biomarker.

Recent Advances in Aptamer Discovery and Applications

Aptamers are short, single-stranded DNA, RNA, or synthetic XNA molecules that can be developed with high affinity and specificity to interact with any desired targets. They have been widely used in facilitating discoveries in basic research, ensuring food safety and monitoring the environment. Furthermore, aptamers play promising roles as clinical diagnostics and therapeutic agents. This review provides update on the recent advances in this rapidly progressing field of research with particular emphasis on generation of aptamers and their applications in biosensing, biotechnology and medicine. The limitations and future directions of aptamers in target specific delivery and real-time detection are also discussed.

Therapeutic aptamers in discovery, preclinical and clinical stages

The aptamer field witnessed steady growth during the past 28 years as evident from the exponentially increasing number of related publications. The field is "coming of age", but like other biomedical research areas facing a global push towards translational research to carry ideas from bench- to bedside, there is pressure to show impact for aptamers at the clinical end. Being easy-to-make, non-immunogenic, stable and high-affinity nano-ligands, aptamers are perfectly poised to move in this direction. They can specifically bind targets ranging from small molecules to complex multimeric structures, making them potentially useful in a limitless variety of therapeutic approaches. This review will summarize efforts made to accomplish the therapeutic promise of aptamers, with a focus on aptamers directly acting as therapeutic molecules, rather than those used in targeted delivery of other drugs. The review will showcase representative examples at various stages of development, covering different disease categories.

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

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

Label-free and enzyme-free sensitive fluorescent method for detection of viable Escherichia coli O157:H7

We have developed a label-free, enzyme-free, modification-free and DNA extraction-free fluorescent aptasensing (LEFA) method for detection of E. coli O157:H7 based on G-quadruplex formation using two ingeniously designed hairpin probes (GHP1 and GHP2). In the presence of E. coli O157:H7, it released the single stranded initiation sequence (IS) resulting in the toehold strand displacement between GHP1 and GHP2, which in turn led to the cyclic reuse of the production of DNA assemblies with numerous G-quadruplex structures and initiation sequences. Then these G-quadruplex structures can be recognized quickly by N-methyl mesoporphyrin IX (NMM) resulting in significantly enhanced fluorescence. The LEFA method was successfully implemented for detecting E. coli O157:H7 with a detection limit of 66 CFU/mL in pure culture, 10 CFU/mL and 1 CFU/mL after pre-incubation of the milk and tap water for 4 and 8 h, respectively. Moreover, the strategy could distinguish viable E. coli O157:H7 from dead E. coli O157:H7 and other species of pathogen cells. Furthermore, the whole process of the strategy is accomplished within 100 min. The results indicated that the approach may be used to effectively control potential microbial hazards in human health, food safety, and animal husbandry.

Supramolecular Analytical Chemistry in Cancer Research

Supramolecular interactions, such as those observed between antibodies and antigens, have been employed in developing analytical methods for several decades. One major area of interest concerns cancer research, where intricate supramolecular designs have emerged to tackle difficult analytes in complex tumor systems. Our increasing knowledge toward supramolecular systems have elicited profound interest in creating more efficient analytical approaches, evidenced by the ever-growing body of literature in the field. Some of the novel tools have indeed facilitated our understanding of cancer biology, through providing previously inaccessible information. In this review, we describe common strategies of developing supramolecular analytical methods and their implementations in cancer research. We provide an overview for each of the approaches and discuss representative examples in recent literature.

Programmable and Multifunctional DNA-Based Materials for Biomedical Applications

DNA encodes the genetic information; recently, it has also become a key player in material science. Given the specific Watson-Crick base-pairing interactions between only four types of nucleotides, well-designed DNA self-assembly can be programmable and predictable. Stem-loops, sticky ends, Holliday junctions, DNA tiles, and lattices are typical motifs for forming DNA-based structures. The oligonucleotides experience thermal annealing in a near-neutral buffer containing a divalent cation (usually Mg²⁺ ) to produce a variety of DNA nanostructures. These structures not only show beautiful landscape, but can also be endowed with multifaceted functionalities. This Review begins with the fundamental characterization and evolutionary trajectory of DNA-based artificial structures, but concentrates on their biomedical applications. The coverage spans from controlled drug delivery to high therapeutic profile and accurate diagnosis. A variety of DNA-based materials, including aptamers, hydrogels, origamis, and tetrahedrons, are widely utilized in different biomedical fields. In addition, to achieve better performance and functionality, material hybridization is widely witnessed, and DNA nanostructure modification is also discussed. Although there are impressive advances and high expectations, the development of DNA-based structures/technologies is still hindered by several commonly recognized challenges, such as nuclease instability, lack of pharmacokinetics data, and relatively high synthesis cost.