Ultrasensitive colorimetric detection of 17β-estradiol: the effect of shortening DNA aptamer sequences

Aptasensor-encapsulating semi-permeable proteinosomes for direct target detection in non-treated biofluids

Detecting biomarkers in biofluids directly without sample treatments makes molecular diagnostics faster and more efficient. Aptasensors, the nucleic acid-based molecular biosensors, can detect a wide range of target molecules, but their susceptibility to degradation and aggregation by nucleases and charged proteins, respectively, limits their direct use in clinical samples. In this work, we demonstrate that when aptasensors are encapsulated in proteinosomes, the protein-based liposome mimics, clinically important small molecules can be sensitively and selectively detected in non-treated specimens, such as 100 % unpurified serum. As serum albumin is used to form the membrane, the nanomeshed proteinosomes become semi-permeable and antifouling, which enables exclusive admission of small molecules while blocking unwanted large proteins. Consequently, the enclosed aptasensors can maintain close-to-optimal performance for target binding, and nucleolytic degradation and electrostatic aggregation are effectively suppressed. Three different structure-switching aptamers specific for estradiol, dopamine, and cocaine, respectively, are demonstrated to fully conserve their high affinities and specificities inside the microcapsules. The shielding effect of proteinosomes is indeed exceptional; the enclosed DNA aptasensors remain completely intact over 18 h in serum and even in an extremely concentrated DNase solution (1 mg/ml, ∼300,000× the serum level). Moreover, the proteinosome-mediated compartmentalization enables independent operation of multiple aptasensors in the same mixture. Hence, simultaneous real-time sensing of two different targets is demonstrated with different operation modes, 'recording' target appearance and 'reporting' target concentration changes. This work is the first demonstration of small-molecule-specific aptasensors operating with optimal performance in serum environments and will find promising applications in molecular diagnostics.

Light-activated, dual-mode fluorescence and colorimetric detection of estradiol with high fidelity based on aptamer's special recognition

The intake of estradiol residue from food will lead to health problems, so the rapid and reliable detection of estradiol residue is essential. Multi-mode assays are inherently self-correcting and self-validating, providing more reliable, interference-resistant, high-fidelity results. Here, we developed a dual-mode method to achieve a rapid, reliable, and sensitive detection of estradiol. The binding of thioflavin T to the cavity sites of estradiol aptamer not only generates a strong fluorescence signal, but also provides light-activated oxidase activity to produce a blue oxidation product. But the specific binding between aptamer and estradiol will compete with the above process. Thus a dual-mode fluorescence and colorimetric detection of estradiol was realized with a detection limit of 0.15 μM or 0.27 μM. Besides, the dual-mode method showed a good selectivity for estradiol detection. The method could detect estradiol in meat food, showing a good application potential to monitor endocrine-disrupting chemical.

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.

Utilizing Deep Learning Algorithms for Signal Processing in Electrochemical Biosensors: From Data Augmentation to Detection and Quantification of Chemicals of Interest

Nanomaterial-based aptasensors serve as useful instruments for detecting small biological entities. This work utilizes data gathered from three electrochemical aptamer-based sensors varying in receptors, analytes of interest, and lengths of signals. Our ultimate objective was the automatic detection and quantification of target analytes from a segment of the signal recorded by these sensors. Initially, we proposed a data augmentation method using conditional variational autoencoders to address data scarcity. Secondly, we employed recurrent-based networks for signal extrapolation, ensuring uniform signal lengths. In the third step, we developed seven deep learning classification models (GRU, unidirectional LSTM (ULSTM), bidirectional LSTM (BLSTM), ConvGRU, ConvULSTM, ConvBLSTM, and CNN) to identify and quantify specific analyte concentrations for six distinct classes, ranging from the absence of analyte to 10 μM. Finally, the second classification model was created to distinguish between abnormal and normal data segments, detect the presence or absence of analytes in the sample, and, if detected, identify the specific analyte and quantify its concentration. Evaluating the time series forecasting showed that the GRU-based network outperformed two other ULSTM and BLSTM networks. Regarding classification models, it turned out signal extrapolation was not effective in improving the classification performance. Comparing the role of the network architectures in classification performance, the result showed that hybrid networks, including both convolutional and recurrent layers and CNN networks, achieved 82% to 99% accuracy across all three datasets. Utilizing short-term Fourier transform (STFT) as the preprocessing technique improved the performance of all datasets with accuracies from 84% to 99%. These findings underscore the effectiveness of suitable data preprocessing methods in enhancing neural network performance, enabling automatic analyte identification and quantification from electrochemical aptasensor signals.

Aptamer-Protein Interactions: From Regulation to Biomolecular Detection

Serving as the basis of cell life, interactions between nucleic acids and proteins play essential roles in fundamental cellular processes. Aptamers are unique single-stranded oligonucleotides generated by in vitro evolution methods, possessing the ability to interact with proteins specifically. Altering the structure of aptamers will largely modulate their interactions with proteins and further affect related cellular behaviors. Recently, with the in-depth research of aptamer-protein interactions, the analytical assays based on their interactions have been widely developed and become a powerful tool for biomolecular detection. There are some insightful reviews on aptamers applied in protein detection, while few systematic discussions are from the perspective of regulating aptamer-protein interactions. Herein, we comprehensively introduce the methods for regulating aptamer-protein interactions and elaborate on the detection techniques for analyzing aptamer-protein interactions. Additionally, this review provides a broad summary of analytical assays based on the regulation of aptamer-protein interactions for detecting biomolecules. Finally, we present our perspectives regarding the opportunities and challenges of analytical assays for biological analysis, aiming to provide guidance for disease mechanism research and drug discovery.

Sensitive detection of 17β-estradiol at a picomolar level using an aptamer-assisted liquid crystal-based optical sensor

A liquid crystal (LC)-based aptasensor was developed that can detect 17β-estradiol (E2) at the picomolar level. This aptasensor is based on competitive reactions of the aptamer that interacts with cetyl trimethyl ammonium bromide (CTAB) and E2 at the aqueous/LC interface. The long alkyl chain of CTAB anchored the 4-cyano-4'-pentylbiphenyl (5CB) to a homeotropic state and controls the local anchoring depending on the extent of electrostatic interaction with the aptamer. Upon addition of the aptamer solution to the CTAB-saturated LC layer, LCs change from dark to bright optical response. This is due to the perturbed orientation of 5CB at the aqueous/LC interface as a result of electrostatic attraction of the cationic group of CTAB and the phosphate group of the aptamer. The conformational change of the aptamer due to specific binding with E2 weakens the electrostatic attraction between CTAB and aptamer. When specific binding becomes relatively dominant, CTAB induces the orientation of LCs to the homeotropic state, resulting in a dark optical image observed. We also analyzed the change in the optical response of LCs according to the interfacial events and compared the grayscale values of the optical image for each concentration of E2 to determine the detection limit. Accordingly, the detection limit of the E2 sensor was found to be 3.1 pM (0.8 pg/ml) in Tris-buffered saline (TBS), and 6.8 pM (1.9 pg/ml) in human urine. The LC-based optical aptasensor was thus shown to be highly sensitive and selective with no requirement for complex analysis equipment.

A "turn-on" fluorescence resonance energy transfer aptasensor based on carbon dots and gold nanoparticles for 17β-estradiol detection in sea salt

17β-estradiol is abused in the food industry. Excess 17β-estradiol can disturb the endocrine system or cause many diseases including obesity, diabetes, cardiac-cerebral vascular disease, and cancers in the human body. A "turn-on" fluorescence resonance energy transfer (FRET) aptasensor based on carbon dots (CDs) and gold nanoparticles (AuNPs) was developed for the detection of 17β-estradiol. A thiol-modified oligonucleotide was conjugated to AuNPs and amino modified oligonucleotide was linked to CDs. The 17β-estradiol aptamer was hybridized with the two oligonucleotides, shortening the distance between CDs and AuNPs. With 360 nm UV light excitation, FRET occurred between CDs and AuNPs. The system was "turn-off". When 17β-estradiol was detected, the aptamer specifically bound to 17β-estradiol, and the FRET system was destroyed, leading to the "turn-on" phenomenon. The fluorescence intensity recovery was detected in the concentration range of 400 pM to 5.5 μM. The limit of detection (LOD) was 245 pM. The FRET aptasensor demonstrated good selectivity for 17β-estradiol detection. Reasonable spiked recoveries were obtained in sea salt samples. It showed the potential for estrogen detection in food safety and environmental applications.

Highly sensitive colorimetric aptasensor for 17β-estradiol detection in milk based on the repetitive-loop aptamer

Trace of 17β-estradiol (E2) contamination in food has been a concern for its negative impacts on human health, leading to the need for an E2-monitoring system. This work reported a new simple, sensitive, and colorimetric E2 detection based on the designed repetitive-loop aptamer and gold nanoparticles (AuNPs). The designed aptamers (L2-L5) exhibited a higher binding capability to E2 than the original truncated aptamer (L1). Although L3-L5 aptamers exhibited the highest binding capability, only L3-aptasensor demonstrated the sensitive detection of E2 in a range of 0.05-0.8 nM, with the limit of detection at 13.1 pM. The developed L3-aptasensor was 7.7-folds more sensitive for E2 detection than the L1-aptasensor. It selectively detected E2, but not the other tested chemicals with similar structures: progesterone, genistein, diethylstilbestrol, bisphenol A, and chloramphenicol. The L3-aptasensor efficiently detected E2 spiked in milk samples within the precision acceptance criterion of recovery rates (100.1%-113.0%) and the relative standard deviations (5.24%-11.06%). These results demonstrated the development of a new aptasensor based on the designed repetitive-loop aptamer that could enhance E2-detection sensitivity and be potentially used for detecting E2 in milk samples with high accuracy and reliability.

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.

Capture-SELEX of DNA Aptamers for Estradiol Specifically and Estrogenic Compounds Collectively

Estrogenic compounds such as estrone (E1), 17β-estradiol (E2), and 17α-ethynylestradiol (EE2) are serious environmental contaminants due to their potent biological activities. At least six selections were previously reported to obtain DNA aptamers for E2, highlighting its environmental importance. A careful analysis revealed that the previous aptamers either are too long or do not bind optimally. Herein, a series of new aptamers were obtained from the capture-SELEX method with dissociation constants down to 30 nM as determined by isothermal titration calorimetry (ITC). Two aptamers were converted to structure-switching fluorescent biosensors, which achieved a limit of detection down to 3.3 and 9.1 nM E2, respectively. One aptamer showed similar binding affinities to all the three estrogens, while the other aptamer is more selective for E2. Both aptamers required Mg²⁺ for binding. The proposed sensors were successfully applied in the determination of E2 in wastewater. Moreover, comparisons were made with previous aptamers based on primary sequence alignment and secondary structures. Among previously reported truncated aptamers, ITC showed binding only in one of them. The newly selected aptamers have the combined advantages of small size and high affinities.

Ultrasensitive Automatic Detection of Small Molecules by Membrane Imaging of Single Molecule Assays

Determination of trace amounts of targets or even a single molecule target has always been a challenge in the detection field. Digital measurement methods established for single molecule counting of proteins, such as single molecule arrays (Simoa) or dropcast single molecule assays (dSimoa), are not suitable for detecting small molecule, because of the limited category of small molecule antibodies and the weak signal that can be captured. To address this issue, we have developed a strategy for single molecule detection of small molecules, called small molecule detection with single molecule assays (smSimoa). In this strategy, an aptamer is used as a recognition element, and an addressable DNA Nanoflower (DNF) attached on the magnetic beads surface, which exhibit fluorescence imaging, is employed as the output signal. Accompanied by digital imaging and automated counting analysis, E2 at the attomolar level can be measured. The smSimoa breaks the barrier of small molecule detection concentration and provides a basis for high throughput detection of multiple substances with fluorescence encoded magnetic beads.

Role of Estradiol Hormone in Human Life and Electrochemical Aptasensing of 17β-Estradiol: A Review

Estradiol is known as one of the most potent estrogenic endocrine-disrupting chemicals (EDCs) that may cause various health implications on human growth, metabolism regulation, the reproduction system, and possibly cancers. The detection of these EDCs in our surroundings, such as in foods and beverages, is important to prevent such harmful effects on humans. Aptamers are a promising class of bio-receptors for estradiol detection due to their chemical stability and high affinity. With the development of aptamer technology, electrochemical aptasensing became an important tool for estradiol detection. This review provides detailed information on various technological interventions in electrochemical estradiol detection in solutions and categorized the aptasensing mechanisms, aptamer immobilization strategies, and electrode materials. Moreover, we also discussed the role of estradiol in human physiology and signaling mechanisms. The level of estradiol in circulation is associated with normal and diseased conditions. The aptamer-based electrochemical sensing techniques are powerful and sensitive for estradiol detection.

Enhancing Electrochemical Biosensor Performance for 17β-Estradiol Determination with Short Split-Aptamers

Chronic exposure of 17β-estradiol (E2) even at low concentration can disorganize the endocrine system and lead to undesirable health problems in the long run. An electrochemical biosensor for rapid detection of E2 in water samples was successfully developed. The biosensor was based on split DNA aptamers attached onto poly (methacrylic acid-co-n butyl acrylate-succinimide) microspheres deposited on polypyrrole nanowires coated electrode (PPY/PMAA-NBA). The sandwich paired of split DNA aptamers used were truncated from 75 mer parent aptamers. These two strands of 12-mer and 14-mer split DNA aptamers were then immobilized on the PMAA-NBA microspheres. In the presence of E2, the split DNA aptamers formed an apt12-E2-apt14 complex, where the binding reaction on the electrode surface led to the detection of E2 by differential pulse voltammetry using ferrocyanide as a redox indicator. Under optimum conditions, the aptasensor detected E2 concentrations in the range of 1 × 10^-4 M to 1 × 10^-12 M (R² = 0.9772) with a detection limit of 4.8 × 10^-13 M. E2, which were successfully measured in a real sample with 97-104% recovery and showed a good correlation (R² = 0.9999) with the established method, such as high-performance liquid chromatography. Interactions between short and sandwich-type aptamers (split aptamers) demonstrated improvement in aptasensor performance, especially the selectivity towards several potential interferents.

Accounting for Interaction Kinetics between Gold Nanoparticles and Aptamers Enables High-Performance Colorimetric Sensors

DNA aptamers have emerged as promising probes for challenging analytes that cannot be easily detected by conventional probes, including small-molecule targets. Among the different signal transduction approaches, gold nanoparticle (AuNP) aggregation assays have been widely used to generate a colorimetric response from aptamer-target interactions. This sensor design relies on the competition between the aptamer adsorbing to the AuNP surface versus interacting with the target, whereby target binding reduces the number of adsorbed aptamers that destabilizes AuNPs toward salt-induced aggregation, thereby inducing a color change. However, this thermodynamic framework overlooks the potential influence of interaction kinetics of different aptamer conformations with AuNP surfaces and with targets in solution or near surfaces. Here, we show that aptamers become more strongly adsorbed on AuNPs over time, and these trapped aptamers are less responsive toward the target analyte. By varying the sequence of addition in sensing assays, we demonstrate that these interaction kinetics have a significant effect on the sensor response and thereby produce an effective sensor for methamphetamine (meth) at biologically relevant levels in oral fluids. Along with underpinning new tools for assay development, this new knowledge also highlights the need for aptamer selection strategies that evolve aptamer sequences based on the functionality that they need to exhibit in an actual sensor.

Unravelling the binding mode of a methamphetamine aptamer: a spectroscopic and calorimetric investigation

Nucleic acid aptamers are bio-molecular recognition agents that bind to their targets with high specificity and affinity, and hold promise in a range of biosensor and therapeutic applications. In the case of small molecule targets, their small size and limited number of functional groups constitute challenges for their detection by aptamer-based biosensors because bio-recognition events may both be weak and produce poorly transduced signals. The binding affinity is principally used to characterize aptamer-ligand interactions; however a structural understanding of bio-recognition is arguably more valuable in order to design a strong response in biosensor applications. Using a combination of nuclear magnetic resonance, circular dichroism, and isothermal titration calorimetry, we propose a binding model for a new methamphetamine aptamer and determine the main interactions driving complex formation. These measurements reveal only modest structural changes to the aptamer upon binding and are consistent with a conformational selection binding model. The aptamer-methamphetamine complex formation was observed to be entropically driven, apparently involving hydrophobic and electrostatic interactions. Taken together, our results exemplify a means of elucidating small molecule-aptamer binding interactions, which may be decisive in the development of aptasensors and therapeutics, and may contribute to a deeper understanding of interactions driving aptamer selection.

Plasmonic Nanomaterials for Colorimetric Biosensing: A Review

In the last few decades, plasmonic colorimetric biosensors raised increasing interest in bioanalytics thanks to their cost-effectiveness, responsiveness, and simplicity as compared to conventional laboratory techniques. Potential high-throughput screening and easy-to-use assay procedures make them also suitable for realizing point of care devices. Nevertheless, several challenges such as fabrication complexity, laborious biofunctionalization, and poor sensitivity compromise their technological transfer from research laboratories to industry and, hence, still hamper their adoption on large-scale. However, newly-developing plasmonic colorimetric biosensors boast impressive sensing performance in terms of sensitivity, dynamic range, limit of detection, reliability, and specificity thereby continuously encouraging further researches. In this review, recently reported plasmonic colorimetric biosensors are discussed with a focus on the following categories: (i) on-platform-based (localized surface plasmon resonance, coupled plasmon resonance and surface lattice resonance); (ii) colloid aggregation-based (label-based and label free); (iii) colloid non-aggregation-based (nanozyme, etching-based and growth-based).

Highly sensitive and selective lateral flow aptasensor for anti-coagulant dabigatran etexilate determination in blood

Dabigatran etexilate (DBG) is a new anticoagulant drug (commercially sold under the names Pradaxa® and Pradax™) that replaces Warfarin, the landmark agent for anticoagulation therapy. Inadequate administration of DBG or in the cases of massive bleeding that occurs after renal impairment, DBG therapy can carry a substantial life-threatening risks. One of the major limitations of DBG treatment is the lack of a simple and quick tool for measuring its level in blood in the case of massive bleedings or emergency operations. In this work, we have incorporated a previously isolated aptamer for DBG to develop a simple competitive lateral flow aptasensor (LFA) for the determination of DBG in buffer and blood samples. A full-length 60-mer aptamer as well as a truncated 38-mer aptamer were conjugated to gold nanoparticles (AuNPs) via thiol-Au coupling chemistry. After appropriate AuNP surface passivation steps, the aptamer's core region was hybridized with 8-mer biotinylated sequences. The conjugated particles could be capture on the test line by the interaction of the biotin molecules with a previously deposited streptavidin. Incubation of the conjugated particles with DBG causes the aptamer to undergo a conformational change that releases the 8-mer biotinylated sequences and result in the disappearance of the test line. Lysozyme protein was used to construct the control line that non-specifically interacts with the conjugated particles whether or not the target compound is present. The developed LFA achieves 20 nM detection level in buffer and blood samples, operates within the nanomolar range, and shows excellent selectivity against potential interfering molecules. The developed sensor could help assessing the levels of DBG in medical conditions that require rapid interventions.

Selection and characterization of DNA aptamers for the rat major urinary protein 13 (MUP13) as selective biorecognition elements for sensitive detection of rat pests

Among invasive mammalian predators, rats represent a major threat, endangering ecosystem functioning worldwide. After rat-control operations, detecting their continued presence or reinvasion requires more sensitive and lower cost detection technologies. Here, we develop a new sensing paradigm by using a specific rat urine biomarker (MUP13) to unambiguously signal the presence of rats. As the first step towards a new remote surveillance technology, aptamers were selected to MUP13 using the Flu-Mag SELEX method. Six aptamer candidates were initially screened by dot blot and two of them (Apt-2.5 and Apt-1.4) exhibited high affinity and specificity. Both aptamers were further characterized by bead-based assay to confirm affinity and selectivity. The lead aptamer candidates were then applied to fluorescence anisotropy (FA) and surface plasmon resonance (SPR)-based biosensor platforms, showing dissociation constants in the nanomolar range and high specificity towards their target. The SPR biosensor had limits of detection of 13.8 and 7.5 nM for Apt-2.5 and Apt-1.4, respectively, which are more than three orders of magnitude lower than the physiological concentrations found in rat urine. Selectivity of the aptamers, when comparing with other major urinary proteins, was excellent, indicating strong efficacy in specific detection of rats. In order to validate the aptamer Apt-2.5 for use with real world samples a FA-based assay was performed on a rat urine sample. The assay showed that the aptamer could detect recombinant MUP13 spiked in filtered urine and the natural MUP13 in unfiltered urine, as a first step into translation to real world application. These are the first known assays to detect and quantify a MUP biomarker of rats.

Single-Round DNA Aptamer Selection by Combined Use of Capillary Electrophoresis and Next Generation Sequencing: An Aptaomics Approach for Identifying Unique Functional Protein-Binding DNA Aptamers

In DNA aptamer selection, existing methods do not discriminate aptamer sequences based on their binding affinity and function and the reproducibility of the selection is often poor, even for the selection of well-known aptamers like those that bind the commonly used model protein thrombin. In the present study, a novel single-round selection method (SR-CE selection) was developed by combining capillary electrophoresis (CE) with next generation sequencing. Using SR-CE selection, a successful semi-quantitative and semi-comprehensive aptamer selection for thrombin was demonstrated with high reproducibility for the first time. Selection rules based on dissociation equilibria and kinetics were devised to obtain families of analogous sequences. Selected sequences of the same family were shown to bind thrombin with high affinity. Furthermore, data acquired from SR-CE selection was mined by creating sub-libraries that were categorized by the functionality of the aptamers (e. g., pre-organized aptamers versus structure-induced aptamers). Using this approach, a novel fluorescent molecular recognition sensor for thrombin with nanomolar detection limits was discovered. Thus, in this proof-of-concept report, we have demonstrated the potential of a "DNA Aptaomics" approach to systematically design functional aptamers as well as to obtain high affinity aptamers.

Synthesis and Characterization of Bis-1,2,3-Triazole Ligand and its Corresponding Copper Complex for the Development of Electrochemical Affinity Biosensors

The bis-triazole ligand and its corresponding copper complexes were synthesized and characterized for the first time and proposed as new labels for the development of electrochemical aptasensors. The bis-triazole ligand was prepared from methyl 1,6-heptadiyne-4-carboxylate and 2-(azidomethyl)phenol using classical CuAAC in presence of different copper salts. The X-ray structure of bis-triazole showed a symmetry center (C1). UV-Vis and X-band EPR spectra showed that the coordination capacity of the bis-triazole ligand was improved in the presence of triethylamine due to deprotonation of the triazole and phenolate moieties. After complexation with copper, the obtained complex was successfully attached to an anti-estradiol aptamer through thiol-maleimide coupling, and the resulting labelled aptamer was immobilized on a carbon screen-printed electrode by carbodiimide coupling. The electrochemical response of the resulting sensor was shown to decrease in the presence of estradiol, demonstrating that the developed complexes can be applied for the development of aptasensors.

Electrochemical aptasensor for 17β-estradiol using disposable laser scribed graphene electrodes

17β-Estradiol (E2), the strongest of the three major physiological estrogens in females, is an important factor in the female reproductive system. The abnormal level of E2 causes health issues, such as weak bones, urinary tract infections and even depression. Here, we present a novel, sensitive and selective, electrochemical aptasensor for detection of 17β-estradiol (E2). The E2 recognition aptamer was split into two fragments: the first fragment, functionalised with adamantane, is attached to poly(β-cyclodextrin) (poly(β-CD))-modified electrode surface through host-guest interactions between the adamantane and poly(β-CD). The second fragment, labelled with gold nanoparticles, forms the stem-loop structure with the first fragment only in the presence of E2. That specific recognition process triggers the change in the electrochemical signal (a change in the peak current from reduction of AuNPs), recorded by means of differential pulse voltammetry (DPV). The feasibility of the sensing design was firstly investigated on the commercially available glass carbon electrodes (GCE), with achieved a linear detection range of 1.0 × 10^-13 to 1.0 × 10^-8 M and a limit of detection (LoD) 0.7 fM. The sensing methodology was then translated onto single-use, disposable, laser-scribed graphene electrodes (LSGE) on a plastic substrate. The dynamic sensing range of E2 on LSGE was found to be 1.0 × 10^-13 to 1.0 × 10^-9 M, with a LoD of 63.1 fM, comparable to these of GCE. The successful translation of the developed E2 aptasensor from GCE to low-cost, disposable LSGE highlights a potential of this sensing platform in commercial, portable sensing detection systems for E2 and similar targets of biological interest.

Molecular detection using aptamer-modified gold nanoparticles with an immobilized DNA brush for the prevention of non-specific aggregation

Gold nanoparticles (AuNPs) are often used for biosensing. In particular, aptamer-modified AuNPs are often used for colorimetric molecular detection, where target molecule-induced AuNP aggregates can be recognized by a color change from red to blue. However, non-specific aggregation could be induced by various compounds, leading to false-positive results. In this work we employed high-density ssDNA modification on the AuNP surface to prevent non-specific aggregation. The covalently immobilized DNA brush was used as an anchor for an aptamer specific for the target molecule. Herein, as a proof-of-concept study, we demonstrated detection of estradiol (E2), one of the endocrine-disrupting estrogen molecules as a model target, in the presence of antibiotic kanamycin (KN) as a model of co-contaminating compounds that induce non-specific aggregation of AuNPs. We also developed a smartphone dark field microscope (DFM) to visualize AuNP aggregation. Our previous study demonstrated that the observation of light scattering by AuNP aggregates with DFM can be applied for versatile molecular detection. In this work, we could successfully detect E2 with the smartphone DFM, and the results were verified by the results from a conventional benchtop DFM. This study would contribute to the future field applicability of AuNP-based sensors.

We demonstrated molecular detection using aptamer-modified gold nanoparticles with DNA-brush for the prevention of non-specific aggregation and smartphone darkfield microscopy.

Ultrasensitive Detection of 17β-Estradiol (E2) Based on Multistep Isothermal Amplification

17β-Estradiol (E2) can cause an adverse effect on the human endocrine system even at the nanomolar level. Measurements of very low levels of E2 remain a critical challenge due to insufficient sensitivity. In this study, a multistep isothermal amplification fluorescence strategy was constructed, which could realize the exponential amplification of target E2. Specifically, strand displacement reaction (SDA), rolling circle amplification (RCA), and multiprimed rolling circle amplification (MRCA) were combined in a series to quantify trace complementary strand of E2 (cDNA). The E2 aptamer and cDNA were hybridized and modified on the magnetic beads. E2 could bind to its aptamer and cause the release of the cDNA. Then, cDNA would combine with the template DNA, initiating the SDA-RCA-MRCA. The molecular beacons, possessing low background signal, whose fluorescence was quenched in the state of chain folding, could be specifically recognized by the long single-stranded DNA (L-ssDNA) generated by the multistep isothermal amplification triggered by cDNA, and then the fluorescence of the molecular beacons could be restored. Therefore, the E2 could be quantitatively detected by the recovery fluorescence intensity. The fluorescence value showed a good linear relationship with the concentration of E2 in the range of 0.001836-183.6 nM, and the limit of detection (LOD) was as low as 63.09 fM. In addition, the recovery rates of this method spiked in milk and water were 80.8-107.0%, respectively. This method has the advantage of multistep isothermal amplification to obtain abundant fluorescence signals, which may provide a new possibility for highly sensitive detection of other small-molecule targets.

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.

Development of a Gold Nanoparticle-Based Colorimetric Sensor for Water for Injection At-Line Impurity Testing

The best-known rapid test using gold nanoparticles (AuNPs) is the human chorionic gonadotropin pregnancy test. AuNPs are a powerful tool in point-of-care testing because of their flexibility, modifiability, and visibility. Here, we report a method to detect impurities for at-line process control in water-for-injection (WFI) manufacturing through the example of endotoxins. If a distinct concentration of these amphipathic molecules, originated from gram-negative bacteria, enters the human body, it will result in septic shock, followed by organ failure and possibly death. Every fluid given parenterally is subject to strict regulatory requirements and therefore endotoxin testing. Through use of traditional methods like the limulus amebocyte lysate (LAL) test, it takes more than 2 h to complete. With the presented method, one-fifth of the sample volume is sufficient compared with the LAL test. Once the assay components have been mixed, the result can be interpreted visually within 2 min without the use of further instruments.

Myocardial infarction biomarker C-reactive protein detection on nanocomposite aptasensor

Myocardial infarction (MI) is considered as one of the major life-threatening health issues worldwide. Growing number of cases every year is demanding rapid, portable, and early detection by the sensing devices for the identification of MI. This research work introduces a modified interdigitated electrode (IDE) sensing surface constructed with single-walled carbon nanotube (SWCN) to detect the cardiac biomarker, C-reactive protein (CRP). CRP-specific aptamer was conjugated with gold nanoparticle and attached on SWCN-constructed IDE surface. This probe-modified sensing surface has reached the limit of CRP detection to 10 pM on a linear regression curve with the regression coefficient of R² = 0.9223 [y = 0.9198x - 0.4326]. Further, control molecules, such as random aptamer sequence and nontarget cardiac biomarker (Troponin I), did not show the current response, indicating the specific CRP detection. This sensing strategy helps to detect the lower level of CRP and diagnose the MI at its earlier stages.

Using Simple-Structured Split Aptamer for Gold Nanoparticle-based Colorimetric Detection of Estradiol

Demand for the detection of estradiol, which is a naturally occurring hormone, has been increasing. Gold nanoparticle-based colorimetric aptasensors have been developed for estradiol detection; however, the long sequence of aptamers due to the formation of the secondary structure likely affects the sensitivity of the aptasensors. Herein, a sensitive colorimetric biosensor is developed for label-free detection of estradiol by using an estradiol-specific split aptamer. The results demonstrate that a superior response is observed when a split aptamer with a high free energy of the secondary structure (ΔG > -3 kcal/mol) is used, in comparison to that observed using a split aptamer with a low free energy of the secondary structure (ΔG < -3 kcal/mol) at 27°C. After selecting the appropriate split aptamer, the standard calibration curve obtained for estradiol has a detection limit of 6.7 nM, with a linear range of 6.7 nM - 66.7 μM in the logarithmic scale. Furthermore, this assay is sensitive, easy-to-operate, inexpensive, and non-time-consuming (provides results within 50 min), thereby showing potential for clinical applications (detection of other small molecular targets).

Selection and truncation of aptamers for ultrasensitive detection of sulfamethazine using a fluorescent biosensor based on graphene oxide

We developed a fluorescent aptamer/graphene oxide (GO)-based biosensor to detect sulfamethazine (SMZ) residues in animal-derived foods. The SMZ-bound aptamers were identified and screened with an improved GO-SELEX technique using non-immobilizing ssDNA library. After seven rounds of selection, six SMZ aptamers were sequenced and analyzed for secondary structure, and their affinity and specificity were assessed by binding assays. The truncated aptamer (SMZ1S: 5'-CGTTAGACG-3') with a unique stem-loop structure showed the highest affinity (K_d = 24.6 nM) to SMZ and was used to develop a GO-based fluorescent aptasensor. The binding mechanism between SMZ1S and SMZ was further analyzed by molecular docking. Under optimal conditions, the fluorescent aptasensor showed low detection limits (0.35 ng/mL) and a wide dynamic linear range (from 2 to 100 ng/mL). The aptasensor was also validated against real samples spiked with SMZ, which showed a fluorescence recovery from 93.9 to 108.8% and a coefficient of variation of < 12.7%. Taken together, these results suggest that this novel aptasensor can be used to sensitively, selectively, and accurately detect SMZ residues in foods. Schematic illustration of fluorescent aptasensor based on aptamer/graphene oxide complex detection of of SMZ.

GOLD SELEX: a novel SELEX approach for the development of high-affinity aptamers against small molecules without residual activity

GOLD SELEX, a novel SELEX approach has been developed that obviates the need for target immobilization for aptamer development. The approach purely relies on the affinity of the aptamers towards its target, to get detached from the gold nanoparticle (GNP) surface (weak attraction) after binding with its target. Thus, only the completely detached aptamers are selected for the next round of SELEX. This, in-process, also addresses the issue of residual binding and thus improves the sensitivity of the developed aptamers. As a proof of concept for establishing the utility of the approach for small molecules, we have developed aptamers against dichlorvos (DV), a pesticide in just 8 rounds. Using these aptamer candidates, we have developed an aptamer-NanoZyme (GNP having peroxidase mimic activity) based colorimetric assay. The developed aptamer displayed high affinity (K_d in sub micromolar range) and selectivity for DV. The developed assay could detect as low as 15 μM DV. The best-performing aptamer was also able to work in real samples like river water and commercial apple juice. The GOLD SELEX approach developed in this study, we believe, can act as a template for future SELEX strategy development and can replace the conventional SELEX strategy.

A Critical Factor for Quantifying Proteins in Unmodified Gold Nanoparticles-Based Aptasensing: The Effect of pH

Unmodified gold nanoparticles (AuNPs)-based aptasensing (uGA) assay has been widely implemented in the determination of many different targets, but there are few reports on protein detection using uGA. Here, we designed a uGA assay for protein detection including the elimination of interfering proteins. Positively charged protein can be absorbed directly on the surface of AuNPs to form “protein corona”, which results in the aggregation of AuNPs even without salt addition, thereby preventing target protein detection. To overcome this problem, we systematically investigated the effect of modifying the pH of the solution during the uGA assay. A probe solution with a pH slightly higher than the isoelectric points (pI) of the target protein was optimal for protein detection in the uGA assay, allowing the aptamer to selectively detect the target protein. Three proteins (beta-lactoglobulin, lactoferrin, and lysozyme) with different pI were chosen as model proteins to validate our method. Positively charged interfering proteins (with pIs higher than the optimal pH) were removed by centrifugation of protein corona/AuNPs aggregates before the implementation of actual sample detection. Most importantly, the limit of detection (LOD) for all three model proteins was comparable to that of other methods, indicating the significance of modulating the pH. Moreover, choosing a suitable pH for a particular target protein was validated as a universal method, which is significant for developing a novel, simple, cost-effective uGA assay for protein detection.

Paper-based microfluidic aptasensors

For in-situ disease markers detection, point-of-care (POC) diagnosis has great advantages in speed and cost compared with traditional techniques. The rapid diagnosis, prognosis, and surveillance of diseases can significantly reduce disease-related mortality and trauma. Therefore, increasing attention has been paid to the POC diagnosis devices due to their excellent diagnosis speed and portability. Over the past ten years, paper-based microfluidic aptasensors have emerged as a class of critical POC diagnosis devices and various aptasensors have been proposed to detect various disease markers. However, most aptasensors need further improvement before they can actually enter the market and be widely used. There is thus an urgent need to sort out the key points of preparing the aptasensors and the direction that needs to be invested in. This review summarizes the representative articles in the development of paper-based microfluidic aptasensors. These works can be divided into paper-based optical aptasensors and paper-based electrochemical aptasensors according to their output signals. Significant focus is applied to these works according to the following three parts: (1) The ingenious design of device structure; (2) Application and synthesis of nanomaterial; (3) The detection principle of the proposed aptasensor. This is a detailed and comprehensive review of paper-based microfluidic aptasensors. The accomplishments and shortcomings of the current aptasensors are outlined, the development direction and the future prospective are given. It is hoped that the research in this review can provide a reference for further development of more advanced, more effective paper-based microfluidic aptasensors for POC disease markers diagnosis.

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.

Design of a ratiometric fluorescence sensor based on metal organic frameworks and Ru(bpy)32+-doped silica composites for 17β-Estradiol detection

17β-Estradiol (E2), an important endocrine disrupting compound, could be quantitatively detected by fluorescence resonance energy transfer (FRET) aptasensor, designed in this paper. Metal organic frameworks have large specific surface area and easily modifiable groups, which are helpful for the construction of aptasensor. Specifically, streptavidin was immobilized on the synthesized MIL-53-NH₂ by covalent bonding, and further linked with the biotin modified E2 aptamer (apt) through specific bonding between avidin and biotin to obtain the FRET donor probe (MIL-53-apt). Meanwhile, complementary DNA (cDNA) modified Ru(bpy)₃²⁺-doped silica nanoparticles (RuSiO₂-cDNA) were prepared through covalent bonding. They acted as the FRET acceptor probe, since its absorption spectrum showed large overlap with the emission spectrum of MIL-53-apt. In the presence of E2, aptamer modified donor probes tended to bind with E2, owing to their higher selectivity and affinity. Therefore, the optimal distance between FRET pairs was broken, resulting in the fluorescence emission recovery of donor and the fluorescence emission of acceptor decreased. Under optimal conditions, this proposed aptasensor displayed sensitive detection of E2 ranging from 0.5 to 1000 nM with a detection limit of 0.2 nM. Furthermore, the sensor provides a promising method for rapid and sensitive detection of other small biological molecules.

Selection and characterisation of triclosan-specific aptamers using a fluorescence microscope-imaging assay

This study reports a fluorescence microscope-imaging assay for determining the binding characteristics of single-stranded DNA aptamers selected against the antibacterial agent, triclosan. The imaging assay utilises fluorescently labelled aptamers and target-immobilised matrices. Upon binding of triclosan-specific aptamers to triclosan-conjugated matrices, the binding complex was visualised and the image was captured with the aid of a fluorescence microscope. Subsequently, the fluorescent intensities of aptamer-bound matrices were analysed using dedicated image-processing software and correlated to known concentrations of selected input aptamers. Thus, by plotting fluorescence intensities against different aptamer concentrations, binding isotherms were generated to determine aptamer K_d values. The imaging assay was applied to characterise the binding affinities and specificities of ten triclosan-specific aptamers H1-H10. One of the candidate aptamers, H6, showed a K_d value of 378 nM, which was comparable with previously published K_d values for aptamer-generated against triclosan analogous. In addition, the utility of the imaging assay for aptamer characterisation was compared with a commonly used affinity column-binding assay. It was concluded that the imaging assay was superior to alternative assays in terms of accuracy, simplicity, and reproducibility.

Mapping the binding region of aptamer targeting small molecule: Dabigatran etexilate, an anti-coagulant

Aptamers are single-stranded DNA or RNA, which have attracted considerable scientific interest due to their characteristic of specific and selective binding to target molecules. They are evolved from the in vitro process known as systematic evolution of ligands by exponential enrichment (SELEX). This paper reports a simple experimental approach to elucidate the binding region of small targets binding aptamers. A previously isolated 60-mer aptamer for the anti-coagulant dabigatran etexilate (DBG) was used for this investigation. Complimentary sequences labelled with a fluorophore and a quencher were used for testing the binding region by change in the fluorescence signal. The full-length aptamer was truncated to multiple shorter copies including a 38 nucleotides sequence that showed 47 fold high affinity compared to the original aptamer. Circular dichroism spectroscopy (CD) measurements indicate that the 38-mer is remarkably more sensitive than the parent aptamer. The truncated 38-mer sequence was used to construct a turn-on fluorescence sensor with the detection limit of 1 nM. The performance of the sensor was examined in blood serum samples and showed excellent recovery percentages exceeding 98%. The reported screening protocol could be applied to the growing small targets aptasensors that require efficient binding aptamer sequences coupled with optimum signal transduction methods.

High affinity truncated aptamers for ultra-sensitive colorimetric detection of bisphenol A with label-free aptasensor

The widespread exposure of bisphenol A (BPA) presents a significant risk to human health. A rapid, ultra-sensitive and label-free colorimetric aptasensor using high affinity truncated aptamers was developed for BPA detection. Truncated 38-mer and 12-mer aptamers specific for BPA were obtained through rationally truncation from 63-mer BPA aptamer. The dissociation constants (K_d) of 38-mer and 12-mer aptamers were determined to be 13.17 nM and 27.05 nM. Then, truncated aptamers were used in label-free colorimetric detection assays based on gold nanoparticles (AuNPs). The limit of detections of aptasensors using 38-mer and 12-mer aptamers were 7.60 pM and 14.41 pM, which were 265-fold and 140-fold lower than that of the aptasensor using 63-mer aptamer, respectively. The recovery rates in milk, orange juice and mineralized water samples were 93.88% to 107.30%. Therefore, the developed BPA colorimetric aptasensor using truncated aptamers has great application prospects in food safety control and environmental monitoring.