Critical evaluation of aptamer binding for biosensor designs

A sensitive tobramycin electrochemical aptasensor based on multiple signal amplification cascades

The residue of tobramycin, a broad spectrum antibiotic commonly used in animal husbandry, has evitable impact on human health, which may cause kidney damage, respiratory paralysis, neuromuscular blockade and cross-allergy in humans. Sensitive monitoring of tobramycin in animal-derived food products is therefore of great importance. Herein, a new aptamer electrochemical biosensor for sensing tobramycin with high sensitivity is demonstrated via exonuclease III (Exo III) and metal ion-dependent DNAzyme recycling and hybridization chain reaction (HCR) signal amplification cascades. Tobramycin analyte binds aptamer-containing hairpin probe to switch its conformation to expose the toehold sequence, which triggers Exo III-based catalytic digestion of the secondary hairpin to release many DNAzyme strands. The substrate hairpins immobilized on the Au electrode (AuE) are then cyclically cleaved by the DNAzymes to form ssDNAs, which further initiate HCR formation of lots of long methylene blue (MB)-tagged dsDNA polymers on the AuE. Subsequently electro-oxidation of these MB labels thus exhibit highly enhanced currents for sensing tobramycin within the 5-1000 nM concentration range with an impressive detection limit of 3.51 nM. Furthermore, this strategy has high selectivity for detecting tobramycin in milk and shows promising potential for detect other antibiotics for food safety monitoring.

Development of a CRISPR/Cas12a-facilitated fluorescent aptasensor for sensitive detection of small molecules

The integration of Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR) and CRISPR-associated proteins (Cas) exhibits superior performance in biosensor construction. And the distinctive role of aptamers in target recognition has long been a focal point of research. Through the combination of Cas12a with cis-cleavage activity and aptamer with specific recognition, a simple and rapid fluorescent biosensor has been constructed. Interestingly, with modified fluorescent and quenching groups at two ends, aptamers play a dual role: primarily as the elements for target recognition and additionally functioning act as the fluorescent probe for signal output. Coupling with cis-cleavage of Cas12a, the demand of additional signal probes is eliminated, thus simplifying the reaction system and enhancing result accuracy. Taking okadaic acid (OA) as a representative small molecule model to evaluate the sensor's performance, a simple and straightforward detection method was established. Following this, the universality of the constructed fluorescent aptasensor was validated by incorporating an adenosine triphosphate (ATP) aptamer. Consequently, the CRISPR/Cas12a-assisted aptasensor was demonstrated to serve as a versatile detection platform for small molecules in food safety and clinical diagnostics. In the forthcoming research endeavors, it can be further extended for applications in environmental analysis and various other fields.

Simple solution and paper-based fluorescent aptasensors for toxic metal ions, thallium(l) and lead(ll)

Heavy metal ions, such as thallium(I) and lead(II) are environmental toxicants known to cause a severe threat to human and ecosystem health. This work investigates aptamers and intercalating chromophore-based complexes for the detection of these toxic species. In one method, a selective label-free "turn-on" biosensor was developed using a G-quadruplex-intercalating agent, berberine. Fluorescence, melting temperature (Tm), and circular dichroism analysis confirmed the affinity and selectivity results, illustrating the potential of these aptasensor methods for improving detection limits. These fluorescence assays were found to perform with a detection limit of 3.4 μM for Tl(I) and 0.84 nM for Pb(II). Furthermore, the assays were challenged successfully with Tl(I) and Pb(II) spiked into river water samples. We next developed paper-based fluorescent assays for Tl(I) and Pb(II), where the aptamer/berberine complex was spotted onto the paper test zone. When Tl(I) or Pb(II) ions solutions were spotted onto the top of the test zone and the spot was illuminated with a portable UV light (365 nm), a strong green fluorescence could be easily visualized with the naked eye. The lowest detection limits achieved with these fluorescent paper-based assays for Tl(I) and Pb(II) were 1.1 nM and 1.6 nM, respectively. The two fluorescent approaches presented here have the potential to be the basis of rapid, fast, and cost-efficient screening assays for these toxic species.

DNA aptamers for common buffer molecules: possibility of buffer interference in SELEX

During a typical aptamer selection experiment, buffer molecules are used at the 10 to 50 mM range, whereas target molecules could be used at much lower concentrations even in low μM levels. Therefore, doubts existed regarding the potential enrichment of buffer binding aptamers, particularly for failed selections that cannot validate binding of enriched sequences. In this study, we used two common buffer molecules, Tris and HEPES, as target molecules. While we successfully isolated aptamers for Tris buffer, our attempts to generate aptamers for HEPES buffer failed. Thioflavin T (ThT) fluorescence spectroscopy showed the dissociation constant (Kd) of the Tris buffer aptamer to be 2.9 mM, while isothermal titration calorimetry showed a Kd of 43 μM. NMR spectroscopy also confirmed aptamer binding. Finally, we discussed the implications of this buffer selection work and recommended the use of certain buffers.

Ultrasensitive monitoring of PCB77 in environmental samples using a visible-driven photoelectrochemical sensing platform coupling with exonuclease I assisted in target recycling

Due to the urgent need for detecting trace amounts of 3,3',4,4'-tetrachlorobiphenyl (PCB77) in the environment, we have developed an efficient and visible-driven photoelectrochemical (PEC) sensing platform based on carbon quantum dots (CQDs) modified titanium dioxide nanorods (TiO2 NRs), coupling with exonuclease I (Exo I) assisted in target recycling for significant signal amplification. CQDs/TiO2 NRs with high visible-light absorption ability and electron-hole separation efficiency is used as photoactive substrate for anchoring anti-PCB77 aptamer and its complementary DNA (cDNA). With the addition of PCB77, the specific interaction between PCB77 and its aptamer forces aptamer to separate from the electrode surface, resulting in an increase in photocurrent density. Adding Exo I in the test system, a self-catalytic target cycle was motivated, which significantly increased the PEC signal by more than twice, achieving signal amplification. The relationship between the photocurrent density changes and the concentrations of PCB77 are utilized to achieve quantitative detection of PCB77. The designed PEC sensing platform has good analytical performance with a detection limit as low as 0.33 pg L-1, high selectivity and stability. Moreover, the PEC sensor is successfully used to evaluate the content of PBC77 in the environment samples. The established sensing platform provides a simple and efficient method for detecting trace amounts of PCB77 in the environment.

Ligand-Induced Folding in a Dopamine-Binding DNA Aptamer

Aptamers are often employed as molecular recognition elements in the development of different types of biosensors. Many of these biosensors take advantage of the aptamer having a ligand-induced structure-formation binding mechanism. However, this binding mechanism is poorly understood. Here we use isothermal titration calorimetry, circular dichroism spectroscopy and NMR spectroscopy to study the binding and ligand-induced structural change exhibited by a dopamine-binding DNA aptamer. We analysed a series of aptamers where we shorten the terminal stem that contains the 5' and 3' termini of the aptamer sequence. All aptamers bind dopamine in an enthalpically driven process coupled with an unfavorable entropy. A general trend of the aptamer having a weaker binding affinity is observed as the terminal stem is shortened. For all aptamers studied, numerous signals appear in the imino region of the 1H NMR spectrum indicating that new structure forms with ligand binding. However, it is only when this region of structure formation in the aptamer is brought close to the sensor surface that we obtain a functional electrochemical aptamer-based biosensor.

Process, advances, and perspectives of graphene oxide-SELEX for the development of aptamer molecular probes: A comprehensive review

BACKGROUND

Aptamers are screened via the systematic evolution of ligands by exponential enrichment (SELEX) and are widely used in molecular diagnostics and targeted therapies. The development of efficient and convenient SELEX technology has facilitated rapid access to high-performance aptamers, thereby advancing the aptamer industry. Graphene oxide (GO) serves as an immobilization matrix for libraries in GO-SELEX, making it suitable for screening aptamers against diverse targets.

RESULTS

This review summarizes the detailed steps involved in GO-SELEX, including monitoring methods, various sublibrary acquisition methods, and practical applications from its inception to the present day. In addition, the potential of GO-SELEX in the development of broad-spectrum aptamers is explored, and its current limitations for future development are emphasized. This review effectively promotes the application of the GO-SELEX technique by providing valuable insights and assisting researchers interested in conducting related studies.

SIGNIFICANCE AND NOVELTY

To date, no review on the topic of GO-SELEX has been published, making it challenging for researchers to initiate studies in this area. We believe that this review will broaden the SELEX options available to researchers, ensuring that they can meet the growing demand for molecular probes in the scientific domain.

Recent advances in portable devices for environmental monitoring applications

Environmental pollution remains a major societal problem, leading to serious impacts on living organisms including humans. Human activities such as civilization, urbanization, and industrialization are major causes of pollution. Imposing stricter rules helps control environmental pollutant levels, creating a need for reliable pollutant monitoring in air, water, and soil. The application of traditional analytical techniques is limited in low-resource areas because they are sophisticated, expensive, and bulky. With the development of biosensors and microfluidics technology, environmental monitoring has significantly improved the analysis time, low cost, portability, and ease of use. This review discusses the fundamentals of portable devices, including microfluidics and biosensors, for environmental control. Recently, publications reviewing microfluidics and biosensor device applications have increased more than tenfold, showing the potential of emerging novel approaches for environmental monitoring. Strategies for enzyme-, immunoassay-, and molecular-based analyte sensing are discussed based on their mechanisms and applications. Microfluidic and biosensor platforms for detecting major pollutants, including metal ions, pathogens, pesticides, and antibiotic residues, are reviewed based on their working principles, advantages, and disadvantages. Challenges and future trends for the device design and fabrication process to improve performance are discussed. Miniaturization, low cost, selectivity, sensitivity, high automation, and savings in samples and reagents make the devices ideal alternatives for in-field detection, especially in low-resource areas. However, their operation with complicated environmental samples requires further research to improve the specificity and sensitivity. Although there is a wide range of devices available for environmental applications, their implementation in real-world situations is limited. This study provides insights into existing issues that can be used as references and a comparative analysis for future studies and applications.

Advances in Aptamer-Based Biosensors for the Detection of Foodborne Mycotoxins

Foodborne mycotoxins (FBMTs) are toxins produced by food itself or during processing and transportation that pose an enormous threat to public health security. However, traditional instrumental and chemical methods for detecting toxins have shortcomings, such as high operational difficulty, time consumption, and high cost, that limit their large-scale applications. In recent years, aptamer-based biosensors have become a new tool for food safety risk assessment and monitoring due to their high affinity, good specificity, and fast response. In this review, we focus on the progress of single-mode and dual-mode aptasensors in basic research and device applications over recent years. Furthermore, we also point out some problems in the current detection strategies, with the aim of stimulating future toxin detection systems for a transition toward ease of operation and rapid detection.

Construction of a DNA walker nanomachine aptasensor for simultaneous detection of dual-cancer biomarkers

While it is recognized that early diagnosis of cancer-related biomarkers can become an effective avenue for timely treatment and successfully improve patient survival, it remains challenging to get accurate inspection results. Currently, most reported cancer biomarker sensing methods are focused on the quantitative detection of a single type of biomarker, which makes accurate medical diagnostics difficult. In this work, we constructed a DNA walker nanomachine aptasensor based on gold nanoparticles for the simultaneous sensing of dual cancer biomarkers. The aptamers, labelled with a fluorophore, hybridized with complementary strands on the gold nanoparticle surface, serve as a walking track. Target analytes bind to their specific aptamers, leading to the dissociation of the unstable double-strand spherical nucleic acid. Exonuclease I (Exo I) selectively digested the aptamers bound with the target analytes, then the released targets go back to the next apamers on the gold nanopareticles surface for walking. The use of spherical nucleic acid probes improved the sensitivity of analyte detection. Exo I provided a driving power for target recycling and considerably improved the sensitivity of the aptasensor as well. The DNA walker nanomachine aptasensor was successfully applied for the detection of carcinoembryonic antigen (CEA) in the range of 0.167 to 3.34 ng mL-1, and mucin-1 (MUC-1) in the same range. Moreover, we used the two aptamers to construct the DNA walker nanomachine and achieved the simultaneous detection of CEA and MUC-1, thus having great potential for biomolecular logic gate construction and early disease diagnosis.

Colorimetric biosensor based on aptamer recognition-induced multi-DNA release and peroxidase-mimicking three-way junction DNA-Ag/PtNCs for the detection of Salmonella typhimurium

Salmonella typhimurium, as a major foodborne pathogen, poses a serious threat to public health safety worldwide. Here, we present a colorimetric biosensor based on aptamer recognition-induced multi-DNA release and peroxidase-mimicking three-way junction DNA-silver/platinum bimetallic nanoclusters (3WJ/DNA-Ag/PtNCs) for the detection of S. typhimurium. In this method, S. typhimurium specifically binds to the aptamer and releases multiple cDNAs to form the three-way junction DNA structure and synthesize silver/platinum bimetallic nanoclusters, which induces signaling changes. Interestingly and importantly, the use of 3WJ/DNA as the template for synthesizing Ag/PtNCs gives the method an extremely low background signal. Under the optimal conditions, the constructed biosensor had a linear response range of 2.6 × 102-2.6 × 106 CFU/mL and a detection limit of 2.6 × 102 CFU/mL for the detection of S. typhimurium. In addition, the proposed method can effectively detect S. typhimurium in milk.

Atomically Co-dispersed nitrogen-doped carbon for sensitive electrochemical immunoassay of breast cancer biomarker CA15-3

The development of an ultrasensitive and precise measurement of a breast cancer biomarker (cancer antigen 15-3; CA15-3) in complex human serum is essential for the early diagnosis of cancer in groups of healthy populations and the treatment of patients. However, currently available testing technologies suffer from insufficient sensitivity toward CA15-3, which severely limits early large-scale screening of breast cancer patients. We report a versatile electrochemical immunoassay method based on atomically cobalt-dispersed nitrogen-doped carbon (Co-NC)-modified disposable screen-printed carbon electrode (SPCE) with alkaline phosphatase (ALP) and its metabolite, ascorbic acid 2-phosphate (AAP), as the electrochemical labeling and redox signaling unit for sensitive detection of low-abundance CA15-3. During electrochemical detection by differential pulse voltammetry (DPV), it was found that the Co-NC-SPCE electrode did not have a current signal response to the AAP substrate; however, it had an extremely favorable response current to ascorbic acid (AA). Based on the above principle, the target CA15-3-triggered immunoassay enriched ALP-catalyzed AAP produces a large amount of AA, resulting in a significant change in the system current signal, thereby realizing the highly sensitive detection of CA15-3. Under the optimal AAP substrate concentration and ALP catalysis time, the Co-NC-SPCE-based electrochemical immunoassay demonstrated a good DPV current for CA15-3 in the assay interval of 1.0 mU/mL to 10,000 mU/mL, with a calculated limit of detection of 0.38 mU/mL. Since Co-NC-SPCE has an excellent DPV current response to AA and employs split-type scheme, the constructed electrochemical immunoassay has the merits of high preciseness and anti-interference, and its clinical diagnostic results are comparable to those of commercial kits.

Freeze-Driven Synthesis of DNA Hairpin-Conjugated Gold Nanoparticle Biosensors for Dual-Mode Detection

Freeze-based immobilization of deoxyribonucleic acid (DNA) oligonucleotides on gold nanoparticles (AuNPs) is highly efficient for single-stranded oligonucleotides but typically does not accommodate structures such as snap-cooled DNA hairpins (Sc-HPs) and snap-cooled molecular beacons (Sc-MBs) frequently used for biorecognition applications. Recognizing this limitation, we have developed a modified, freeze-based technique specifically designed to enable the adsorption of such hairpin oligonucleotides onto AuNP surfaces while ensuring that they retain their biosensing capabilities. Successful hairpin oligonucleotide conjugation of varying lengths to a wide range of AuNP diameters was corroborated by dynamic light scattering, ζ-potential, and UV-vis spectrophotometry. Moreover, we conducted a thorough evaluation of this modified method, confirming the retention of the sensing functions of Sc-HPs and Sc-MBs. This advancement not only offers a more efficient route for DNA hairpin conjugation but also elucidates the underlying biorecognition functions, with implications for broader applications in molecular diagnostics.

Turn-off enzyme activity of histidine-rich peptides for the detection of lysozyme

An assay that integrates histidine-rich peptides (HisRPs) with high-affinity aptamers was developed enabling the specific and sensitive determination of the target lysozyme. The enzyme-like activity of HisRP is inhibited by its interaction with a target recognized by an aptamer. In the presence of the target, lysozyme molecules progressively assemble on the surface of HisRP in a concentration-dependent manner, resulting in the gradual suppression of enzyme-like activity. This inhibition of HisRP's enzyme-like activity can be visually observed through color changes in the reaction product or quantified using UV-visible absorption spectroscopy. Under optimal conditions, the proposed colorimetric assay for lysozyme had a detection limit as low as 1 nM and exhibited excellent selectivity against other nonspecific interferents. Furthermore, subsequent research validated the practical applicability of the developed colorimetric approach to saliva samples, indicating that the assay holds significant potential for the detection of lysozymes in samples derived from humans.

Emerging biosensor probes for glycated hemoglobin (HbA1c) detection

Glycated hemoglobin (HbA1c), originating from the non-enzymatic glycosylation of βVal1 residues in hemoglobin (Hb), is an essential biomarker indicating average blood glucose levels over a period of 2 to 3 months without external environmental disturbances, thereby serving as the gold standard in the management of diabetes instead of blood glucose testing. The emergence of HbA1c biosensors presents affordable, readily available options for glycemic monitoring, offering significant benefits to small-scale laboratories and clinics. Utilizing nanomaterials coupled with high-specificity probes as integral components for recognition, labeling, and signal transduction, these sensors demonstrate exceptional sensitivity and selectivity in HbA1c detection. This review mainly focuses on the emerging probes and strategies integral to HbA1c sensor development. We discussed the advantages and limitations of various probes in sensor construction as well as recent advances in diverse sensing strategies for HbA1c measurement and their potential clinical applications, highlighting the critical gaps in current technologies and future needs in this evolving field.

A dual amplified gold nanoparticle-based biosensor for ultrasensitive and selective detection of fibrin

Ultrasensitive, selective, and non-invasive detection of fibrin in human serum is critical for disease diagnosis. So far, the development of high-performance and ultrasensitive biosensors maintains core challenges for biosensing. Herein, we designed a novel ribbon nanoprobe for ultrasensitive detection of fibrin. The probe contains gold nanoparticles (AuNPs) that can not only link with homing peptide Cys-Arg-Glu-Lys-Ala (CREKA) to recognize fibrin but also carry long DNA belts to form G-quadruplex-based DNAzyme, catalyzing the chemiluminescence of luminol-hydrogen peroxide (H2O2) reaction. Combined with the second amplification procedure of rolling circle amplification (RCA), the assay exhibits excellent sensitivity with a detection limit of 0.04 fmol L-1 fibrin based on the 3-sigma. Furthermore, the biosensor shows high specificity on fibrin in samples because the structure of antibody-fibrin-homing peptide was employed to double recognize fibrin. Altogether, the simple and inexpensive approach may present a great potential for reliable detection of biomarkers.

A review on magnetic beads-based SELEX technologies: Applications from small to large target molecules

This review summarizes the stepwise strategy and key points for magnetic beads (MBs)-based aptamer selection which is suitable for isolating aptamers against small and large molecules via systematic evolution of ligands by exponential enrichment (SELEX). Particularities, if any, are discussed according to the target size. Examples targeting small molecules (<1000 Da) such as xenobiotics, toxins, pesticides, herbicides, illegal additives, hormones, and large targets such as proteins (biomarkers, pathogens) are discussed and presented in tabular formats. Of special interest are the latest advances in more efficient alternatives, which are based on novel instrumentation, materials or microelectronics, such as fluorescence MBs-SELEX or microfluidic chip system-assisted MBs-SELEX. Limitations and perspectives of MBs-SELEX are also reviewed. Taken together, this review aims to provide practical insights into MBs-SELEX technologies and their ability to screen multiple potential aptamers against targets from small to large molecules.

Precision-SELEX aptamer screening for the colorimetric and fluorescent dual-readout aptasensing of AFB1 in food

As nucleic acid-based affinity elements, aptamers have attracted significant attention for a wide range of analytical applications. Although several aflatoxin B1 (AFB1) aptamers have been identified, they are unsuitable for overcoming the unavoidable cross-reactions from interferents in complex food matrices due to their poor binding affinities and specificities. Herein, a novel precision-systematic evolution of ligands by exponential enrichment (P-SELEX) strategy through introducing the counter (matrix without target AFB1) and positive (with AFB1) screening steps was implemented to accurately identify AFB1 aptamers. A DNA aptamer A-42-2 at a 24-nt length was selected finally, which possessed nanomolar-level affinity of 5.55 nM, high specificity to other interferents, and strong anti-cross-reactivity ability for matrix components. Then, an A-42-2 aptamer-based ultra-sensitive colorimetric and fluorescent dual-readout aptasensor was fabricated for AFB1 detection in three kinds of complex food samples rich in starch without cross-reactions. The aptasensor displayed outstanding detection capacity with a wide liner range of 0.25-30 nM (1.95-234.4 μg/kg), while the detection limit for colorimetric measurement as low as 0.22 nM (1.72 μg/kg) and 0.048 nM (0.20 μg/kg) for fluorescent determination. P-SELEX is ideal for screening and applying aptamers in complex food matrices, creating more opportunities for the efficient and cost-effective development of high-quality aptamers and aptasensors for other targets.

Aptamers for nanobodies: A nontoxic alternative to toxic ochratoxin A in immunoassays

To measure toxins using immunoassays, hazardous toxin standards need to be added for quantification. To solve this problem, we propose to use aptamers as competitors to replace toxin standards. In this work, aptamers specific for ochratoxin A (OTA) nanobodies were selected using a DNA library containing a 36 nucleotide random region. The obtained sequences were highly aligned and the best competitor was identified to be a sequence named apt2-OT based on an indirect competitive enzyme-linked immunosorbent assay (ELISA). The Kd of apt2-OT was measured to be 2.86 μM using local surface plasmon resonance spectroscopy. The optimal apt2-OT was identified to substitute the OTA standard with a concentration needed for 50% inhibition of binding (IC50) of 3.26 μM based on a nontoxic direct competitive ELISA. The equivalence relationship between the aptamer and OTA was established in a flour sample, and a recovery experiment was performed. The detection limit for this method was 0.23 ng/mL, with a linear range from 0.25 to 10.50 ng/mL. The recovery rate was 97.5%-115.5%. This study provides a low-cost, rapid and environmentally friendly alternative to the development of immunoassays for toxins.

A binary system based DNA tetrahedron and fluorogenic RNA aptamers for highly specific and label-free mRNA imaging in living cells

Developing simple, rapid and specific mRNA imaging strategy plays an important role in the early diagnosis of cancer and the new drugs development. Herein, we have established a novel binary system based DNA tetrahedron and fluorogenic RNA aptamers for highly specific and label-free mRNA imaging in living cells. This developed system consisted of tetrahedron probe A (TPA) and tetrahedron probe B (TPB). TK1 mRNA was chosen as the study model. After TPA and TPB enter into the live cells, the TK1 mRNA induces TPA and TPB to approach and activate the fluorescent aptamer, resulting in enhanced fluorescent signal in the presence of small molecules of DFHBI-1T. By this design, the high specificity label-free detection of nucleic acids was achieved with a detection limit of 1.34 nM. Confocal fluorescence imaging experiments had proved that this strategy could effectively distinguish the TK1 mRNA expression level between normal cell and cancer cell. The developed method is expected to provide a new tool for early diagnosis of diseases and new drug development.

Assessing Aptamer-Analyte Binding Kinetics by Microfluidic Fluorescence Microscopy

Kinetic measurement plays a crucial role in understanding aptamer binding mechanisms and identifying appropriate aptamers for clinical and research applications. Current techniques, while well established, generally require large sample volumes, bulky and expensive instruments operated by trained personnel, and are hence not readily accessible to resource-limited research laboratories. This paper presents a fluorescence microscopy-based microfluidic assay for measuring aptamer-analyte binding kinetics in a simple and cost-effective manner. Kinetic measurements are achieved by monitoring time-course fluorescence of fluorescently labeled aptamers as they bind to the targets trapped in a microfluidic chip. Fluorescence measurements are performed on a standard fluorescence microscope and are accessible to laboratories with only modest resources. Moreover, microfluidic technology allows efficient and cost-effective immobilization of small amounts of target molecules or live cells as well as flow-based manipulation of aptamers for the measurements. Kinetic measurements of aptamer binding to immunoglobulin E protein and CCRF-CEM cells have yielded results consistent with those obtained from established methods, demonstrating the potential utility of our method for exploring aptamer-target interactions and identifying aptamers that best suit specific given biomedical applications.

Are Aptamers Really Promising as Receptors for Analytical Purposes? Insights into Anti-Lysozyme DNA Aptamers through a Multitechnique Study

Aptamers are recognition elements increasingly used for the development of biosensing strategies, especially in the detection of proteins or small molecule targets. Lysozyme, which is recognized as an important biomarker for various diseases and a major allergenic protein found in egg whites, is one of the main analytical targets of aptamer-based biosensors. However, since aptamer-based strategies can be prone to artifacts and data misinterpretation, rigorous strategies for multifaceted characterization of the aptamer-target interaction are needed. In this work, a multitechnique approach has been devised to get further insights into the binding performance of the anti-lysozyme DNA aptamers commonly used in the literature. To study molecular interactions between lysozyme and different anti-lysozyme DNA aptamers, measurements based on a magneto-electrochemical apta-assay, circular dichroism spectroscopy, fluorescence spectroscopy, and asymmetrical flow field-flow fractionation were performed. The reliability and versatility of the approach were proved by investigating a SELEX-selected RNA aptamer reported in the literature, that acts as a positive control. The results confirmed that an interaction in the low micromolar range is present in the investigated binding buffers, and the binding is not associated with a conformational change of either the protein or the DNA aptamer. The similar behavior of the anti-lysozyme DNA aptamers compared to that of randomized sequences and polythymine, used as negative controls, showed nonsequence-specific interactions. This study demonstrates that severe testing of aptamers resulting from SELEX selection is the unique way to push these biorecognition elements toward reliable and reproducible results in the analytical field.

A label-free aptasensor for colorimetric detection of food toxin: Mediation of catalytically active gold nanozymes and smartphone imaging strategy

A portable colorimetric aptasensor was developed on the surface of a plastic sheet for on-site detection of acrylamide. The mechanism of aptasensor is based on the disruption of the aptamer complex with its complementary strand on the sensing zone, and subsequently, the catalytic activity of gold nanoparticles (AuNPs) for the reduction process of 4-nitrophenol (4-NP) in the presence of sodium borohydride (NaBH4). A yellow-to-colorless change of the sample solution revealed the target presence, easily discernible by the naked eye. The acrylamide quantification was accomplished using the smartphone imaging readout technique. The aptasensor detected the acrylamide concentration in the range of 0.01-500 nmol L-1 with a detection limit of 0.0024 nmol L-1. Coffee, potato chips, bread, and lake water samples were successfully analyzed by the aptasensor for their acrylamide content. The introduced aptasensor can pave a facile, cost-effective, portable, and user-friendly sensing tool for food safety control and environmental monitoring.

Recent progress of SELEX methods for screening nucleic acid aptamers

Nucleic acid aptamers are oligonucleotide sequences screened by an in vitro methodology called Systematic Evolution of Ligands by Exponential Enrichment (SELEX). Known as "chemical antibodies", aptamers can achieve specific recognition towards the targets through conformational changes with high affinity, and possess multiple attractive features including, but not limited to, easy and inexpensive to prepare by chemical synthesis, relatively stable and low batch-to-batch variability, easy modification and signal amplification, and low immunogenicity. Now, aptamers are attracting researchers' attentions from more than 25 disciplines, and have showed great potential for application and economic benefits in disease diagnosis, environmental detection, food security, drug delivery and discovery. Although some aptamers exist naturally as the ligand-binding elements of riboswitches, SELEX is a recognized method for aptamers screening. After thirty-two years of development, a series of SELEX methods have been investigated and developed, as well as have shown unique advantages to improve sequence performances or to explore screening mechanisms. This review would mainly focus on the novel or improved SELEX methods that are available in the past five years. Firstly, we present a clear overview of the aptamer's history, features, and SELEX development. Then, we highlight the specific examples to emphasize the recent progress of SELEX methods in terms of carrier materials, technical improvements, real sample-improved screening, post-SELEX and other methods, as well as their respects of screening strategies, implementation features, screening parameters. Finally, we discuss the remaining challenges that have the potential to hinder the success of SELEX and aptamers in practical applications, and provide the suggestions and future directions for developing more convenient, efficient, and stable SELEX methods in the future.

Ultrasensitive fluorescence immunoassay of pepsinogen I based on enzyme-triggered decomposition of AuNCs/MnO2

Gastric cancer is a prevalent malignant tumor of the gastrointestinal tract accompanied by a high mortality rate; therefore, early gastric cancer screening is critical for improving patient survival. In this study, we present a facile fluorescence immunoassay for highly sensitive screening of pepsinogen I (PG I) based on a one-pot biomimetic mineralization process for the synthesis of gold nanocluster-anchored manganese dioxide (AuNCs/MnO2) nanosheets. MnO2 first quenches the fluorescence of AuNCs through the Förster resonance energy transfer effect, whereas the introduction of ascorbic acid (AA) leads to the decomposition of MnO2 and rapidly recovers the fluorescence of AuNCs. Based on the above principles and phenomena, we developed a sensitive fluorescence immunoassay for the in situ generation of AA to detect PG I. Specifically, in the presence of PG I, the sandwich-type immunoreactivity-enriched alkaline phosphatase-labeled secondary antibody catalyzes the production of AA from the substrate, which enhances the fluorescence intensity. Under optimized conditions, the fluorescence intensity increased linearly with the concentration of PG I (0.05 to 200 ng mL-1) with a limit of detection (LOD) of 0.013 ng mL-1 (S/N = 3). The designed sensing platform has good stability (more than one year) and excellent anti-interference capability and demonstrates satisfactory accuracy for detection in real samples compared to commercial ELISA kits.

An ultrasensitive Cd2+ detection biosensor based on DNAzyme and CRISPR/Cas12a coupled with hybridization chain reaction

The detection of cadmium is essential because it poses a significant threat to human health and the environment. Recent advancements in biosensors that detect nonnucleic-acid targets using CRISPR/Cas12a in combination with aptamers or DNAzymes show promising performance. Herein, we integrated DNAzyme, hybridization chain reaction (HCR) and CRISPR/Cas12a into a single biosensor for the first time and realized the ultrasensitive detection of Cd2+. A single phosphorothioate ribonucleobase (rA)-containing oligonucleotide (PS substrate) and a Cd2+-specific DNAzyme (Cdzyme) are used for Cd2+ recognition, releasing short single-stranded DNA. Then, the HCR is triggered by the cleavage products for signal transduction and amplification. Next, the trans-cleavage activity of Cas12a is activated due to the presence of crRNA complementary strands and PAM sites in the HCR products. As a result, FQ-reporters are cleaved, and the fluorescence values can be easily read using a fluorometer, allowing Cd2+ quantification by measuring the fluorescent signal. The Cd2+ detection biosensor is ultrasensitive with a detection limit of 1.25 pM. Moreover, the biosensor shows great stability under different pH and various anion conditions. The proposed sensor was utilized for environmental water sample detection, demonstrating the dependability of the detection system. Considering the high sensitivity and reliable performance of the assay, it could be further used in environmental monitoring. In addition, the design strategy reported in this study could extend the application of CRISPR/Cas12a in heavy metal detection.

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

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

Light-up split aptamers: binding thermodynamics and kinetics for sensing

Due to their programmable structures, many aptamers can be readily split into two halves while still retaining their target binding function. While split aptamers are prevalent in the biosensor field, fundamental studies of their binding are still lacking. In this work, we took advantage of the fluorescence enhancement property of a new aptamer named OTC5 that can bind to tetracycline antibiotics to compare various split aptamers with the full-length aptamer. The split aptamers were designed to have different stem lengths. Longer stem length aptamers showed similar dissociation constants (Kd) to the full-length aptamer, while a shorter stem construct showed an 85-fold increase in Kd. Temperature-dependent fluorescence measurements confirmed the lower thermostability of split aptamers. Isothermal titration calorimetry indicated that split aptamer binding can release more heat but have an even larger entropy loss. Finally, a colorimetric biosensor using gold nanoparticles was designed by pre-assembling two thiolated aptamer halves, which can then link gold nanoparticles to give a red-to-blue color change.

A carbon quantum layer modified BiVO4 photoelectrochemical aptamer biosensor for ultra-sensitive cTnI biomarker detection based on the interface nephelauxetic effect and heterojunction assistance

The sensitivity and specificity of a semiconductor photoelectrochemical (PEC) aptamer biosensor are determined by the separation and transport of the photoinduced carriers as well as aptamer probe immobilization. In this study, an in situ thermal transformation organic polymer strategy was employed to produce an ∼2.5 nm carbon quantum layer on the surface of the BiVO4(BVO) photoanode. Experimental tests and theoretical calculations have revealed that this carbon quantum layer-coated BVO(C@BVO) heterostructure could generate surface charge depletion regions through an interface nephelauxetic effect. These charge depletion regions facilitated the efficient immobilization of DNA aptamer probes of the acute myocardial infarction biomarker cardiac troponin I (cTnI), while showing almost no immobilization capability on a pure-phase C quantum layer or BVO crystals. Simultaneously, the formation of the C@BVO heterostructure also enhanced the directional transport of photo-generated holes from BVO to the C quantum layer. Due to the above reasons, the C@BVO PEC aptamer biosensor achieved a linear detection range for cTnI from 10-14 g L-1 to 10-10 g L-1, with a record detection limit (LOD) of ∼0.33 × 10-14 g L-1 (N > 3). Meanwhile, the biosensor also demonstrated well the detection reproducibility and specificity for cTnI detection. Therefore, the strategy of using a carbon quantum layer-coated PEC electrode shows good potential to develop PEC biosensors with high sensitivity, specificity, and robustness.

Ratiometric fluorescent aptasensor for convenient detection of ochratoxin A in beer and orange juice

Based on the principle of fluorescence resonance energy transfer (FRET), a simple ratiometric fluorescent aptasensor for convenient detection of ochratoxin A (OTA), a Group IIB carcinogen secreted by some fungi, was established. Initially, the anti-OTA aptamer with a quadruplex structure was flanked with FAM and BHQ1, and its partially complementary DNA (cDNA) was tagged with Cy3. In the absence of OTA, this aptamer hybridized with the cDNA strand forming a DNA duplex structure, in which BHQ1 was adjacent to Cy3 and distant from FAM. Due to the FRET principle, the fluorescence intensity emitted by Cy3 (FCy3) was quenched by BHQ1, and the fluorescence intensity emitted by FAM (FFAM) recovered. In the presence of OTA, the prepared aptamer preferred to bind with OTA instead of cDNA, forming an aptamer-OTA complex structure in which BHQ1 was adjacent to FAM and distant from Cy3. As a result, FFAM was quenched and FCy3 was restored. OTA can be accurately detected via the determination of the FCy3/FFAM ratio value. Under optimal conditions, this ratiometric fluorescent aptasensor offers excellent OTA detection in the range of 0.6 nmol L-1-5 μmol L-1, with a limit of detection (LOD) of 0.3 nmol L-1. This ratiometric aptasensor showed the advantages of easy operation, accuracy and sensitive analysis. Good specificity of this aptasensor was demonstrated. This ratiometric aptasensor could be used for the detection of OTA in real samples, e.g. beer and orange juice, showing its promising application potential.

Rational design of a ratiometric fluorescent aptasensor for patulin in traditional Chinese medicine through the studies of the interaction mechanism between its DNA aptamer and the target molecule

Patulin (PAT) is a kind of mycotoxin which must be monitored for the sake of quality and safety in traditional Chinese medicine (TCM) owing to its harm to human health. On this account, a rationally designed ratiometric fluorescent aptasensor was developed based on the studies of the interaction mechanism between PAT and its aptamer (PAT-APT). First, CD spectroscopy, molecular docking, and molecular dynamic simulation were applied to investigate the details on how PAT-APT binds with its target molecule. The results indicated that the structure of PAT-APT changed to a certain extent and was stabilized after binding with PAT. C-11, C-37 and C-38 were the key sites for the recognition and interaction between PAT-APT and its target. Second, based on these results, a ratiometric aptasensor was designed using fluorescence resonance energy transfer (FRET) and synchronous fluorescence spectroscopy. A complementary sequence (cDNA) to the aptamer with an appropriate length and hybridization position was obtained through rational design and optimization. Both PAT-APT and cDNA were labeled using a pair of fluorophores, which could generate FRET when the two single-stranded oligonucleotides hybridized. The accurate detection of PAT could be realized according to the change ratio of the fluorescence intensity at the corresponding wavelengths of the two fluorophores before and after the assay. The aptasensor achieved an ultralow limit of detection of 0.16 nM, perfect selectivity, and satisfactory practicability in complex TCM samples. To our knowledge, this is the first aptasensor for PAT designed through the interaction mechanism between its aptamer and the target molecule. Moreover, the assay for PAT is cost-effective, does not need complicated pretreatment and only takes less than an hour. In summary, this study makes a contribution to the safety control of TCM and provides a thinking mode from mechanism to rational design to conquer the problem of sensitive aptasensing of one component in a complex system.

Quantitative Comparison of Capture-SELEX, GO-SELEX, and Gold-SELEX for Enrichment of Aptamers

Since 1990, numerous methods for aptamer selection have been developed, although a quantitative comparison of their sequence enrichment is lacking. In this study, we compared the enrichment factors of three library-immobilization SELEX methods (capture-SELEX, GO-SELEX, and gold-SELEX). We used a spiked library that contained multiple DNA aptamers with different affinities for adenosine. The aptamer separation efficiency was measured using qPCR, and all of the three methods showed a very low DNA release (<1%) in the presence of 100 μM adenosine. Among these, barely any DNA was released from the gold nanoparticles. Deep sequencing was used to compare the enrichment of three aptamers: Ade1301, Ade1304, and the classical aptamer. Enrichment up to 30 to 50-fold was observed only for the capture-SELEX method, whereas the other two methods showed enrichment factors below 1. By blocking the primer-binding regions of the library, GO-SELEX reached up to 14% enrichment. Finally, the enrichment of aptamers based on nonspecific release and target-induced release was discussed, and the advantages of capture-SELEX were rationalized. Taken together, these results indicate that capture-SELEX is a much more efficient method for enriching aptamers.

A cocktail therapeutic strategy based on clofarabine-containing aptamer-PROTAC for enhanced cancer therapy

By introducing a therapeutic nucleoside analogue tail to the parent Aptamer-PROTACs, a PROTAC-cocktail system (ApTCs-3X) was designed and evaluated. ApTCs-3X exhibited improved nuclease resistance and efficiently degraded target protein with subcellular localization preference. This cocktail therapy results in enhanced therapeutic outcomes, making it suitable for advancing PROTAC in combination therapy.

Integrating Ligands into Nucleic Acid Systems

Signal transduction from non-nucleic acid ligands (small molecules and proteins) to structural changes of nucleic acids plays a crucial role in both biomedical analysis and cellular regulations. However, how to bridge between these two types of molecules without compromising the expandable complexity and programmability of the nucleic acid nanomachines is a critical challenge. Compared with the previously most widely applied transduction strategies, we review the latest advances of a kinetically controlled approach for ligand-oligonucleotide transduction in this Concept article. This new design works through an intrinsic conformational alteration of the nucleic acid aptamer upon the ligand binding as a governing factor for nucleic acid strand displacement reactions. The functionalities and applications of this transduction system as a ligand converter on biosensing and DNA computation are described and discussed. Furthermore, we propose some potential scenarios for utilization of this ligand transduction design to regulate gene expression through synthetic RNA switches in the cellular contexts. Finally, future perspectives regarding this ligand-oligonucleotide transduction platform are also discussed.

Capture-SELEX for Chloramphenicol Binding Aptamers for Labeled and Label-Free Fluorescence Sensing

Chloramphenicol (CAP) is a potent antibiotic. Due to its side effects, CAP is currently banned in most countries, but it is still found in many food products and in the environment. Developing aptamer-based biosensors for the detection of CAP has interested many researchers. While both RNA and DNA aptamers were previously reported for CAP, they were all obtained by immobilization of the CAP base, which omitted the two chlorine atoms. In this work, DNA aptamers were selected using the library-immobilized method and free unmodified CAP. Three families of aptamers were obtained, and the best one named CAP1 showed a dissociation constant (Kd) of 9.8 μM using isothermal titration calorimetry (ITC). A fluorescent strand-displacement sensor showed a limit of detection (LOD) of 14 μM CAP. Thioflavin T (ThT) staining allowed label-free detection of CAP with a LOD of 1 μM in buffer, 1.8 μM in Lake Ontario water, and 3.6 μM in a wastewater sample. Comparisons were made with previously reported aptamers, and ITC failed to show binding of a previously reported 80-mer aptamer. Due to the small size and well-defined secondary structures of CAP1, this aptamer will find analytical applications for environmental and food monitoring.

Cross-Binding of Four Adenosine/ATP Aptamers to Caffeine, Theophylline, and Other Methylxanthines

The classical DNA aptamer for adenosine and ATP was selected twice using ATP as the target in 1995 and 2005, respectively. In 2022, this motif appeared four more times from selections using adenosine, ATP, theophylline, and caffeine as targets, suggesting that this aptamer can also bind methylxanthines. In this work, using thioflavin T fluorescence spectroscopy, this classical DNA aptamer showed Kd values for adenosine, theophylline, and caffeine of 9.5, 101, and 131 μM, respectively, and similar Kd values were obtained using isothermal titration calorimetry. Binding to the methylxanthines was also observed for the newly selected Ade1301 aptamer but not for the Ade1304 aptamer. The RNA aptamer for ATP also had no binding to the methylxanthines. Molecular dynamics simulations were performed using the classical DNA and RNA aptamers based on their NMR structures, and the simulation results were consistent with the experimental observations, explaining the selectivity profiles. This study suggests that a broader range of target analogues need to be tested for aptamers. For the detection of adenosine and ATP, the Ade1304 aptamer is a better choice due to its better selectivity.

Aggregates-based fluorescence sensing technology for food hazard detection: Principles, improvement strategies, and applications

Aggregates often exhibit modified or completely new properties compared with their molecular elements, making them an extraordinarily advantageous form of materials. The fluorescence signal change characteristics resulting from molecular aggregation endow aggregates with high sensitivity and broad applicability. In molecular aggregates, the photoluminescence properties at the molecular level can be annihilated or elevated, leading to aggregation-causing quenching (ACQ) or aggregation-induced emission (AIE) effects. This change in photoluminescence properties can be intelligently introduced in food hazard detection. Recognition units can combine with the aggregate-based sensor by joining the aggregation process, endowing the sensor with the high specificity of analytes (such as mycotoxins, pathogens, and complex organic molecules). In this review, aggregation mechanisms, structural characteristics of fluorescent materials (including ACQ/AIE-activated), and their applications in food hazard detection (with/without recognition units) are summarized. Because the design of aggregate-based sensors may be influenced by the properties of their components, the sensing mechanisms of different fluorescent materials were described separately. Details of fluorescent materials, including conventional organic dyes, carbon nanomaterials, quantum dots, polymers and polymer-based nanostructures and metal nanoclusters, and recognition units, such as aptamer, antibody, molecular imprinting, and host-guest recognition, are discussed. In addition, future trends of developing aggregate-based fluorescence sensing technology in monitoring food hazards are also proposed.

Aptamers 101: aptamer discovery and in vitro applications in biosensors and separations

Aptamers are single-stranded nucleic acids that bind and recognize targets much like antibodies. Recently, aptamers have garnered increased interest due to their unique properties, including inexpensive production, simple chemical modification, and long-term stability. At the same time, aptamers possess similar binding affinity and specificity as their protein counterpart. In this review, we discuss the aptamer discovery process as well as aptamer applications to biosensors and separations. In the discovery section, we describe the major steps of the library selection process for aptamers, called systematic evolution of ligands by exponential enrichment (SELEX). We highlight common approaches and emerging strategies in SELEX, from starting library selection to aptamer-target binding characterization. In the applications section, we first evaluate recently developed aptamer biosensors for SARS-CoV-2 virus detection, including electrochemical aptamer-based sensors and lateral flow assays. Then we discuss aptamer-based separations for partitioning different molecules or cell types, especially for purifying T cell subsets for therapeutic applications. Overall, aptamers are promising biomolecular tools and the aptamer field is primed for expansion in biosensing and cell separation.

Integrating Water Purification with Electrochemical Aptamer Sensing for Detecting SARS-CoV-2 in Wastewater

Wastewater analysis of pathogens, particularly SARS-CoV-2, is instrumental in tracking and monitoring infectious diseases in a population. This method can be used to generate early warnings regarding the onset of an infectious disease and predict the associated infection trends. Currently, wastewater analysis of SARS-CoV-2 is almost exclusively performed using polymerase chain reaction for the amplification-based detection of viral RNA at centralized laboratories. Despite the development of several biosensing technologies offering point-of-care solutions for analyzing SARS-CoV-2 in clinical samples, these remain elusive for wastewater analysis due to the low levels of the virus and the interference caused by the wastewater matrix. Herein, we integrate an aptamer-based electrochemical chip with a filtration, purification, and extraction (FPE) system for developing an alternate in-field solution for wastewater analysis. The sensing chip employs a dimeric aptamer, which is universally applicable to the wild-type, alpha, delta, and omicron variants of SARS-CoV-2. We demonstrate that the aptamer is stable in the wastewater matrix (diluted to 50%) and its binding affinity is not significantly impacted. The sensing chip demonstrates a limit of detection of 1000 copies/L (1 copy/mL), enabled by the amplification provided by the FPE system. This allows the integrated system to detect trace amounts of the virus in native wastewater and categorize the amount of contamination into trace (<10 copies/mL), medium (10-1000 copies/mL), or high (>1000 copies/mL) levels, providing a viable wastewater analysis solution for in-field use.

Recent advances in electrochemical nanomaterial-based aptasensors for the detection of cancer biomarkers

New technologies have provided suitable tools for rapid diagnosis of cancer which can reduce treatment costs and even increase patients' survival rates. Recently, the development of electrochemical aptamer-based nanobiosensors has raised great hopes for early, sensitive, selective, and low-cost cancer diagnosis. Here, we reviewed the flagged recent research (2021-2023) developed as a series of biosensors equipped with nanomaterials and aptamer sequences (nanoaptasensors) to diagnose/prognosis of various types of cancers. Equipping these aptasensors with nanomaterials and using advanced biomolecular technologies have provided specified biosensing interfaces for more optimal and reliable detection of cancer biomarkers. The primary intention of this review was to present and categorize the latest innovations used in the design of these diagnostic tools, including the hottest surface modifications and assembly of sensing bioplatforms considering diagnostic mechanisms. The main classification is based on applying various nanomaterials and sub-classifications considered based on the type of analyte and other vital features. This review may help design subsequent electrochemical aptasensors. Likewise, the up-to-date status, remaining limitations, and possible paths for translating aptasensors to clinical cancer assay tools can be clarified.

Surfactant-Assisted Label-Free Fluorescent Aptamer Biosensors and Binding Assays

Using DNA staining dyes such as SYBR Green I (SGI) and thioflavin T (ThT) to perform label-free detection of aptamer binding has been performed for a long time for both binding assays and biosensor development. Since these dyes are cationic, they can also adsorb to the wall of reaction vessels leading to unstable signals and even false interpretations of the results. In this work, the stability of the signal was first evaluated using ThT and the classic adenosine aptamer. In a polystyrene microplate, a drop in fluorescence was observed even when non-binding targets or water were added, whereas a more stable signal was achieved in a quartz cuvette. Equilibrating the system can also improve signal stability. In addition, a few polymers and surfactants were also screened, and 0.01% Triton X-100 was found to have the best protection effect against fluorescence signal decrease due to dye adsorption. Three aptamers for Hg²⁺, adenosine, and cortisol were tested for their sensitivity and signal stability in the absence and presence of Triton X-100. In each case, the sensitivity was similar, whereas the signal stability was better for the surfactant. This study indicates that careful control experiments need to be designed to ensure reliable results and that the reliability can be improved by using Triton X-100 and a long equilibration time.

Integrated technologies for continuous monitoring of organs-on-chips: Current challenges and potential solutions

Organs-on-chips (OoCs) are biomimetic in vitro systems based on microfluidic cell cultures that recapitulate the in vivo physicochemical microenvironments and the physiologies and key functional units of specific human organs. These systems are versatile and can be customized to investigate organ-specific physiology, pathology, or pharmacology. They are more physiologically relevant than traditional two-dimensional cultures, can potentially replace the animal models or reduce the use of these models, and represent a unique opportunity for the development of personalized medicine when combined with human induced pluripotent stem cells. Continuous monitoring of important quality parameters of OoCs via a label-free, non-destructive, reliable, high-throughput, and multiplex method is critical for assessing the conditions of these systems and generating relevant analytical data; moreover, elaboration of quality predictive models is required for clinical trials of OoCs. Presently, these analytical data are obtained by manual or automatic sampling and analyzed using single-point, off-chip traditional methods. In this review, we describe recent efforts to integrate biosensing technologies into OoCs for monitoring the physiologies, functions, and physicochemical microenvironments of OoCs. Furthermore, we present potential alternative solutions to current challenges and future directions for the application of artificial intelligence in the development of OoCs and cyber-physical systems. These "smart" OoCs can learn and make autonomous decisions for process optimization, self-regulation, and data analysis.

An aptamer array for discriminating tetracycline antibiotics based on binding-enhanced intrinsic fluorescence

Tetracyclines are a class of antibiotics with a similar four-ringed structure. Due to this structural similarity, they are not easily differentiated from each other. We recently selected aptamers using oxytetracycline as a target and focused on an aptamer named OTC5, which has similar affinities for oxytetracycline (OTC), tetracycline (TC), and doxycycline (DOX). Tetracyclines exhibit an intrinsic fluorescence that is enhanced upon aptamer binding, allowing convenient binding assays and label-free detection. In this study, we analyzed the top 100 sequences from the previous selection library. Three other sequences were found to differentiate between different tetracyclines (OTC, DOX, and TC) by the selective enhancement of their intrinsic fluorescence. Among them, the OTC43 aptamer was more selective for OTC with a limit of detection (LOD) of 0.7 nM OTC, OTC22 was more selective for DOX (LOD 0.4 nM), and OTC2 was more selective for TC (0.3 nM). Using these three aptamers to form a sensor array, principal component analysis was able to discriminate between the three tetracyclines from each other and from the other molecules. This group of aptamers could be useful as probes for the detection of tetracycline antibiotics.

A simple and programmable dual-mode aptasensor for the ultrasensitive detection of multidrug-resistant bacteria

Accurately identifying multidrug-resistant (MDR) bacteria from clinical samples has long been a challenge. Herein, we report a simple and programmable dual-mode aptasensor called DAPT to reliably detect MDR bacteria. The DAPT method comprises two elements, namely the mode of dynamic light scattering (Mode-DLS) for ultrasensitive detection and the mode of fluorescence (Mode-Flu) for reliable quantification as a potent complement. Benefiting from the states of aptamer-modified gold nanoparticles (AptGNPs) sensitively changing from dispersion to aggregation, the proposed Mode-DLS achieved the rapid, specific, and ultrasensitive detection of methicillin-resistant Staphylococcus aureus (MRSA) at the limit of detection (LOD) of 4.63 CFU mL^-1 in a proof-of-concept experiment. Simultaneously, the Mode-Flu ensured the accuracy of the detection, especially at a high concentration of bacteria. Moreover, the feasibility and universality of the DAPT platform was validated with four other superbugs by simply reprogramming the corresponding sequence. Overall, the proposed DAPT method based on a dual-mode aptasensor can provide a universal platform for the rapid and ultrasensitive detection of pathogenic bacteria due to its superior programmability.

Combining bioinspired nanochannels with ferrocene doped MoS2 nanoplates: Application to ratiometric electrochemical detection of let-7a

Sensitive and accurate detection of tumor suppressor genes is vastly important to the related therapeutic research. Herein, a ratiometric electrochemical method for let-7a detection was established by integrating a ferrocene (Fc) doped MoS₂ nanoplates modified electrode into the nanochannels-based biosensing platform. The ratiometric signal was developed by the redox current of methylene blue (MB) which reflects the target recognition occurred into the nanochannels and the redox current of Fc which corrects the slight signal deviation caused by some analyte-independent factors. And thus, the ratio of peak current of MB and Fc (I_MB/I_Fc) measured at differential pulse voltammogram varied precisely with the increment of the concentration of let-7a incubated in the bioinspired nanochannels. The strategy of spherical DNAzyme induced deposition in nanochannels was utilized to further amplify the signal. Under optimal conditions, a wide linear dynamic range of 50 aM to 10 pM spanning five orders of magnitude was obtained. The developed electrochemical method, with attomole level of detection limit, was successfully applied to the determination of let-7a in human serum and tumor cells. The study not only offers a new route for reliable nucleic acid detection, but also provides an excellent opportunity to extend the application of the two-dimensional transition-metal dichalcogenides.

Machine Learning Directed Aptamer Search from Conserved Primary Sequences and Secondary Structures

Computer-aided prediction of aptamer sequences has been focused on primary sequence alignment and motif comparison. We observed that many aptamers have a conserved hairpin, yet the sequence of the hairpin can be highly variable. Taking such secondary structure information into consideration, a new algorithm combining conserved primary sequences and secondary structures is developed, which combines three scores based on sequence abundance, stability, and structure, respectively. This algorithm was used in the prediction of aptamers from the caffeine and theophylline selections. In the late rounds of the selections, when the libraries were converged, the predicted sequences matched well with the most abundant sequences. When the libraries were far from convergence and the sequences were deemed challenging for traditional analysis methods, this algorithm still predicted aptamer sequences that were experimentally verified by isothermal titration calorimetry. This algorithm paves a new way to look for patterns in aptamer selection libraries and mimics the sequence evolution process. It will help shorten the aptamer selection time and promote the biosensor and chemical biology applications of aptamers.

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.

Measuring the Affinities of RNA and DNA Aptamers with DNA Origami-Based Chiral Plasmonic Probes

Reliable characterization of binding affinities is crucial for selected aptamers. However, the limited repertoire of universal approaches to obtain the dissociation constant (K_D) values often hinders the further development of aptamer-based applications. Herein, we present a competitive hybridization-based strategy to characterize aptamers using DNA origami-based chiral plasmonic assemblies as optical reporters. We incorporated aptamers and partial complementary strands blocking different regions of the aptamers into the reporters and measured the kinetic behaviors of the target binding to gain insights on aptamers' functional domains. We introduced a reference analyte and developed a thermodynamic model to obtain a relative dissociation constant of an aptamer-target pair. With this approach, we characterized RNA and DNA aptamers binding to small molecules with low and high affinities.

Recent advances in gold nanoparticle-based colorimetric aptasensors for chemical and biological analyses

Aptasensors are amazing among many currently formed procedures due to their excellent particularity, selectivity and responsiveness. These biosensors get more popular in combination with gold nanoparticles (AuNPs) to detect chemical and biological molecules. The response of AuNPs by changing color provides a simple explanation of outcomes. The authors review the recent developments in AuNP-based colorimetric aptasensors designed to sense different chemical and biological molecules. They summarize the procedure of AuNP-based detection and the ordinary instances of currently formed AuNP-based colorimetric procedures. Furthermore, their uses for detecting different analytes based on analyte types are given and the present challenges, overview, and positive views for forming new aptasensors are also regarded.