Screening and application of a truncated aptamer for high-sensitive fluorescent detection of metronidazole

Multicolor emissive carbon dot-based fluorometric analysis platform for rapid quantification and discrimination of nitroimidazole antibiotic residues

The development of efficient, rapid, portable, and accurate analysis of veterinary drug residues in food matrices is in great demand for food safety assessment. Here, we have developed a smartphone-integrated platform for fluorometric quantification of metronidazole (MNZ) residues and constructed a sensor array for discrimination of different nitroimidazole antibiotics (NIIMs). Multicolor CDs (B-CDs, C-CDs, Y-CDs, and R-CD) were prepared and showed different fluorescence response to MNZ. The fluorescence of C-CDs was quenched Because of the inner filter effect (IFE) between the C-CDs and MNZ, while that of R-CDs was enhanced due to the passivation of surface defects by MNZ. Based on the response pattern, the fluorometric quantification of MNZ based on the fluorescence images of C-CD + R-CD system (R/G values) was achieved with a low detection limit of 0.45 μM. By designing a smartphone-integrated platform, the analysis can be completed within 20 min. In addition, a fluorescence sensor array based C-CDs and R-CDs was also developed. The unique fingerprint of each NIIMs was obtained by linear discriminant analysis (LDA) of the response patterns, indicating an effective discrimination of five NIIMs. Moreover, the platform was used for quantification of MNZ in food samples and the recoveries were within 84.0-106.3 % with relative standard deviations 1.2-10.2 %. Therefore, the proposed method shows great potential as a universal platform for rapid detection of veterinary drug residues.

A lateral flow strip for on-site detection of homocysteine based on a truncated aptamer

An elevated level of homocysteine (Hcy) in serum is closely related to the development of various diseases. Therefore, homocysteine has been widely employed as a biomarker in medical diagnosis and the on-site detection of homocysteine is highly desired. In this study, a truncated highly specific aptamer for homocysteine was screened and used to design a lateral flow strip (LFS) for the detection of homocysteine. The aptamer was derived from a previously reported sequence. Based on the result of molecular docking, the original sequence was subjected to truncation, resulting in a reduction of the length from 66 nt to 55 nt. Based on the truncated aptamer, the LFS was designed for the detection of homocysteine. In the presence of homocysteine, the aptamer selectively binds to it, releasing cDNA from the aptamer/cDNA duplex. This allows cDNA to bind to the capture probe immobilized on the T zone of the strip, resulting in a red signal on the T zone from gold nanoparticles (AuNPs). The strip enables the visual detection of homocysteine in 5 min. Quantitative detection can be facilitated with the aid of ImageJ software. In this mode, the linear detection range for homocysteine is within 5-50 μM, with a detection limit of 4.18 μM. The strip has been effectively utilized for the detection of homocysteine in human serum. Consequently, the combination of the truncated aptamer and the strip offers a method that is sensitive, quick, and economical for the on-site detection of homocysteine.

Screening and Application of DNA Aptamers for Heparin-Binding Protein

Rapid detection of heparin-binding protein (HBP) is essential for timely intervention in sepsis cases. Current detection techniques are usually antibody-based immunological methods, which have certain problems, such as complexity and slow detection, and fall short in meeting the urgency of clinical needs. The application of an aptamer can address these concerns well. In this study, HBP-specific DNA aptamers were screened first. Among which, Apt-01, Apt-02, and Apt-13 had a high affinity for HBP, exhibiting impressive KD values of 3.42, 1.44, and 1.04 nmol/L, respectively. Then, the aptamer of HBP and its partially complementary primer probe were combined to form double-stranded DNA (dsDNA) and synthesize a circular DNA template. The template is complementary to the primer probe, but due to the presence of dsDNA, ExoIII cleaves C2-13 as an RCA primer probe, rendering the template unable to recognize the primer probe and preventing the RCA reaction from proceeding. When the target is present, it competes with the adapter for recognition and releases C2-13, exposing its 3' end. After initiating the RCA at room temperature and reacting with SYBR GreenII at 37 °C for 20 min, fluorescence changes can be observed and quantitatively analyzed at a 530 nm wavelength, achieving quantitative biological analysis. Apt-01 was used to develop a fluorescent biosensor for HBP detection, which exhibited a good linear range (0.01 nmol/L to 10 nmol/L) and detection limit (0.0056 nmol/L). This advancement holds the potential to lay a solid groundwork for pioneering sensitive and specific methods for HBP detection and to significantly enhance the diagnostic processes for sepsis.

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.

Composite of a thiacalix[4]arene-copper(I) metal-organic framework and mesoporous carbon for efficient electrochemical detection of antibiotics

Abundant use of nitrofurantoin (NFT) and metronidazole (MTZ) antibiotics has led to excessive residues in the environments and humans, resulting in serious damage to the human body and ecosystem. Therefore, effective detection of NFT and MTZ is exceedingly necessary. In this regard, metal-organic frameworks (MOFs) are promising materials as electrochemical sensors. Herein, we synthesized a new two-dimensional thiacalix [4]arene-copper (I) MOF (Cu-TC4A-M). This MOF was mixed with mesoporous carbon (MC) to a give Cu-TC4A-M@MC composite. In addition, the sensors of Cu-TC4A-M@MC(2:1)/GCE and Cu-TC4A-M@MC(1:2)/GCE were achieved (GCE = glassy carbon electrode), and then were applied for effectively detecting NFT and MTZ, respectively. Markedly, the two sensors exhibited satisfactory linear detection range, anti-interference, reproducibility and stability. When they were utilized in the real samples, such as human serum, urine, tap water and lake water, satisfactory recoveries were attained. The relative standard deviations (RSDs) were in the range of 1.16 % ∼ 1.92 % for NFT and 0.95 % ∼ 2.33 % for MTZ. This work provided a new application prospect for the thiacalix [4]arene-based MOFs as promising candidate materials for NFT and MTZ detection.

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.

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.

Synthesis of Isolated DNA Aptamer and Its Application of AC-Electrothermal Flow-Based Rapid Biosensor for the Detection of Dengue Virus in a Spiked Sample

Dengue fever is an infectious disease caused by the dengue virus (DENV) and is transmitted by mosquitoes in tropical and subtropical regions. The early detection method at a low cost is essential. To address this, we synthesized the isolated DENV aptamer for fabricating a rapid electrochemical biosensor on a Au interdigitated microgap electrode (AuIMGE). The DENV aptamers were generated using the SELEX (systemic evolution of ligands by exponential enrichment) method for binding to DENV surface envelope proteins. To reduce the manufacturing cost, unnecessary nucleotide sequences were excluded from the isolation process of the DENV aptamer. To reduce the detection time, the alternating current electrothermal flow (ACEF) technique was applied to the fabricated biosensor, which can shorten the detection time to 10 min. The performance of the biosensor was evaluated using cyclic voltammetry (CV) and electrochemical impedance spectroscopy (EIS). In the diluted DENV protein solution, the linear range of the concentrations was from 1 pM to 1 μM and the LOD was 76.7 fM. Moreover, the proposed biosensor detected DENV in a diluted spiked sample at a linear range of 10-6 to 106 TCID50/mL, while the detection performance was proven with an LOD of 1.74 × 10-7 TCID50/mL along with high selectivity.

Improving aptamer performance: key factors and strategies

Aptamers are functional single-stranded oligonucleotide fragments isolated from randomized libraries by Systematic Evolution of Ligands by Exponential Enrichment (SELEX), exhibiting excellent affinity and specificity toward targets. Compared with traditional antibody reagents, aptamers display many desirable properties, such as low variation and high flexibility, and they are suitable for artificial and large-scale synthesis. These advantages make aptamers have a broad application potential ranging from biosensors, bioimaging to therapeutics and other areas of application. However, the overall performance of aptamer pre-selected by SELEX screening is far from being satisfactory. To improve aptamer performance and applicability, various post-SELEX optimization methods have been developed in the last decade. In this review, we first discuss the key factors that influence the performance or properties of aptamers, and then we summarize the key strategies of post-SELEX optimization which have been successfully used to improve aptamer performance, such as truncation, extension, mutagenesis and modification, splitting, and multivalent integration. This review shall provide a comprehensive summary and discussion of post-SELEX optimization methods developed in recent years. Moreover, by discussing the mechanism of each approach, we highlight the importance of choosing the proper method to perform post-SELEX optimization.

Selection and truncation of aptamers as fluorescence sensing platforms for selective and sensitive detection of nitrofurazone

Nitrofurazone (NFZ) is an antibiotic banned in many countries, as its residue seriously harms the human body. Herein, anti-NFZ aptamers were selected and identified based on the magnetic bead SELEX technique using a ssDNA library with a full length of 90 nucleotides (nt). Five full sequence candidate aptamers (NFZ8, NFZ24, NFZ28, NFZ34, and NFZ70) were obtained by secondary structure analysis. We optimized the entire sequence to obtain a truncated aptamer, a 16 nt sequence (NFZ8-1:5'-GTTCTATTGAAAAAAC-3') that showed the highest affinity for NFZ (K_d = 76.11 nM). The binding site of NFZ and aptamer NFZ8-1 was found to be "GAA" by molecular docking. In addition, utilizing the most special truncated aptamer NFZ8-1 as the identification probe, a graphene oxide fluorescent aptasensor is an innovative for the detection of NFZ residue that showed a wide linear reach from 1.25 to 160 ng/mL and a low limit of detection of 1.13 ng/mL. In the actual water environment sample detection, the recovery rate ranged from 95.21 to 113.66%, and the coefficient of variation ranged from 3.53 to 11.24%. These results demonstrate that the NFZ-truncated aptamer applied to the aptasensor provides a novel methodology for recognizing NFZ residues.

Screening of a Sialyllactose-Specific Aptamer and Engineering a Pair of Recognition Elements with Unique Fluorescent Characteristics for Sensitive Detection of Sialyllactose

A single-stranded DNA (ssDNA) aptamer specific for 6'-sialyllactose (6'-SL) was screened through magnetic separation-based SELEX and post-SELEX truncation and used to construct unique aptamer bio-dots for sensitive detection of 6'-SL. Eighteen rounds of screening were conducted during the SELEX process. The ssDNA aptamer Apt9 (K_d = 152.3 nM) with a length of 79 nucleotides (nt) was demonstrated as the optimal aptamer candidate after affinity and specificity evaluation. Then, Apt9 was truncated and optimized according to secondary structure and molecular docking. A 35 nt truncated aptamer Apt9-1 (K_d = 91.75 nM) with higher affinity than Apt9 was finally obtained. Furthermore, Apt9-1 was used to synthesize bio-dots as a new recognition element of 6'-SL, and the aminobenzene boric acid functionalized carbon dots were employed as the other recognition element. With the respective fluorescent characteristics, the two quantum dots (QDs) were made a pair to construct a 6'-SL fluorescent biosensor. The linear detection range of the biosensor is 10 μM to 5 mM, and the detection limit is 0.9 μM. With the advantages of time-saving, high efficiency, and simplicity in the actual sample detection, the screened aptamer and dual-QD-based biosensor have broad application prospects in 6'-SL detection.

Screening of Single-Stranded DNA Aptamer Specific for Florfenicol and Application in Detection of Food Safety

In this work, the single-stranded DNA (ssDNA) aptamers specific to florfenicol (FF) and having a high binding affinity were prepared using the magnetic bead-based systematic evolution of ligands by the exponential enrichment technique (MB-SELEX). After 10 rounds of the MB-SELEX screening, aptamers that can simultaneously recognize FF and its metabolite florfenicol amine (FFA) were obtained. The aptamer with the lowest dissociation constant (Kd) was truncated and optimized based on a secondary structure analysis. The optimal aptamer selected was Apt-14t, with a length of 43 nt, and its dissociation constant was 4.66 ± 0.75 nM, which was about 7 times higher than that of the full-length sequence. The potential binding sites and interactions with FF were demonstrated by molecular docking simulations. In addition, a colorimetric strategy for nanogold aptamers was constructed. The linear detection range of this method was 0.00128–500 ng/mL and the actual detection limit was 0.00128 ng/mL. Using this strategy to detect florfenicol in actual milk and eggs samples, the spiked recoveries were 88.9–123.1% and 84.0–112.2%, respectively, and the relative standard deviation was less than 5.6%, showing high accuracy.

Study on Metronidazole Acid-Base Behavior and Speciation with Ca2+ for Potential Applications in Natural Waters

Metronidazole (MNZ) is an antibiotic widely used for the treatment of various infectious diseases and as an effective pesticide agent for the cultivation of chickens and fish. Its high resistance to purification processes and biological activity has led to the classification of MNZ as an emerging contaminant. A speciation study, aimed to define the acid-base properties of MNZ and its interaction with Ca²⁺, commonly present in natural waters, is reported. The protonation constants of MNZ, as well as the formation constant value of Ca²⁺-MNZ species, were obtained by potentiometric titrations in an aqueous solution, using NaCl as background salt at different ionic strengths (0.15, 0.5, 1 mol L⁻¹) and temperature (15, 25 and 37 °C) conditions. The acid-base behavior and the complexation with Ca²⁺ were also investigated by ¹H NMR and UV-Vis titrations, with results in very good agreement with the potentiometric ones. The dependence of the formation constants on the ionic strength and temperature was also determined. The sequestering ability of MNZ towards Ca²⁺ was defined by the empirical parameter pL_0.5 at different pH and temperature values. The speciation of MNZ simulating sea water conditions was calculated.

Split aptamer acquisition mechanisms and current application in antibiotics detection: a short review

Antibiotic contamination is becoming a prominent global issue. Therefore, sensitive, specific and simple technology is desirable the demand for antibiotics detection. Biosensors based on split aptamer has gradually attracted extensive attention for antibiotic detection due to its higher sensitivity, lower cost, false positive/negative avoidance and flexibility in sensor design. Although many of the reported split aptamers are antibiotics aptamers, the acquisition and mechanism of splitting is still unknow. In this review, six reported split aptamers in antibiotics are outlined, including Enrofloxacin, Kanamycin, Tetracycline, Tobramycin, Neomycin, Streptomycin, which have contributed to promote interest, awareness and thoughts into this emerging research field. The study introduced the pros and cons of split aptamers, summarized the assembly principle of split aptamer and discussed the intermolecular binding of antibiotic-aptamer complexes. In addition, the recent application of split aptamers in antibiotic detection are introduced. Split aptamers have a promising future in the design and development of biosensors for antibiotic detection in food and other field. The development of the antibiotic split aptamer meets many challenges including mechanism discovery, stability improvement and new biosensor development. It is believed that split aptamer could be a powerful molecular probe and plays an important role in aptamer biosensor.

Rapid and label-free detection of aflatoxin B1 using a rationally truncated aptamer and via circular dichroism measurement

We describe a simple aptamer assay for the rapid analysis of aflatoxin B1 (AFB1), a potently carcinogenic fungal metabolite. The original anti-AFB1 aptamer was rationally truncated, obtaining a short aptamer that displayed better performance. Different concentrations of AFB1 were detected by measuring the circular dichroism spectra of this short aptamer. The detection limit reached 0.6 nM, which was lower than that of the original aptamer (80 nM).

Polyvinylpyrrolidone-assisted synthesis of highly water-stable cadmium-based metal-organic framework nanosheets for the detection of metronidazole

Recently, much effort has been dedicated to ultra-thin two-dimensional metal–organic framework (2D MOF) nanosheets due to their outstanding properties, such as ultra-thin morphology, large specific surface area, abundant modifiable active sites, etc. However, the preparation of high-quality 2D MOF nanosheets in good yields still remains a huge challenge. Herein, we report 2D cadmium-based metal–organic framework (Cd-MOF) nanosheets prepared in a one-pot polyvinylpyrrolidone (PVP)-assisted synthesis method with high yield. The Cd-MOF nanosheets were characterized with good stability and dispersion in aqueous systems, and were highly selective and sensitive to the antibiotic metronidazole (MNZ) with low limit of detection (LOD: 0.10 μM), thus providing a new and promising fluorescent sensor for rapid detection of MNZ in aqueous solution.

Except PVP was added for Cd-MOF nanosheets, the preparation process of bulk and Cd-MOF nanosheets was similar.

Recent Advances in Micro/Nanomaterial-Based Aptamer Selection Strategies

Aptamers are artificial nucleic acid ligands that have been employed in various fundamental studies and applications, such as biological analyses, disease diagnostics, targeted therapeutics, and environmental pollutant detection. This review focuses on the recent advances in aptamer discovery strategies that have been used to detect various chemicals and biomolecules. Recent examples of the strategies discussed here are based on the classification of these micro/nanomaterial-mediated systematic evolution of ligands by exponential enrichment (SELEX) platforms into three categories: bead-mediated, carbon-based nanomaterial-mediated, and other nanoparticle-mediated strategies. In addition to describing the advantages and limitations of the aforementioned strategies, this review discusses potential strategies to develop high-performance aptamers.

Screening and application of a broad-spectrum aptamer for acyclic guanosine analogues

Acyclic guanosine analogues, a class of widely used antiviral drugs, can cause chronic toxicity and virus resistance. Therefore, it is essential to establish rapid and accurate methods to detect acyclic guanosine analogues. In this study, five acyclic guanosine analogues (acyclovir, famciclovir, ganciclovir, penciclovir, and valaciclovir) were used as positive targets to obtain broad-spectrum aptamers through Capture-SELEX technology. Real-time quantitative PCR (Q-PCR) was used to monitor the aptamer SELEX process. After the sixteen rounds of selection against mixed targets, sequences were obtained by high-throughput sequencing (HTS). Furthermore, a broad-spectrum aptamer, named CIV6, was found as the higher performance aptamer that was suitable for five acyclic guanosine analogues by graphene oxide (GO) polarization and fluorescence assay. Finally, the aptamer CIV6 was used to construct GO fluorescence assay to detect five acyclic guanosine analogues. The limits of detection (LOD) of acyclovir, famciclovir, ganciclovir, penciclovir, and valaciclovir were 0.48 ng·mL^-1, 0.53 ng·mL^-1, 0.50 ng·mL^-1, 0.56 ng·mL^-1, and 0.38 ng·mL^-1, respectively.

Screening Aptamers that Are Specific for Beclomethasone and the Development of Quantum Dot-Based Assay

We developed an aptamer that was specific for beclomethasone (BEC) via systematic evolution of ligands by exponential enrichment (SELEX). Development was monitored by real-time quantitative PCR (Q-PCR) and the enriched library was sequenced by high-throughput sequencing. Forty-seven aptamer candidates were obtained; of these, BEC-6 showed the highest affinity (K_d = 0.15 ± 0.02 μM) and did not cross-react with other BEC analogs. We also developed a quantum dot-based assay (QDA) for the detection of BEC that was based upon a quantum dot (QD) composite probe. Under optimized reaction conditions, the linear range of this method for BEC was 0.1 to 10 μM with a low detection limit (LOD) of 0.1 μM. Subsequently, the method was used to detect BEC in Traditional Chinese Medicine (TCM) with a mean recovery of 81.72-91.84%. This is the first report to describe the development of an aptamer against BEC; BEC-6 can also be engineered into QDA for the detection of BEC.

In silico approach for Post-SELEX DNA aptamers: A mini-review

Aptamers are short oligonucleotides that possess high specificity and affinity against their target. Generated via Systematic Evolution of Ligands by Exponential Enrichment, (SELEX) in vitro, they were screened and enriched. This review covering the study utilizing bioinformatics tools to analyze primary sequence, secondary and tertiary structure prediction, as well as docking simulation for various aptamers and their ligand interaction. Literature was pooled from Web of Science (WoS) and Scopus databases until December 18, 2020 using specific search string related to DNA aptamers, in silico, structure prediction, and docking simulation. Out of 330 published articles, 38 articles were assessed in the analysis based on the predefined inclusion and exclusion criteria. It was found that Mfold and RNA Composer web server is the most popular tool in secondary and tertiary structure prediction of DNA aptamers, respectively. Meanwhile, in docking simulation, ZDOCK and AutoDock are preferred to analyze binding interaction in the aptamer-ligand complex. This review reports a brief framework of recent developments of in silico approaches that provide predictive structural information of ssDNA aptamer.