Aptamer functionalized magnetic hydrophobic polymer with synergetic effect for enhanced adsorption of alternariol from wheat

A new adsorbent based on aptamer functionalized magnetic hydrophobic polymer (MHbPA) was developed for specific and efficient adsorption of alternariol (AOH). Through the synergistic effect of aptamer-AOH affinity and hydrophobic interaction of polymer, enhanced adsorption properties had been realized, in which AOH aptamer was the first selected through capture-SELEX with good specificity and affinity, and the targeting polymer was designed based on the hydrophobicity of AOH to increase the interaction. The proposed MHbPA demonstrated a high adsorption capacity of 187.6 ng/mg for AOH. The adsorption behavior was considered as Langmuir adsorption model and pseudo-secondary kinetic adsorption model. Notably, the adsorption of AOH in wheat powder samples could be accomplished within 10 mins with acceptable recoveries. The as designed adsorbent with synergistic effect provides new insights into the development of enhanced pretreatment materials for mycotoxin monitoring in complex food matrices with specific aptamer and targeting polymer.

Selection and Characterization of DNA Aptamers for Cytidine and Uridine

Cytidine and uridine are two essential pyrimidine ribonucleotides, and accurate detection of these nucleosides holds significant biological importance. While many aptamers were reported to bind purines, little success was achieved for pyrimidine binding. This study employs the library-immobilization capture-SELEX technique to isolate aptamers capable of selectively binding to cytidine and uridine. First, a selection was performed using a mixture of cytidine and uridine as the target. This selection led to the isolation of a highly selective aptamer for cytidine with a dissociation constant (Kd ) of 0.9 μM as determined by isothermal titration calorimetry (ITC). In addition, a dual-recognition aptamer was also discovered, which exhibited selective binding to both cytidine and uridine. Subsequently, a separate selection was carried out using uridine as the sole target, and the resulting uridine aptamer displayed a Kd of 4 μM based on a thioflavin T fluorescence assay and a Kd of 102 μM based on ITC. These aptamers do not have a strict requirement of metal ions for binding, and they showed excellent selectivity since no binding was observed with their nucleobases or nucleotides. This study has resulted three aptamers for pyrimidines, which can be employed in biosensors and DNA switches.

Selective Hemin Binding by a Non-G-quadruplex Aptamer with Higher Affinity and Better Peroxidase-like Activity

Previous aptamers for porphyrins and metalloporphyrins were all guanine-rich sequences that can fold in G-quadruplex structures. Due to stacking-based binding, these aptamers can hardly tell different porphyrins apart, and they can also bind other planar molecules, hindering their practical applications. In this work, we used the capture selection method to obtain aptamers for hemin and protoporphyrin IX (PPIX). The hemin aptamer (Hem1) features two highly conserved repeating binding loops, and it cannot form a G-quadruplex, which was supported by its Mg2+ -dependent but K+ -independent hemin binding and CD spectroscopy. Isothermal titration calorimetry revealed much higher enthalpy change for the new aptamer, and the best aptamer showed a Kd of 43 nM hemin. Hem1 can also enhance the peroxidase-like activity of hemin. This work demonstrates that aptamers have alternative ways to bind porphyrins allowing selective recognition of different porphyrins.

Generation of a high-affinity DNA aptamer for on-site screening of toxic aristolochic acid I in herbal medicines and botanical products

Aristolochic Acid I (AAI) is an environmental and foodborne toxin found in the Aristolochia and Asarum species of plants that are widespread all over the world. Therefore, there is an urgent need to develop a sensitive and specific biosensor for identifying AAI. Aptamers as a powerful biorecognition element provide the most viable options for solving this problem. In this study, we used library-immobilized SELEX to isolate an AAI-specific aptamer with a K_D value of 86 ± 13 nM. To verify the practicability of the selected aptamer, a label-free colorimetric aptasensor was designed. This aptasensor exhibited a low detection limit of 225 nM. Besides, it had been further applied for the determination of AAI in real samples and the recoveries ranged from 97.9% to 102.4%. In the future, AAI aptamer will provide a promising tool for safety evaluation in various fields of agriculture, food, and medication.

A novel electrochemical aptasensor for ultrasensitive detection of herbicide prometryn based on its highly specific aptamer and Ag@Au nanoflowers

Herbicide prometryn has become a common pollutant in aquatic environments and caused adverse impacts on ecosystems. This study developed an ultrasensitive electrochemical aptasensor for prometryn based on its highly affinitive and specific aptamer and Ag@Au nanoflowers (Ag@AuNFs) for signal amplification. Firstly, this study improved the Capture-SELEX strategy to screen aptamers and obtained aptamer P60-1, which had a high affinity (Kd: 23 nM) and could distinguish prometryn from its structural analogues. Moreover, the typical stem-loop structure in aptamer P60-1 was found to be the binding pocket for prometryn. Subsequently, an electrochemical aptasensor for prometryn was established using multiwalled carbon nanotubes and reduced graphene oxide as electrode substrate, Ag@Au NFs as signal amplification element, and aptamer P60-1 as recognition element. The aptasensor had a detection range of 0.16-500 ng/mL and a detection limit of 60 pg/mL, which was much lower than those of existing detection methods. The aptasensor had high stability and good repeatability, and could specifically detecting prometryn. Furthermore, the utility of the aptasensor was validated by measuring prometryn in environmental and biological components. Therefore, this study provides a robust and ultrasensitive aptasensor for accurate detection for prometryn pollution.

Screening and identification of a DNA aptamer to construct the label-free fluorescent aptasensor for ultrasensitive and selective detection of clothianidin residue in agricultural products

Clothianidin pesticide not only pollutes the ecological environment, but also poses a potential threat to human health. Thus, it is of great importance to develop efficient and accurate methods to recognize and detect clothianidin residues in agricultural products. Aptamer has the advantages of easy modification, high affinity and good stability, which is particularly suitable as a recognition biomolecule for pesticide detection. However, the aptamer against clothianidin has not been reported. Herein, the aptamer (named CLO-1) had good selectivity and strong affinity (K_d = 40.66 ± 3.47 nM) to clothianidin pesticide, which was screened for the first time by Capture-SELEX strategy. The binding effect of CLO-1 aptamer to clothianidin was further studied by circular dichroism (CD) spectroscopy and molecular docking technique. Finally, the CLO-1 aptamer was used as the recognition molecule to construct a label-free fluorescent aptasensor using GeneGreen dye as sensing signal for the highly sensitive detection of clothianidin pesticide. The constructed fluorescent aptasensor had the limit of detection (LOD) as low as 5.527 μg L^-1 for clothianidin, and displayed good selectivity against other competitive pesticides. The aptasensor was applied to detect the clothianidin spiked in tomatoes, pears and cabbages, and the recovery rate was good in the range of 81.99%-106.64%. This study provides a good application prospect for the recognition and detection of clothianidin.

Selected ssDNA aptamers-graphene oxide based fluorescent biosensor to detect sulfameter in milk

The abuse of sulfameter (SME) in animal husbandry can cause drug resistance and toxic or allergic reactions in humans. Therefore, it is very important to establish a simple, inexpensive and efficient method for detecting SME in food. In this work, we propose a single fluorescent aptamer/graphene oxide (GO)-based biosensor to detect SME residues in milk. Aptamers that specifically bind to SME were screened by capture-SELEX using an ssDNA library immobilized on magnetic beads. The 68 active candidate aptamers were chemically synthesized for specificity and affinity characterization. Among the aptamers, the aptamer sulf-1 revealed the highest affinity (K_d =77±15 nM) to SME and was selected to construct a GO-based fluorescent biosensor for real milk sample detection. Under optimal conditions, the single fluorescent aptasensor had a wide linear range (R² was 0.997) from 7 to 336 ng/mL and low detection limit of 3.35 ng/mL that was calculated with a 3 SD/slope. The single fluorescent method was also validated by SME-fortified milk samples, showing average recoveries ranging from 99.01% to 104.60% with a relative standard deviation below 3.88%. These results demonstrate that this novel aptamer sensor provides an opportunity for sensitive, convenient and accurate detection of SME residues in milk.

RNA Capture-SELEX on Streptavidin Magnetic Beads

SELEX has enabled the selection of aptamers, nucleic acids that can bind a defined ligand, in some cases with exceptionally high affinity and specificity. The SELEX protocol has been adapted many times to fit a variety of needs. This protocol describes such an adaptation, namely, RNA-Capture SELEX that we have used to successfully develop small molecule-binding RNA aptamers. Our proposed method specifically selects not only for excellent binding but also for conformational switching. In consequence, we found this SELEX method to be particularly suitable for identifying aptamers for further application in synthetic riboswitch engineering.

Selection and characterization of bispecific aptamers against malachite green and leucomalachite green

In order to develop multi-residues rapid detection, the bispecific aptamers against malachite green (MG) and leucomalachite green (LMG) were isolated by the capture systematic evolution of ligands by exponential enrichment (Capture-SELEX). After thirteen rounds of selection, the enriched ssDNA pools were sent for high-throughput sequencing. Nine aptamer candidates (A1-A9) were picked out to test their specificity by gold nanoparticles (AuNPs) colorimetric assay. Three aptamers (A2, A3, A5) with good selectivity were truncated to verify their affinity by fluorescence assay. Finally, three truncated aptamers (A2-a, A3-a, A5-a) with bispecificity and high affinity were identified. For LMG, the dissociation constant (Kd) of them were 8.4 ± 0.8 nM, 8.2 ± 1.2 nM, and 13.7 ± 1.4 nM, respectively. For MG, Kd of them were 3.4 ± 0.3 μM, 2.3 ± 0.2 μM, 3.0 ± 0.2μM. Among them, A3-a is the best. Our work will provide novel probes for the development of multi-residues rapid detection as well as opportunities for multiple target aptamer discovery.

Selection of Aptamer for N-Methyl Mesoporphyrin IX to Develop Porphyrin Metalation DNAzyme

Mesoporphyrin IX (MPIX) contains a planar macrocycle center that can interact with various divalent metal ions through the exposed binding sites, leading to the metalation of MPIX. The DNA aptamers for porphyrin molecules usually display different catalytic functions (termed deoxyribozymes or DNAzymes), which can accelerate such chemical reactions. Inspired by this, an affinity chromatography selection approach was designed for identifying a porphyrin metalation DNAzyme. In our experiment, N-methyl mesoporphyrin IX (NMM), an analog of MPIX, is used as the target molecule, owing to its stable and high fluorescence enhancement after combining with specific oligonucleotides. Our results showed that the selected aptamer Nm1 is capable of binding to NMM with a low micromolar dissociation constant (0.75 ± 0.08 μM) and displays a catalytic activity for MPIX metalation with 3.3-fold rate enhancement. The protocol for isolation of such a porphyrin metalation DNAzyme is described in detail here.

Efficient Method to Identify Synthetic Riboswitches Using RNA-Based Capture-SELEX Combined with In Vivo Screening

Synthetic riboswitches are a promising tool for conditional gene expression. In vitro selected aptamers used as binding domains for the design of RNA-based switches have to exhibit excellent binding affinity as well as ligand binding-induced structural changes. Selection via Capture-SELEX favors the enrichment of aptamers which exhibit both characteristics. For the Capture-SELEX, an RNA pool is used that gets immobilized onto a capture oligonucleotide by hybridization. Addition of the ligand frees the aptamers by their binding to the ligand, resulting in the release from the capture oligonucleotide through structural changes. These sequences get reverse transcribed, PCR amplified, and used for the following selection rounds. In this publication, we present a detailed protocol for Capture-SELEX, followed by screening in yeast to identify aptamers suitable for the design of synthetic riboswitches.

Highly selective and sensitive detection of glutamate by an electrochemical aptasensor

An electrochemical aptamer-based sensor was developed for glutamate, the major excitatory neurotransmitter in the central nervous system. Determining glutamic acid release and glutamic acid levels is crucial for studying signal transmission and for diagnosing pathological conditions in the brain. Glutamic acid-selective oligonucleotides were isolated from an ssDNA library using the Capture-SELEX protocol in complex medium. The selection permitted the isolation of an aptamer 1d04 with a dissociation constant of 12 µM. The aptamer sequence was further used in the development of an electrochemical aptamer sensor. For this purpose, a truncated aptamer sequence named glu1 was labelled with a ferrocene redox tag at the 3'-end and immobilized on a gold electrode surface via Au-thiol bonds. Using 6-mercapto-1-hexanol as the backfill, the sensor performance was characterized by alternating current voltammetry. The glu1 aptasensor showed a limit of detection of 0.0013 pM, a wide detection range between 0.01 pM and 1 nM, and good selectivity for glutamate in tenfold diluted human serum. With this enzyme-free aptasensor, the highly selective and sensitive detection of glutamate was demonstrated, which possesses great potential for implementation in microelectrodes and for in vitro as well as in vivo monitoring of neurotransmitter release.

Selection and identification of a DNA aptamer for ultrasensitive and selective detection of λ-cyhalothrin residue in food

Pyrethroid pesticides residues will not only pollute the environment, but also cause high toxicity to the human body. It is significant to establish an efficient and accurate method for pyrethroid detection in food. Considering that the common biomolecules like antibody is complicated and easy to inactivate, it is urgent to find a new type of biomolecule to specifically recognize pyrethroid pesticides. This study proposed the Capture-SELEX strategy to firstly select λ-cyhalothrin aptamer by immobilizing random ssDNA library. High-throughput sequencing was performed on the enriched ssDNA library through multiple Capture-SELEX rounds. Comprehensively inspecting structural similarity and homology, six sequences were chosen from five families for further analysis. The results showed that the aptamer (named LCT-1) could specifically recognize λ-cyhalothrin with the strongest affinity (K_d = 50.64 ± 4.33 nmol L^-1). Molecular docking results revealed that the binding sites between λ-cyhalothrin and LCT-1 aptamer are mainly related to the bases A-5, C-6, C-28, A-29, C-30, G-31 and G-32. The LCT-1 aptamer was truncated to a shorter sequence (named as LCT-1-39) by removing other irrelevant bases, and its K_d value was determined as (10.27 ± 1.33) nmol·L^-1 by Microscale Thermophoresis (MST). Both LCT-1 and LCT-1-39 aptamers were employed as recognition molecules to establish the colorimetric aptasensors for λ-cyhalothrin detection, which displayed good repeatability and reproducibility. The detection limit of the aptasensors were individually calculated as 0.0197 μg ml^-1 and 0.0186 μg ml^-1, and their recovery rate of λ-cyhalothrin in pear and cucumber samples was in the range of 82.93-95.50%. This article provides a promising application for the detection of λ-cyhalothrin.

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.

Preparation of DNA aptamer and development of lateral flow aptasensor combining recombinase polymerase amplification for detection of erythromycin

Erythromycin has polluted our aquatic environment for decades, leading to the risk of bacterial resistance and harmful effects on human beings, wildlife and ecosystem. There is an urgent demand of developing a portable tool capable of detecting erythromycin on site. In this study, ten aptamer candidates against erythromycin were prepared through Capture-SELEX (systematic evolution of ligands by exponential enrichment) process in 20 rounds. Aptamer candidate Ery_06 with the highest enrichment was chosen for further study, whose affinity was characterized by gold nanoparticles colorimetric assay, quartz crystal microbalance with dissipation and agarose chasing diffusion assay. It was determined by SYBR Green I fluorimetric assay that the characterized aptamer binds to erythromycin with high affinity (Kd: 20 ± 9 nM). Its specificity was also characterized by distinguishing erythromycin from different antibiotics tested. A novel lateral flow aptasensor was constructed by using the newly identified aptamer combined with recombinase polymerase amplification (RPA) and lateral flow strip (LFS). Aptamer acted as a sensing element anchoring on the surface of solid phase could be eluted by erythromycin. RPA functioned to amplify and convert the signal to be visible on LFS. The lateral flow was completed in 15 min, achieving a detection limit of 3 pM. The application feasibility of the aptasensor was proved by the detection of tap water samples spiked with erythromycin.

Capture-SELEX for aptamer selection: A short review

The emerging aptamer, developed through the systematic evolution of ligands by exponential enrichment (SELEX) process, has revolutionized and facilitated the discoveries in basic research. Among all SELEX technology, Capture-SELEX is a variant of the in vitro selection process, which is suitable for isolating aptamers against small molecules. Capture-SELEX library was developed to enable the immobilization of the oligonucleotides instead of the target molecules during the aptamer selection process. The review provides an update on the recent-advances in this new screening method with particular emphasis on key points of capture protocol and its applications. The limitations and the prospects of the Capture-SELEX are also discussed. We hope that present review will inspire more researchers to understand the selection problems from the perspective of Capture-SELEX. Moreover, it will open new pave to improve the efficiency and success of screening to meet the growing demand for aptasensor discovery in small molecules.

Selection and application of ssDNA aptamers against spermine based on Capture-SELEX

Spermine contamination ranks as one of the food safety issues, it will cause some adverse reactions if the intake of spermine is excessive in human body. So it is of great significance to establish fast and efficient analysis method to detect spermine in foods. In this study, the spermine aptamers with high affinity and specificity were obtained by the capture systematic evolution of ligands by exponential enrichment (Capture-SELEX) technique. Forty-one aptamer sequences were obtained by cloning and sequencing, and were divided into eight families based on homology and secondary structure analysis. The affinity and specificity of candidate aptamers was analyzed by isothermal titration calorimetry (ITC) and fluorescence assay. The aptamers named APJ-6 was picked out as the optimal aptamer that recognizes spermine specifically with the Kd value of 9.648 ± 0.896 nM. In order to verify the practicability of the selected aptamers, the sensitive aptamer-based fluorescene assay was designed. Under optimized conditions, this aptasensor exhibited a low detection limit of 0.052 nM, as well as a linear within the range of 0.1-20 nM. Besides, it has been further applied for the determination of spermine in pork samples and the recoveries ranged from 86.45% to 98.15%, showing its great potential for sensitive analysis in food safety control.

RNA-based Capture-SELEX for the selection of small molecule-binding aptamers

Despite their wide applicability, the selection of small molecule-binding RNA aptamers with both high affinity binding and specificity is still challenging. Aptamers that excel at both binding and structure switching are particularly rare and difficult to find. Here, we present the protocol of a Capture-SELEX that specifically allows the in vitro selection of small-molecule binding aptamers, which are essential building blocks for the design process of synthetic riboswitches and biosensors. Moreover, we provide a comparative overview of our proposed methodology versus alternative in vitro selection protocols with a special focus on the design of the pool. Finally, we have included detailed notes to point out useful tips and pitfalls for future application.

Selection, Characterization, and Application of ssDNA Aptamer against Furaneol

Furaneol is an aroma compound which occurs naturally in foods and is used as an artificial flavor. Detection of furaneol is required in food science and food processing industry. Capture- Systematic Evolution of Ligands by EXponential enrichment (SELEX) protocol was applied for the isolation of an aptamer binding to furaneol, a small volatile organic substance contributing to the flavor of various products. Thirteen cycles of selection were performed. The resulting DNA pool was cloned, using blunt-end cloning, and ninety-six plasmids were sequenced and analyzed. Eight oligonucleotides were selected as aptamer candidates and screened for the ability to bind to furaneol, using three different methods—magnetic-beads associated elution assay, SYBR Green I assay, and exonuclease protection assay. One of the candidates was further characterized as an aptamer. The apparent equilibrium constant was determined to be (1.1 ± 0.4) µM, by the fluorescent method. The reported aptamer was applied for development of the ion-sensitive field-effect transistor (ISFET)-based biosensor, for the analysis of furaneol, in the concentration range of 0.1–10 µM.

Selection of DNA aptamers against penicillin G using Capture-SELEX for the development of an impedimetric sensor

This paper describes for the first time the selection of aptamers selective to penicillin. Aptamers were selected using a specific process called Capture-SELEX (Systematic Evolution of Ligands by Exponential Enrichment). This technique is based on the selection of DNA aptamers using penicillin G in solution while the ssDNA library is fixed on a support. One aptamer showing a good affinity to penicillin was finally selected and tested in electrochemical sensor configuration, using electrochemical impedance spectroscopy as detection technique. The developed aptasensor allowed the detection of penicillin in a wide concentration range, comprised between 0.4 and 1000µgL^-1 Such performance was compatible with milk analysis, as the maximum residue limit tolerated in this matrix is 4µgL^-1. The selectivity of the developed sensor was also studied, showing that the sensor was also able to bind other beta-lactam antibiotics, although with a weaker affinity. Finally the sensor was used for detection of penicillin G in milk. It was shown that a simple sample treatment with isopropanol followed by filtration was sufficient to eliminate matrix effects, allowing the determination of penicillin in milk at concentrations compatible with legislation requirements.