Electrochemical aptasensor for sulfadimethoxine detection based on the triggered cleavage activity of nuclease P1 by aptamer-target complex

A fluorescent aptasensor for enzyme-free and sensitive detection of kanamycin based on entropy-driven strand displacement reaction

BACKGROUND

Kanamycin is an antibiotic that can easily cause adverse side effects if used improperly. Due to the extremely low concentrations of kanamycin in food, quantitative detection of kanamycin becomes a challenge. As one of the DNA self-assembly strategies, entropy-driven strand displacement reaction (EDSDR) does not require enzymes or hairpins to participate in the reaction, which greatly reduces the instability of detection results. Therefore, it is a very beneficial attempt to construct a highly sensitive and specific fluorescence detection method based on EDSDR that can detect kanamycin easily and quickly while ensuring that the results are effective and stable.

RESULTS

We created an enzyme-free fluorescent aptamer sensor with high specificity and sensitivity for detecting kanamycin in milk by taking advantage of EDSDR and the high specific binding between the target and its aptamer. The specific binding can result in the release of the promoter chain, which then sets off the pre-planned EDSDR cycle. Fluorescent label modification on DNA combined with the fluorescence quenching-recovery mechanism gives the sensor impressive fluorescence response capabilities. The research results showed that within the concentration range of 0.1 nM-50 nM, there was a good relationship between the fluorescence intensity of the solution and the concentration of kanamycin. Specificity experiments and actual sample detection experiments confirmed that the biosensor could achieve highly sensitive and specific detection of trace amounts of kanamycin in food, with a detection limit of 0.053 nM (S/N = 3).

SIGNIFICANCE

To our knowledge, this is the first strategy to combine EDSDR with fluorescence to detect kanamycin in food. Accurate results can be obtained in as little as 90 min with no enzymes or hairpins involved in the reaction. Furthermore, our enzyme-free biosensing method is straightforward, highly sensitive, and extremely specific. It has many possible applications, including monitoring antibiotic residues and food safety.

A fluorescent aptasensor for quantification of cocaine mediated by signal amplification characteristics of UiO-66/AuNPs nanocomposite

Due to the detrimental effects of cocaine on the human body such as organ damage, paranoia, immunodeficiency, cardiovascular disease, blood pressure, and stress, it is highly required to develop sensing approaches for its rapid and facile determination. Based on the signal enhancement capability of the UiO-66/AuNPs nanocomposite and acting as a capture agent, we designed a cost-effective fluorescent aptasensor for cocaine detection. The cocaine presence in the sample would cause a considerable escalation in the quenching of the fluorescence signal. The aptasensor achieved the linear response range over 0.5 μM-20 μM with a low detection limit of 0.178 μM. The selectivity of the designed aptasensing assay was successfully confirmed by examining several analgesic drugs. The aptasensor was employed for cocaine determination in human serum as the real samples. This method has a substantial benefit the for development of a low-cost and facile tool in medicine and forensic science.

A signal "on-off-on"-type electrochemiluminescence aptamer sensor for detection of sulfadimethoxine based on Ru@Zn-oxalate MOF composites

An "on-off-on"-type electrochemiluminescence (ECL) aptamer sensor based on Ru@Zn-oxalate metal-organic framework (MOF) composites is constructed for sensitive detection of sulfadimethoxine (SDM). The prepared Ru@Zn-oxalate MOF composites with the three-dimensional structure provide good ECL performance for the "signal-on." The MOF structure with a large surface area enables the material to fix more Ru(bpy)₃²⁺. Moreover, the Zn-oxalate MOF with three-dimensional chromophore connectivity provides a medium which can accelerate excited-state energy transfer migration among Ru(bpy)₃²⁺ units, and greatly reduces the influence of solvent on chromophore, achieving a high-energy Ru emission efficiency. The aptamer chain modified with ferrocene at the end can hybridize with the capture chain DNA1 fixed on the surface of the modified electrode through base complementary pairing, which can significantly quench the ECL signal of Ru@Zn-oxalate MOF. SDM specifically binds to its aptamer to separate ferrocene from the electrode surface, resulting in a "signal-on" ECL signal. The use of the aptamer chain further improves the selectivity of the sensor. Thus, high-sensitivity detection of SDM specificity is realized through the specific affinity between SDM and its aptamer. This proposed ECL aptamer sensor has good analytical performance for SDM with low detection limit (27.3 fM) and wide detection range (100 fM-500 nM). The sensor also shows excellent stability, selectivity, and reproducibility, which proved its analytical performance. The relative standard deviation (RSD) of SDM detected by the sensor is between 2.39 and 5.32%, and the recovery is in the range 97.23 to 107.5%. The sensor shows satisfactory results in the analysis of actual seawater samples, which is expected to play a role in the exploration of marine environmental pollution.

An aptamer-based colorimetric/SERS dual-mode sensing strategy for the detection of sulfadimethoxine residues in animal-derived foods

Residues of sulfadimethoxine (SDM) in animal-derived foods have attracted widespread public concern. Herein, we propose an aptamer-based colorimetric/SERS dual-mode sensing strategy for the determination of SDM based on hexadecyl trimethyl ammonium bromide (CTAB) induced aggregation of nanoparticles. In the absence of SDM, the SDM aptamer formed a supramolecular composite with CTAB, and the 4-mercaptopyrimidine functionalized gold nanoparticles (AuNPs@4-MPY) remained dispersed due to the lack of CTAB. Upon the addition of SDM, the SDM aptamer preferentially combined with SDM, resulting in the release of CTAB and subsequent aggregation of AuNPs@4-MPY, and the solution color changed from red to blue and presented a dynamic UV-absorbance curve based on different aggregation states. On the other hand, when, gold-silver core-shell nanoparticles (Au@AgNPs) were added additionally, the released CTAB narrowed the nanogap between AuNPs@4-MPY and Au@AgNPs, thus exhibiting enhanced SERS intensity of 4-MPY. This strategy achieved colorimetric detection of SDM with a linear range of 4.00-200.00 ng mL^-1 and a detection limit of 2.41 ng mL^-1, while SERS had a detection range of 1.20-120.00 ng mL^-1 with a detection limit of 0.89 ng mL^-1. This strategy is simple and cost-effective for the rapid detection of SDM within 20 minutes. It was further applied for the detection of SDM in spiked milk and honey samples with satisfactory recoveries. Therefore, it exhibits great potential for fast and on-site SDM detection.

Dual fluorescent aptasensor for simultanous and quantitative detection of sulfadimethoxine and oxytetracycin residues in animal-derived foods tissues based on mesoporous silica

Herein, we developed a dual fluorescent aptasensor based on mesoporous silica to simultaneously detect sulfadimethoxine (SDM) and oxytetracycline (OTC) in animal-derived foods. We immobilized two types of aptamers modified with FAM and CY5 on the silica surface by base complementary pairing reaction with the cDNA modified with a carboxyl group and finally formed the aptasensor detection platform. Under optimal conditions, the detection range of the aptasensor for SDM and OTC was 3-150 ng/mL (R ² = 0.9831) and 5-220 ng/mL (R ² = 0.9884), respectively. The limits of detection for SDM and OTC were 2.2 and 1.23 ng/mL, respectively. The limits of quantification for SDM and OTC were 7.3 and 4.1 ng/mL, respectively. Additionally, the aptasensor was used to analyze spiked samples. The average recovery rates ranged from 91.75 to 114.65% for SDM and 89.66 to 108.94% for OTC, and all coefficients of variation were below 15%. Finally, the performance and practicability of our aptasensor were confirmed by HPLC, demonstrating good consistency. In summary, this study was the first to use the mesoporous silica-mediated fluorescence aptasensor for simultaneous detection of SDM and OTC, offering a new possibility to analyze other antibiotics, biotoxins, and biomolecules.

A competitive colorimetric aptasensor for simple and sensitive detection of kanamycin based on terminal deoxynucleotidyl transferase-mediated signal amplification strategy

We developed a rapid and sensitive colorimetric biosensor based on competitive recognition between kanamycin (KAN), magnetic beads-kanamycin (MBs-KAN) and aptamer and terminal deoxynucleotidyl transferase (TdT)-mediated signal amplification strategy. In the absence of KAN, aptamers recognize MBs-KAN. TdT can amplify oligonucleotides to the 3'-OH ends of aptamers, with biotin-dUTP being embedded in the long single stranded DNA (ssDNA). Then the assay produced visual readout due to the horseradish peroxidase (HRP)-catalyzed color change of the substrate after the linkage between biotin and streptavidin (SA)-HRP. In the presence of KAN, however, aptamers tend to bind free KAN rather than MBs-KAN. In this case, aptamers are isolated by magnetic separation, resulting in the failure of signal amplification and catalytic signals. This competitive colorimetric sensor showed excellent selectivity toward KAN with the limit of detection (LOD) as low as 9 pM. And recovery values were between 93.8 and 107.8% when spiked KAN in milk and honey samples.

Novel Dual-Signal Electrochemiluminescence Aptasensor Involving the Resonance Energy Transform System for Kanamycin Detection

Based on luminol-capped Pt-tipped Au bimetallic nanorods (NRs) (L-Au-Pt NRs) as the anode emitter and SnS₂ quantum dots (QDs) hybrid Eu metal organic frameworks (MOFs) (SnS₂ QDs@Eu MOFs) as the cathode emitter, a dual-signal electrochemiluminescence (ECL) platform was designed for the ultrasensitive and highly selective detection of kanamycin (KAN). Using a dual-signal output mode, the ratiometric ECL aptasensor largely eliminates false-positives or false-negatives by self-calibration in the KAN assay process. To stimulate the resonance energy transform (RET) system, the KAN aptamer and complementary DNA are introduced for conjugation between the donor and acceptor. With the specific recognition of target KAN by its aptamer, L-Au-Pt NRs-apt partially peels off from the electrode surface. Eventually, the RET system is removed, leading to an increasing cathode signal and a decreasing anode signal. In view of this phenomenon, the ratiometric aptasensor can quantify KAN from 1 pM to 10 nM with a low detection limit of 0.32 pM. This dual-signal ECL aptasensor exhibits great practical potential in environmental monitoring and food safety.

Ultrasensitive electrochemical aptasensor based on palindromic sequence mediated bidirectional SDA and a DNAzyme walker for kanamycin detection

An electrochemical biosensing platform for kanamycin analysis based on SDA and a DNA walker.

Development of Electrochemical Aptasensor for Lung Cancer Diagnostics in Human Blood

We describe the preparation and characterization of an aptamer-based electrochemical sensor to lung cancer tumor markers in human blood. The highly reproducible aptamer sensing layer with a high density (up to 70% coverage) on the gold electrode was made. Electrochemical methods and confocal laser scanning microscopy were used to study the stability of the aptamer layer structure and binding ability. A new blocking agent, a thiolated oligonucleotide with an unrelated sequence, was applied to fill the aptamer layer’s defects. Electrochemical aptasensor signal processing was enhanced using deep learning and computer simulation of the experimental data array. It was found that the combinations (coupled and tripled) of cyclic voltammogram features allowed for distinguishing between the samples from lung cancer patients and healthy candidates with a mean accuracy of 0.73. The capacitive component from the non-Faradic electrochemical impedance spectroscopy data indicated the tumor marker’s presence in a sample. These findings allowed for the creation of highly informative aptasensors for early lung cancer diagnostics.

Aptamer-based diagnostic and therapeutic approaches in animals: Current potential and challenges

Fast and precise diagnosis of infectious and non-infectious animal diseases and their targeted treatments are of utmost importance for their clinical management. The existing biochemical, serological and molecular methods of disease diagnosis need improvement in their specificity, sensitivity and cost and, are generally not amenable for being used as points-of-care (POC) device. Further, with dramatic changes in environment and farm management practices, one should also arm ourselves and prepare for emerging and re-emerging animal diseases such as cancer, prion diseases, COVID-19, influenza etc. Aptamer – oligonucleotide or short peptides that can specifically bind to target molecules – have increasingly become popular in developing biosensors for sensitive detection of analytes, pathogens (bacteria, virus, fungus, prions), drug residues, toxins and, cancerous cells. They have also been proven successful in the cellular delivery of drugs and targeted therapy of infectious diseases and physiological disorders. However, the in vivo application of aptamer-mediated biosensing and therapy in animals has been limited. This paper reviews the existing reports on the application of aptamer-based biosensors and targeted therapy in animals. It also dissects the various modifications to aptamers that were found to be successful in in vivo application of the aptamers in diagnostics and therapeutics. Finally, it also highlights major challenges and future directions in the application of aptamers in the field of veterinary medicine.

Contribution of Nanomaterials to the Development of Electrochemical Aptasensors for the Detection of Antimicrobial Residues in Food Products

The detection of antimicrobial residues in food products of animal origin is of utmost importance. Indeed antimicrobial residues could be present in animal derived food products because of animal treatments for curative purposes or from illegal use. The usual screening methods to detect antimicrobial residues in food are microbiological, immunological or physico-chemical methods. The development of biosensors to propose sensitive, cheap and quick alternatives to classical methods is constantly increasing. Aptasensors are one of the major trends proposed in the literature, in parallel with the development of immunosensors based on antibodies. The characteristics of electrochemical sensors (i.e., low cost, miniaturization, and portable instrumentation) make them very good candidates to develop screening methods for antimicrobial residues in food products. This review will focus on the recent advances in the development of electrochemical aptasensors for the detection of antimicrobial residues in food products. The contribution of nanomaterials to improve the performance characteristics of electrochemical aptasensors (e.g., Sensitivity, easiness, stability) in the last ten years, as well as signal amplification techniques will be highlighted.

Recent Advances in Aptamer Sensors

Recently, aptamers have attracted attention in the biosensing field as signal recognition elements because of their high binding affinity toward specific targets such as proteins, cells, small molecules, and even metal ions, antibodies for which are difficult to obtain. Aptamers are single oligonucleotides generated by in vitro selection mechanisms via the systematic evolution of ligand exponential enrichment (SELEX) process. In addition to their high binding affinity, aptamers can be easily functionalized and engineered, providing several signaling modes such as colorimetric, fluorometric, and electrochemical, in what are known as aptasensors. In this review, recent advances in aptasensors as powerful biosensor probes that could be used in different fields, including environmental monitoring, clinical diagnosis, and drug monitoring, are described. Advances in aptamer-based colorimetric, fluorometric, and electrochemical aptasensing with their advantages and disadvantages are summarized and critically discussed. Additionally, future prospects are pointed out to facilitate the development of aptasensor technology for different targets.

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

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

Determination of sulfadimethoxine in milk with aptamer-functionalized Fe3 O4 /graphene oxide as magnetic solid-phase extraction adsorbent prior to HPLC

An aptamer (Apt) functionalized magnetic material was prepared by covalently link Apt to Fe₃ O₄ /graphene oxide (Fe₃ O₄ /GO) composite by 1-ethyl-3-(3-dimethylaminopropyl) carbodiimide hydrochloride and N-hydroxysuccinimide, and then characterized by FTIR spectroscopy, X-ray diffraction, and vibration sample magnetometry. The obtained composite of Fe₃ O₄ /GO/Apt was employed as magnetic solid-phase extraction adsorbent for the selective preconcentration of sulfadimethoxine prior to analysis by high-performance liquid chromatography. Under the optimal conditions (sample pH of 4.0, sorbent dosage of 20 mg, extraction time of 3 h, and methanol-5% acetic acid solution as eluent), a good linear relationship was obtained between the peak area and concentration of sulfadimethoxine in the range of 5.0 to 1500.0 µg/L with correlation coefficient of 0.9997. The limit of detection (S/N = 3) was 3.3 µg/L. The developed method was successfully applied to the analysis of sulfadimethoxine in milk with recoveries in the range of 75.9-92.3% and relative standard deviations less than 8.1%. The adsorption mechanism of Fe₃ O₄ /GO/Apt toward sulfadimethoxine was studied through the adsorption kinetics and adsorption isotherms, and the results show that the adsorption process fits well with the pseudo-second-order kinetic model and the adsorbate on Fe₃ O₄ /GO/Apt is multilayer and heterogeneous.

A novel strategy for detection of small molecules based on aptamer/gold nanoparticles/graphitic carbon nitride nanosheets as fluorescent biosensor

Herein, a novel ultrasensitive strategy has been developed by designing a label free fluorescent nano-aptasensor for monitoring of small moecules in human plasma. In this nano-aptasensor, graphitic carbon nitride nanosheets were used as fluorescent probe. The fluorescence intensity of the probe was decreased by interaction between graphitic carbon nitride nanosheets and label-free aptamer/gold nanoparticles conjugate, via Fluorescence resonance energy transfer mechanism. Upon addition of the analyte, the fluorescence of graphitic carbon nitride nanosheets was restored due to the aptamer/analyte interaction, and the aggregation of gold nanoparticles in the presence of salt. The influence of various factors on sensing method was investigated, and under the approved conditions, the fluorescence signal showed a linear relation with Digoxin concentration in the range of 10-500 ng L^-1 with limit of detection down to 3.2 ng L^-1 relative standard deviations for 25, 100 and 500 ng L^-1 of analyte concentrations were 2.6, 4.0 and 6.5%, respectively. This strategy provided a simple, rapid, cost effective and reproducible experimental model, with successful application for determination of Digoxin in plasma samples without any pretreatment steps.

Computer-Aided aptamer design for sulfadimethoxine antibiotic: step by step mutation based on MD simulation approach

This study introduces a computational method to design a new aptamer with higher binding affinity to a special target in comparison with the experimentally available aptamers. The method is called step by step mutation based on MD simulation, which includes some steps. First, MD simulation is performed for the SELEX-introduced (native) aptamer in the presence of the target. Afterwards, conformational factor (P_i) is calculated for the simulated system, which obtains the affinity of the aptamer residues to the target. A nucleotide exchange is done for the residue with the least P_i parameter to the nucleotide with the highest P_i value that results in a mutant aptamer. MD simulation is performed for the target-mutant complex, and P_i values are calculated again. The nucleotide exchange is performed similarly, and the designing process is proceeded repeatedly that results in a mutant with the improved specificity to the target. The aptamer affinity to the target is also determined in each step through calculating the binding Gibbs energy (ΔG_Bind) as a reliable parameter. The introduced strategy is utilized efficiently to design a mutant aptamer with improved specificity toward sulfadimethoxine (SDM) antibiotic as a case study. The great difference in the ΔG_Bind values about 579.856 kJ mol^-1 highlights that the M5 mutant possesses the improved specificity toward SDM in comparison with the native aptamer. Besides, the selectivity of the M5 aptamer toward SDM is examined among some conventional interfering compounds by using MD simulation that confirms the applicability of the designed aptamer for further experimental studies.

Highly efficient fluorescence sensing of kanamycin using Endo IV-powered DNA walker and hybridization chain reaction amplification

An ultrasensitive fluorescence sensing strategy for kanamycin (KANA) determination using endonuclease IV (Endo IV)-powered DNA walker, and hybridization chain reaction (HCR) amplification was reported. The sensing system consists of Endo IV-powered 3D DNA walker using for the specific recognition of KANA and the formation of the initiators, two metastable hairpin probes as the substrates of HCR and a tetrahydrofuran abasic site (AP site)-embeded fluorescence-quenched probe for fluorescence signal output. On account of this skilled design of sensing system, the specific binding between KANA and its aptamer activates DNA walker, in which the swing arm can move autonomously along the 3D track via Endo IV-mediated hydrolysis of the anchorages, inducing the formation of initiators that initiates HCR and the following Endo IV-assisted cyclic cleavage of fluorescence reporter probes. The use of Endo IV offers the advantages of simplified and accessible design without the need of specific sequence in DNA substrates. Under the optimal experimental conditions, the fluorescence biosensor shows excellent sensitivity toward KANA detection with a detection limit as low as 1.01 pM (the excitation wavelength is 486 nm). The practical applicability of this strategy is demonstrated by detecting KANA in spiked milk samples with recovery in the range of 98 to 102%. Therefore, this reported strategy might create an accurate and robust fluorescence sensing platform for trace amounts of antibiotic residues determination and related safety analysis. Graphical abstract Highly efficient fluorescence sensing of kanamycin using Endo IV-powered DNA Walker and hybridization chain, reaction amplification, Xiaonan Qu, Jingfeng Wang, Rufeng Zhang, Yihan Zhao, Shasha Li, Yu Wang, Su Liu*, Jiadong Huang, and Jinghua Yu, an ultrasensitive fluorescence sensing strategy for kanamycin determination using endonuclease IV-powered DNA walker, and hybridization chain reaction amplification is reported.