Development of sensitive colorimetric aptasensor based on short DNA aptamer and its application to screening for paraquat residues in agricultural soil.

Paraquat is a widely used herbicide for controlling weeds and grasses in agriculture, and its contaminated residues in agricultural areas are of increasing concern. This work reports the development of the sensitive and easy-to-use colorimetric aptasensor for screening paraquat residues in agricultural soil. The short DNA fragments derived from the original aptamer were analyzed for their capability to interact with paraquat by molecular dynamic simulation. The paraquat-aptasensor was developed using the selected DNA fragment and gold nanoparticles. Its limit of detection (LOD) for paraquat is 2.76 nM, which is more sensitive than the aptasensor with long-length aptamer (LOD = 12.98 nM). The developed aptasensor shows the selectivity to paraquat, but not to other tested herbicides; ametryn, atrazine, difenzoquat, 2,4-D-dimethyl ammonium, and glufosinate. The recovery rates of paraquat detection in the spiked soil samples were in a range of 99.5%-105.1%, with relative standard deviation values of <4%. The developed aptasensor was used to screen for paraquat residues in agricultural soils, and three out of 23 soil samples were tested positive for paraquat, which was confirmed by a high-performance liquid chromatography analysis. These results suggested the potential application of the developed aptasensor to detect paraquat residues in agricultural sites.

Insight into the Covalently Oriented Immobilization of Antibodies on Gold Nanoparticle Probes to Improve Sensitivity in the Colorimetric Detection of Listeria monocytogenes.

In this work, the covalently oriented conjugation of monoclonal Listeria monocytogenes antibody (mAb-Lis) to amino-terminated oligo(ethylene glycol)-capped gold nanoparticles (NH2-TEG-AuNPs) was studied. After NH2-TEG-AuNPs were synthesized, the amino-terminated ligands on the particles were then linked to the carboxyl groups in the mAb-Lis through EDC/NHS chemistry. By maintaining the pH of the solution at ∼5, the Fc region of the antibody could preferably attach to the particle surface, providing a specific Fab region that was available for binding with the target pathogen. The resulting mAb-NH-TEG-AuNPs could act as a colorimetric probe for L. monocytogenes based on a particular antigen-antibody interaction, which resulted in a drastic aggregation of particles. This caused the color of the colloidal solution to transition from red-pink to purple or even gray depending on the pathogen concentration. To perform quantitative analysis, the absorbance ratio of A650/A534 was monitored as a function of L. monocytogenes concentration using a spectrophotometer. The detection limit was very low at 11 CFU/mL. Furthermore, a lateral flow strip (LFS) was fabricated as a portable device for onsite utilization. LFS detection could be completed by the naked eye and by a smartphone. The detection limit of LFS was estimated to be 103 CFU/mL. Our methods exhibited a substantial improvement in sensitivity compared to that of previous studies on immuno-based nanoparticles. The assay could be completed in 15 min, and no cross reactivity by any pathogen was found. Hence, the designed AuNPs exhibit great promise for use in monitoring L. monocytogenes for food safety and in other applications.

Insight into the Molecular Mechanisms of AuNP-Based Aptasensor for Colorimetric Detection: A Molecular Dynamics Approach.

Colorimetric aptasensor based on assembly of salt-induced gold nanoparticles (AuNPs) is a promising biosensor. However, the molecular mechanism of the aptasensor is far from being fully understood. Herein, molecular dynamics (MD) simulation was used to investigate molecular interactions in the detection of ochratoxin A (OTA) including the following: (i) the molecular recognition of the anti-OTA aptamer, (ii) OTA-aptamer interactions in monovalent (Na+) and divalent (Mg2+) electrolytes, (iii) the binding mode of citrate on the AuNP surface, (iv) interactions of the aptamer with citrate-capped AuNPs, and (v) a detailed mechanism of the aptasensor. Our MD simulations revealed a specific binding of the OTA-aptamer complex, compared with OTB and warfarin. Compared with Na+, Mg2+ ions exerted a more effective attractive force between OTA and anti-OTA aptamer. Three different binding modes of citrate on AuNP surfaces were found. The kinetics of the adsorption of unfolded aptamers onto the citrate-capped AuNP was also elucidated. Most importantly, our MD simulation revealed an insightful analysis of the molecular mechanisms in the AuNP-based aptasensor and paved the way for the design of a novel colorimetric aptasensor for other target molecules, which is not limited to OTA detection.

Multifunctional fluorescent Eu-MOF probe for tetracycline antibiotics and dihydrogen phosphate sensing and visualizing latent fingerprints.

The contamination of tetracycline antibiotics and dihydrogen phosphate (H2PO4 -) in food and the environment is one of the major concerns for human health. Herein, a water-stable carboxyl-functionalized europium metal-organic framework (Eu-MOF) was prepared and demonstrated, for the first time, as a dual-responsive fluorescent sensor of tetracycline antibiotics (oxytetracycline (OTC), tetracycline (TC), and doxycycline (DOX)) and H2PO4 - via fluorescent turn-on and turn-off, respectively. Eu-MOF presents a sensitive and selective detection of OTC with a rapid response time (1 min) and good anti-interference ability. The limits of detection (LODs) of 78 nm, 225 nm, and 201 nM were achieved for OTC, TC, and DOX, respectively. Coordination and hydrogen bonding led to energy and electron transfer from the TC to the MOF, contributing to the fluorescent enhancement mechanism. Moreover, Eu-MOF can effectively detect H2PO4 - via fluorescence turn-off with a LOD of 0.70 µM. The interactions between H2PO4 - and MOF interrupt the energy transfer from ligand to MOF, leading to fluorescence quenching. In addition, Eu-MOF was successfully applied to determine OTC and H2PO4 - in real samples, obtaining satisfactory recoveries and RSDs. More fascinating, Eu-MOF could be utilized to develop latent fingerprints on various surfaces, providing well-defined fluorescent fingerprint details in which the sweat pores can be seen with the naked eye.

Dual-Responsive Carbon Quantum Dots for the Simultaneous Detection of Cytosine and 5-Methylcytosine Interpreted by a Machine Learning-Assisted Smartphone.

DNA methylation is an epigenetic alteration that results in 5-methylcytosine (5-mC) through the addition of a methyl group to the fifth carbon of a cytosine (C) residue. The methylation level, the ratio of 5-mC to C, in urine might be related to the whole-body epigenetic status and the occurrence of common cancers. To date, never before have any nanomaterials been developed to simultaneously determine C and 5-mC in urine samples. Herein, a dual-responsive fluorescent sensor for the urinary detection of C and 5-mC has been developed. This assay relied on changes in the optical properties of nitrogen-doped carbon quantum dots (CQDs) prepared by microwave-assisted pyrolysis. In the presence of C, the blue-shifted fluorescence intensity of the CQDs increased. However, fluorescence quenching was observed upon the addition of 5-mC. This was primarily due to photoinduced electron transfer as confirmed by the density functional theory calculation. In urine samples, our sensitive fluorescent sensor had detection limits for C and 5-mC of 43.4 and 74.4 µM, respectively, and achieved satisfactory recoveries ranging from 103.5 to 115.8%. The simultaneous detection of C and 5-mC leads to effective methylation level detection, achieving recoveries in the range of 104.6-109.5%. Besides, a machine learning-enabled smartphone was also developed, which can be effectively applied to the determination of methylation levels (0-100%). These results demonstrate a simple but very effective approach for detecting the methylation level in urine, which could have significant implications for predicting the clinical prognosis.

Rapid detection of cancer DNA in human blood using cysteamine-capped AuNPs and a machine learning-enabled smartphone.

DNA methylation occurs when a methyl group is added to a cytosine (C) residue's fifth carbon atom, forming 5-methylcytosine (5-mC). Cancer genomes have a distinct methylation landscape (Methylscape), which could be used as a universal cancer biomarker. This study developed a simple, low-cost, and straightforward Methylscape sensing platform using cysteamine-decorated gold nanoparticles (Cyst/AuNPs), in which the sensing principle is based on methylation-dependent DNA solvation. Normal and cancer DNAs have distinct methylation profiles; thus, they can be distinguished by observing the dispersion of Cyst/AuNPs adsorbed on these DNA aggregates in MgCl2 solution. After optimising the MgCl2, Cyst/AuNPs, DNA concentration, and incubation time, the optimised conditions were used for leukemia screening, by comparing the relative absorbance (ΔA 650/525). Following the DNA extraction from actual blood samples, this sensor demonstrated effective leukemia screening in 15 minutes with high sensitivity, achieving 95.3% accuracy based on the measurement by an optical spectrophotometer. To further develop for practical realisation, a smartphone assisted by machine learning was used to screen cancer patients, achieving 90.0% accuracy in leukemia screening. This sensing platform can be applied not only for leukemia screening but also for other cancers associated with epigenetic modification.

Aptamer-based colorimetric detection of the DNA damage marker 8-oxo-dG using cysteamine-stabilised gold nanoparticles.

8-Oxo-7,8-dihydro-2'-deoxyguanosine (8-oxo-dG) is a crucial biomarker for oxidative DNA damage and carcinogenesis. Current strategies for 8-oxo-dG detection often require sophisticated instruments and qualified personnel. In this study, cysteamine-stabilised gold nanoparticles (cyst-AuNPs) were synthesised and used for colorimetric detection of 8-oxo-dG in urine. Sensing of 8-oxo-dG is based on the anti-aggregation of cyst-AuNPs, mediated by the specific recognition of 8-oxo-dG and its aptamer. In the absence of 8-oxo-dG, the aptamer was adsorbed onto the surface of cyst-AuNPs, resulting in aggregation and the development of a purple colour solution. Upon addition of the target molecule 8-oxo-dG, the aptamer specifically bound to it and could not induce the aggregation of cyst-AuNPs, leading to the dispersion of cyst-AuNPs in the solution. Simple visual examination could be used to monitor the purple-to-red colour change that started at 12 nM, a threshold concentration for visual analysis. The absorbance at 525 nm increased in direct relation to the number of the target molecule 8-oxo-dG. This aptamer/cyst-AuNPs system showed excellent sensing ability for the 8-oxo-dG concentration in the range of 15-100 nM, with a detection limit as low as 10.3 nM and a detection time of 30 min. Interference experiments showed that the developed colorimetric strategy had a good sensitivity. This simple and rapid colorimetric method has successfully been applied to inspect 8-oxo-dG concentration in real urine samples and provided recoveries between 93.6 and 94.1%, with a limit of quantification (LOQ) of 34.3 nM, which was comparable with an enzyme-linked immunosorbent-based detection of 8-oxo-dG. This new, easy-to-use, and rapid method could be used as an alternative and initiative strategy for the development of an on-site analysis of 8-oxo-dG in urine.

Computational Insights into Molecular Adsorption Characteristics of Methylated DNA on Graphene Oxide for Multicancer Early Detection.

DNA methylation is an epigenetic modification involving the transfer of a methyl group to cytosine residues of a DNA molecule. Altered DNA methylation of certain genes is associated with several diseases including cancer. Nanomaterials, such as graphene oxide (GO), offer great potential as sensing elements for methylated DNA (mDNA) detection due to their distinct properties. Understanding molecular interactions between mDNA and GO can make provision for developing a universal cancer screening test. Molecular dynamics (MD) simulation and density functional theory (DFT) calculation have been employed for investigating their detailed macro- and microscale interactions. Based upon the MD simulation, different adsorption levels of methylated and unmethylated DNAs on GO were represented by a contacting surface area (CSA), which depends on surrounding conditions (in water or a MgCl2 solution). In water, the CSAs of the methylated and unmethylated single-stranded DNA (ssDNA) were ≈13 and ≈5 nm2, respectively, representing more preferable adsorption on GO for the methylated ssDNA. In the presence of divalent ions (Mg2+), the CSAs of both methylated and unmethylated DNA molecules were ≈8 nm2, suggesting that there was no significant difference in adsorption in a saline solution. To reveal the electrical property of GO covered by either methylated or unmethylated DNA, its electronic structure was investigated by the DFT calculation. The energy gaps of pristine graphene (pG) and GO adsorbed by 5-methylcytosine (5mC) were 1.6 and 12.9 meV, respectively, while cytosine adsorption resulted in lower energy gaps (1.2 meV for pG and 9.5 meV for GO). When comparing methylated DNA-covered GO with that covered with unmethylated DNA, remarkable differences in electrical conductivity, which were caused by the electronic structure of GO, were observed. These findings will provide a new route for an efficient detection method of DNA methylation, which can further be used to develop a universal cancer test.

pH modulated luminescent switching and discriminative detection of amino acid based on metal-organic framework.

The detection of glutamic (Glu) or aspartic (Asp) acids is vital for human nutrition and diagnosis of disease. Herein, the dht ligand containing hydroxy group (-OH) is used to design and synthesize a 2D luminescent [Cd2(idc)(dht)(H2O)4] (1); H2idc = 4,5-imidazoledicarboxylic acid and H2dht = 2,5-dihydroxyterephthalic acid for sensing amino acids. The compound 1 can discriminatively detect Asp and Glu among other amino acids through blue-shifted emission (yellow → green). The dual sensing mechanism may be attributed to the intermolecular excited-state proton transfer between MOF and water to produce keto form along with the subsequent switching of keto form to enol form by protonation causing the increased band gap energy. This material can serve several benefits in terms of high selectivity, fast response (30s), good reproducibility and low LOD value of 11.34 µM which is less than the harmful concentration of Glu for human health (>400 µM). In addition, 1 shows the broad range detection of Glu covering in safe and unsafe levels. For on-site detection of Glu, MOF-based paper is devised and can be applied through color-scanning application in smartphone. Besides, this sensor can serve to detect Glu in real samples with good recovery.

Role of Surface Functionalization on Cellular Uptake of AuNPs Characterized by Computational Microscopy.

A surface modification of nanoparticles (NPs) provides an effective way to control their interactions with living cells. The complete understanding of interactions between NPs and a cell membrane is a key step for the development of drug delivery. In the present work, the role of different surface charges (anionic, cationic, and zwitterionic) on the internalization through an idealized plasma membrane was investigated using a coarse-grained molecular dynamics (CGMD) technique. The decorated AuNPs used in this in silico study closely imitated those experimentally synthesized, while the idealized plasma membrane model resembled that found in living cells. The mechanism of direct translocation of a 2 nm particle by membrane was observed. The zwitterionic AuNP demonstrates a higher free-energy barrier than the positively and negatively charged AuNPs, resulting in a lack of preference for internalization across the membrane, leading to lower translocation rate and permeability of internalization. Despite the surface coverage, the agglomeration of AuNPs in a physiological condition has been observed resulting in slow unfavorable permeability. Our study highlights that in addition to surface charges, the hydrodynamic size (DH) plays an important role in the permeability of the functionalized AuNPs into the cell membrane. Through our simulations, complete understanding of interactions between ligands-coated AuNPs and the realistic plasma membrane has been established serving as a platform for the novel design of AuNPs in nanomedicine applications.

Development of Low-Cost AuNP-Based Aptasensors with Truncated Aptamer for Highly Sensitive Detection of 8-Oxo-dG in Urine.

8-Oxo-7,8-dihydro-2'-deoxyguanosine (8-oxo-dG), an oxidized form of guanosine residues, is a critical biomarker for various cancers. Herein, a sensitive citrate-capped gold nanoparticle-based aptasensor device has been developed for the detection of 8-oxo-dG in urine. We previously designed a 38-nt anti-8-oxo-dG-aptamer by a computer simulation and the experimental validation has been performed in the present work. The analytical performance of the 38-nt aptamer from the in silico design was compared with the parent 66-nt aptamer. This assay is based on the principle of salt-induced aggregation of citrate-capped gold nanoparticles. Based on this sensing mechanism, the difference between the absorbance in the presence and absence of 8-oxo-dG at λ = 525 nm (ΔA525) increased linearly as a function of 8-oxo-dG concentrations in the ranges of 10-100 and 15-100 nM for 38-nt and 66-nt aptasensors, respectively. This method can provide detection limits of 6.4 nM for 8-oxo-dG in the 38-nt aptasensor and 13.2 nM in the 66-nt aptasensor. Similar to the 66-nt aptamer, the shortened aptamer, 38-nt long, can provide high sensitivity and selectivity with rapid detection time. In addition, using the 38-nt aptamer as a recognition component in the developed portable low-cost device showed high sensitivity in the detection range of 15-100 nM with a detection limit of 12.9 nM, which is much lower than the threshold value (280 nM) for normal human urine. This easy-to-use device could effectively and economically be utilized for monitoring 8-oxo-dG in real urine samples and potentially serve as a prototype for a commercial device.

Combined in silico and in vitro study of an aptasensor based on citrate-capped AuNPs for naked-eye detection of a critical biomarker of oxidative stress.

An elevated level of 8-oxo-7,8-dihydro-2'-deoxyguanosine (8-oxo-dG) in biosamples has been found to correlate to oxidative stress, and it has been assigned as a critical biomarker of various diseases. Herein, insights into the mechanisms of an aptasensor, based on citrate-capped gold nanoparticles (AuNPs), for 8-oxo-dG detection were elucidated using molecular dynamics (MD) simulations and validated experimentally. We found that the binding mechanism for binding between the anti-8-oxo-dG aptamer and 8-oxo-dG has the following characteristic stages: (i) adsorption stage, (ii) binding stage, and (iii) complex stabilization stage. Our simulations also reveal the binding sites between the anti-8-oxo-dG aptamer and 8-oxo-dG formed through hydrogen bonding during complex formation. A shortened anti-8-oxo-dG-aptamer was also engineered using in silico design, which was expected to improve the analytical performance of the colorimetric aptasensor. The mechanisms of the colorimetric aptasensor in the presence and absence of 8-oxo-dG were also investigated, and found to be in good agreement with the experiments. Complete understanding of the mechanism of the colorimetric aptasensor would open the door for development of novel naked-eye aptasensors.

Designing an Aptasensor Based on Cysteamine-Capped AuNPs for 8-Oxo-dG Detection: A Molecular Dynamics Approach and Experimental Validation.

The concentration of 8-oxo-7,8-dihydro-2'-deoxyguanosine (8-oxo-dG) in urine or serum is associated with the degree of oxidative damage of DNA and broadly used as a sensitive biomarker for various diseases. However, determination of a low concentration of 8-oxo-dG in biosamples is not an easy task owing to the complexity of coexisting substances. Herein, we design an aptasensor based on aptamer-mediated aggregation of cysteamine-capped gold nanoparticles (Cyst/AuNPs) for the detection of 8-oxo-dG by molecular dynamics simulation. Our simulations reveal that a positively charged Cyst modified onto the surfaces of AuNP exists in two conformers including gauche and trans. The trans conformer was prevalent on the AuNP surfaces and can stabilize AuNPs in the aqueous solution, even in the presence of 8-oxo-dG. Molecular recognition between 8-oxo-dG and the aptamer was demonstrated and bonding between these biomolecules was thoroughly elucidated. During the complex formation, van der Waals stacking interactions between 8-oxo-dG molecules were observed and found to play a significant role in the binding stability. The sensing mechanism of the colorimetric aptasensor was studied and the feasibility study of the proposed aptasensor was assessed by experimental validation. The experimental results are in good agreement with the computational study. Our in silico design can pave the way for, but is not limited to, a highly sensitive aptasensor for the naked-eye detection of 8-oxo-dG.

Capture Efficiency of Biocompatible Magnetic Nanoparticles in Arterial Flow: A Computer Simulation for Magnetic Drug Targeting.

The primary limitation of magnetic drug targeting (MDT) relates to the strength of an external magnetic field which decreases with increasing distance. Small nanoparticles (NPs) displaying superparamagnetic behaviour are also required in order to reduce embolization in the blood vessel. The small NPs, however, make it difficult to vector NPs and keep them in the desired location. The aims of this work were to investigate parameters influencing the capture efficiency of the drug carriers in mimicked arterial flow. In this work, we computationally modelled and evaluated capture efficiency in MDT with COMSOL Multiphysics 4.4. The studied parameters were (i) magnetic nanoparticle size, (ii) three classes of magnetic cores (Fe3O4, Fe2O3, and Fe), and (iii) the thickness of biocompatible coating materials (Au, SiO2, and PEG). It was found that the capture efficiency of small particles decreased with decreasing size and was less than 5 % for magnetic particles in the superparamagnetic regime. The thickness of non-magnetic coating materials did not significantly influence the capture efficiency of MDT. It was difficult to capture small drug carriers (D<200 nm) in the arterial flow. We suggest that the MDT with high-capture efficiency can be obtained in small vessels and low-blood velocities such as micro-capillary vessels.

Circular dichroism sensor based on cadmium sulfide quantum dots for chiral identification and detection of penicillamine.

A new chemical sensor based on the measuring of circular dichroism signal (CD) was fabricated from cysteamine capped cadmium sulfide quantum dots (Cys-CdS QDs). The chiral-thiol molecules, d-penicillamine (DPA) and l-penicillamine (LPA), were used to evaluate potentials of this sensor. Basically, DPA and LPA provide very low CD signals. However, the CD signals of DPA and LPA can be enhanced in the presence of Cys-CdS QDs. The CD spectra of DPA and LPA exhibited a mirror image profile. Parameters affecting the determination of DPA and LPA were thoroughly investigated in details. Under the optimized condition, the CD signals of DPA and LPA displayed a linear relationship with the concentrations of both enantiomers, ranging from 1 to 35 µM. Detection limits of this sensor were 0.49 and 0.74 µM for DPA and LPA, respectively. To demonstrate a potential application of this sensor, the proposed sensor was used to determine DPA and LPA in real urine samples. It was confirmed that the proposed detection technique was reliable and could be utilized in a broad range of applications.