Label-free fluorescent aptasensor berberine-based strategy for ultrasensitive detection of Hg2+ ion

Fluorescent aptasensors for sensitive detection of lead ions based on structure-switching DNA beacon probe and exonuclease I-mediated signal amplification

Herein, two simple fluorescent signal-on sensing strategies for detecting lead ions (Pb2+) were established based on structure-switching aptamer probes and exonuclease-assisted signal amplification strategies. Two hairpin-structure fluorescent probes with blunt-ended stem arms were designed by extending the base sequence of Pb2+ aptamer (PS2.M) and labelling the probes with FAM (in probe 1) and 2-aminopurine (2-AP) (in probe 2), respectively. In method 1, graphene oxide (GO) was added to adsorb probe 1 and quench the fluorescence emission of FAM to achieve low fluorescent background. In method 2, fluorescent 2-AP molecule inserted into the double-stranded DNA of probe 2 was quenched as a result of base stacking interactions, leading to a simplified, quencher-free approach. The addition of Pb2+ can induce the probes to transform into G-quadruplex structures, exposing single DNA strands at the 3' end (the extended sequences). This exposure enables the activation of exonuclease I (Exo I) on the probes, leading to the cleavage effect and subsequent release of free bases and fluorophores, thereby resulting in amplified fluorescence signals. The two proposed methods exhibit good specificity and sensitivity, with detection limits of 0.327 nM and 0.049 nM Pb2+ for method 1 and method 2, respectively, and have been successfully applied to detect Pb2+ in river water and fish samples. Both detection methods employ the structure-switching aptamer probes and can be completed in two or three steps without the need for complex analytical instruments. Therefore, they have a broad prospect in the sensitive and simple detection of lead ion contamination in food and environmental samples.

Comparison of Double-Stranded DNA at the 5' and 3' Ends of the G-Triplex and Its Application in the Detection of Hg(II)

Leveraging the fluorescence enhancement effect of the G-triplex (G3)/thioflavin T (ThT) catalyzed by the adjacent double-stranded DNA positioned at the 5' terminus of the G3, the G3-specific oligonucleotide (G3MB6) was utilized to facilitate the rapid detection of mercury (Hg(II)) through thymine-Hg(II)-thymine (T-Hg(II)-T) interactions. G3MB6 adopted a hairpin structure in which partially complementary strands could be disrupted with the presence of Hg(II). It prompted the formation of double-stranded DNA by T-Hg(II)-T, inducing the unbound single strand of G3MB6 to spontaneously form a parallel G3 structure, producing a solid fluorescence signal by ThT. Conversely, fluorescence was absent without Hg(II), since no double strand and formation of G3 occurred. The fluorescence intensity of G3MB6 exhibited a positive correlation with Hg(II) concentrations from 17.72 to 300 nM (R2 = 0.9954), boasting a notably low quality of limitation (LOQ) of 17.72 nM. Additionally, it demonstrated remarkable selectivity for detecting Hg(II). Upon application to detect Hg(II) in milk samples, the recovery rates went from 100.3% to 103.2%.

Mercury (II) sensing using a simple turn-on fluorescent graphene oxide based aptasensor in serum and water samples

A simple, highly sensitive, and selective fluorometric aptasensing platform based on aptamer and graphene oxide (GO) is proposed for the determination of mercury (II) ion (Hg2+). In the designed assay, two aptamer probes, a carboxy-fluorescein (FAM) labeled aptamer (aptamer A) and its complementary (aptamer B) with partial complement containing several mismatches and GO as the quencher were used. In the absence of Hg2+, both A and B aptamers were adsorbed on the surface of GO by π-π-stacking, leading to fluorescence quenching of FAM due to fluorescence resonance energy transfer (FRET). Upon exposure to Hg2+, the A and B aptamer strands bind Hg2+ and form T-Hg2+-T complexes, leading to the formation of a stable double-stranded aptamer. The double-stranded aptamer is detached from the GO surface, resulting in the recovery of FAM fluorescence. The fluorescence intensity (FI) of the developed sensor was correlated with the Hg2+ concentration under optimized experimental conditions in two wide linear ranges, even in the presence of 10 divalent cations as interferences. The linear ranges were obtained from 200.0 to 900.0 fM and 5.0 to 33.0 pM, a limit of detection (LOD) of 106.0 fM, and a limit of quantification (LOQ) of 321.3 fM. The concentration of Hg2+ was determined in five real samples containing three water and two serum samples, using spiking and standard addition methods and the results were compared with the spiked amounts and atomic absorption (AAS) as standard method respectively, with acceptable recoveries. Furthermore, in the standard addition method, to overcome the effects of matrix influence of real samples in quantitative predictions, the excitation-emission matrix (EEM) data for samples was simultaneously analyzed by multivariate curve resolution with alternating least squares (MCR-ALS) as a second-order standard addition method (SOSAM).

Development of a split G-quadruplex and DAPI-based fluorescent probe for Hg(II) and Pb(II) ions detection

A novel thymine- and guanine-rich oligonucleotide (ODN-7) was engineered explicitly for the detection of Hg(II) and Pb(II) by a single intercalated dye 4',6-diamidinyl-2-phenylindole (DAPI). Upon the introduction of Hg(II), a rapid formation of T-Hg(II)-T base pairs takes place, triggering the assembly of a split G-quadruplex structure, resulting in a strong fluorescence signal due to DAPI intercalating into the T-Hg(II)-T mismatch. The introduction of Pb(II) initiates an interaction with the split G-quadruplex, causing a significant conformational change in its structure. Consequently, the altered split G-quadruplex structure fails to facilitate the insertion of DAPI into the T-Hg(II)-T complexes, leading to fluorescence quenching. This strategy offers a straightforward means of detecting Hg(II) and Pb(II). Leveraging the split G-quadruplex, the ODN-7 sensor enables the detection limits (3σ) for Hg(II) and Pb(II) to reach an impressive low of 0.39 nM and 4.98 nM, respectively. It exhibited a favorable linear range of 0.39-900 nM for Hg(II) detection (R2 = 0.9993) and 4.98 nM-5 μM for Pb(II) determination (R2 = 0.9953), respectively. Furthermore, the proposed sensor had excellent selectivity for detecting Hg(II) and Pb(II). It was used in milk samples containing mixed Hg(II) and Pb(II) solutions, yielding recovery rates of 99.3-103.8% for Hg(II) detection and 100.1-104.1% for Pb(II) detection.

LABAMPsGCN: A framework for identifying lactic acid bacteria antimicrobial peptides based on graph convolutional neural network

Lactic acid bacteria antimicrobial peptides (LABAMPs) are a class of active polypeptide produced during the metabolic process of lactic acid bacteria, which can inhibit or kill pathogenic bacteria or spoilage bacteria in food. LABAMPs have broad application in important practical fields closely related to human beings, such as food production, efficient agricultural planting, and so on. However, screening for antimicrobial peptides by biological experiment researchers is time-consuming and laborious. Therefore, it is urgent to develop a model to predict LABAMPs. In this work, we design a graph convolutional neural network framework for identifying of LABAMPs. We build heterogeneous graph based on amino acids, tripeptide and their relationships and learn weights of a graph convolutional network (GCN). Our GCN iteratively completes the learning of embedded words and sequence weights in the graph under the supervision of inputting sequence labels. We applied 10-fold cross-validation experiment to two training datasets and acquired accuracy of 0.9163 and 0.9379 respectively. They are higher that of other machine learning and GNN algorithms. In an independent test dataset, accuracy of two datasets is 0.9130 and 0.9291, which are 1.08% and 1.57% higher than the best methods of other online webservers.

Synergistic Effect of Bio-Inspired Nanochannels: Hydrophilic DNA Probes at Inner Wall and Hydrophobic Coating at Outer Surface for Highly Sensitive Detection

During the past few decades, bio-inspired nanochannels have been well developed and applied in biosensing, energy transfer, separation, and so on. Here, inspired by the synergistic effect of biological nanopores, biomimetic solid-state nanochannels with hydrophilic DNA probes at the inner wall (DNA@IW_Hydrophilic ) and hydrophobic coating at the outer surface (None@OS_Hydrophobic ) are designed. To demonstrate their prompted sensing properties, Hg²⁺ and its specific probe are selected as target and hydrophilic DNA probes, respectively. Compared with the traditional solid-state nanochannels with hydrophilic probes distributed on both the inner wall and outer surface, the nanochannels with DNA@IW_Hydrophilic +None@OS_Hydrophobic significantly decrease the limit of detection (LOD) by 10⁵ -fold. The obvious improvement of sensitivity (with LOD of 1 nM) is attributed to the synergistic effect: None@OS_Hydrophobic results in the nanochannel's effective diameter decrease and DNA@IW_Hydrophilic induces a specific sensing target. Meanwhile, nanomolar detection of Hg²⁺ in human serum and in vivo fish muscle are achieved. Through molecular dynamics simulation, the synergistic effect can be confirmed by ion fluxes increasement; the relative carbon nanotube increases from 135.64% to 135.84%. This work improves the understanding of nanochannels' synergistic effect and provides a significant insight for nanochannels with improved sensitivity.

Selective colorimetric sensing of sub-nanomolar Hg2+ based on its significantly enhancing peroxidase mimics of silver/copper nanoclusters

A simple colorimetric sensing strategy for Hg²⁺ ions was developed using silver/copper nanoclusters (Ag/Cu NCs) with excellent selectivity and sensitivity. Bimetallic Ag/Cu NCs were synthesized by using glutathione (GSH) as a template and sodium borohydride as a reducing agent. It was found that the peroxidase-like activity of Ag/Cu NCs was significantly enhanced in the presence of Hg²⁺. Therefore, a colorimetric method based on catalysis was developed to detect Hg²⁺ with a linear concentration range of 0.1-700 nM and a detection limit of 0.05 nM (S/N = 3). The common species have no effect on Hg²⁺ ion detection. Furthermore, this method is applicable to accurately detect Hg²⁺ in real aqueous samples and is reproducible. Therefore, owing to the merits of sensitivity, selectivity, rapid response and visual read-out, it can be promising in the development of a portable Hg²⁺ analyzer for on-site detection.

A novel electrochemical biosensor for ultrasensitive Hg2+ detection via a triple signal amplification strategy

We developed a novel electrochemical biosensor for ultrasensitive Hg2+ detection via a triple signal amplification strategy of a DNA dual cycle, organic-inorganic hybrid nanoflowers (Cu3(PO4)2 HNFs) and gold nanoparticle (AuNP) probe. The DNA dual cycle was triggered by exonuclease III (Exo III) in the presence of Hg2+, and Cu3(PO4)2 HNFs were synthesized as an AuNP probe carrier. The electrochemical biosensor displayed high stability, high sensitivity and excellent specificity, which was improved by up to seven orders of magnitude compared to the World Health Organization (WHO) allowed Hg2+ levels in drinking water. This signal amplification strategy could be easily modified and extended to detect other hazardous heavy metals and nucleic acids.

Reusable, facile, and rapid aptasensor capable of online determination of trace mercury

Herein, we reported a homemade waveguide-based evanescent wave aptasensor for the facile online monitoring of mercury pollution. The aptasensor exploited the high selectivity of hairpin structure-based thymidine-Hg²⁺-thymidine coordination chemistry (T-T mismatch) for Hg²⁺ recognition and the stably regenerable capability of DNA-functionalized waveguide surfaces. The presence of Hg²⁺ caused the T-T mismatch of Cy5.5-labeled T-rich single-stranded DNA sequences. The formed hairpin structures blocked the further hybridization of T-rich single-stranded DNA sequences with the complementary DNA strands that are modified on the waveguide surface; this phenomenon was accompanied by the decrease in the fluorescent signals excited by the evanescent wave. The limit of detection in real water samples was determined to be 0.2 μg/L, which was comparable with that of 0.4 μg/L in an ultrapure water under controlled conditions. And the linear range was observed from 1.4 µg/L to 240.7 µg/L. The negligible environmental matrix effect on the performance ensured the reliability of the proposed aptasensor. Moreover, the cross reactivity of this method toward other investigated metal ions was negligible. Through the delicate surface modification with DNA molecules covalently, the chip was reused at least 31 times with a relative standard deviation (RSD) of less than 19%. A Hg²⁺ pollution accident was successfully detected within 30 min, shedding new light in pollution monitoring, environment restoration, and emergency treatment.

Mercuric ion detection by plasmon-enhanced spectrophotometric ellipsometer using specific oligonucleotide probes

Pollution due to heavy metal ions, including mercury, has become a major issue because of their toxicities. It is required to monitor mercury levels in aqueous media using fast and selective methods with high accuracy. Ellipsometry is a promising technique for instance when it's combined with the plasmon resonance phenomena. We reported a biosensor system available for qualitative/quantitative determination of mercuric ions in aqueous media where both the spectrophotometric ellipsometry and oligonucleotide recognition elements were used. A single step assay using both a linear (ProbeL) and a hair-pin (ProbeH) type oligonucleotide probe as a recognition element, in addition to a sandwich-type (ProbeLS) assay were developed and compared. The detection limits were 0.23 nM, 0.03 nM and 0.15 pM for ProbeL, ProbeH and ProbeLS, respectively. The detection range was between 0.05 nM and 100 nM Hg²⁺ for all assays proposed herein.

Exonuclease I-assisted fluorescence aptasensor for tetrodotoxin

A fluorescence aptasensor for the highly specific and sensitive determination of tetrodotoxin was established with tetrodotoxin-aptamer as the recognition unit, berberine as the signal reporter and exonuclease I as the elimination agent for the background. Berberine has a weak fluorescence emission at 540 nm, and it can form the tetrodotoxin-aptamer/berberine complex, resulted in an increased fluorescence. After introducing exonuclease I, it can degrade the single strand oligonucleotides of tetrodotoxin-aptamer into the single nucleotide in the absence of tetrodotoxin, which lead to dramatic fluorescence quenching, and reduce the background signal of sensing system. Once tetrodotoxin is in the presence, tetrodotoxin-aptamer is converted into the stable neck ring conformation, which resists the degradation of exonuclease I and provides a more rigid micro-environment for the excited state of berberine, and then the strong fluorescence is observed. Based on the above properties, an ultrasensitive label-free fluorescence aptasensor for tetrodotoxin is established. The fluorescence aptasensor shows good analytical performance with the linear increase of fluorescence intensity at the tetrodotoxin concentration from 0.030 nM to 6.0 × 10³ nM. The detection limit of 11.0 pM is much lower than that of other reported sensor methods.

A review: Recent advances in ultrasensitive and highly specific recognition aptasensors with various detection strategies

One of the most studied topics in analytical chemistry and physics is to develop bio-sensors. Aptamers are small single-stranded RNA or DNA oligonucleotides (5-25 kDa), which have advantages in comparison to their antibodies such as physicochemical stability and high binding specificity. They are able to integrate with proteins or small molecules, including intact viral particles, plant lectins, gene-regulation factor, growth factors, antibodies and enzymes. The aptamers have reportedly shown some unique characteristics, including long shelf-life, simple modification to provide covalent bonds to material surfaces, minor batch variation, cost-effectiveness and slight denaturation susceptibility. These features led important efforts toward the development of aptamer-based sensors, known as apta-sensors classified into optical, electrical and mass-sensitive based on the signal transduction mode. This review provided a number of current advancements in selecting, development criteria, and aptamers application with the focus on the effect of apta-sensors, specifically for disease-associated analyses. The review concentrated on the current reports of apta-sensors that are used for evaluating different food and environmental pollutants.

A low-cost paper-based aptasensor for simultaneous trace-level monitoring of mercury (II) and silver (I) ions

Mercury (Hg²⁺) and silver (Ag⁺) ions possess the harmful effects on public health and environment that makes it essential to develop the sensing techniques with great sensitivity for the ions. Metal ions commonly coexist in the different biological and environmental systems. Hence, it is an urgent demand to design a simple method for the simultaneous detection of metal ions, peculiarly in the case of coexisting Hg²⁺ and Ag⁺. This study introduces a low-cost paper-based aptasensor to monitor Hg²⁺ and Ag⁺, simultaneously. The strategy of the sensing array is according to the conformational changes of Hg²⁺- and Ag⁺-specific aptamers and their release from the GO surface after the injection of the target sample on the sensing platform. Through monitoring the fluorescence recovery changes against the concentrations of the ions, Hg²⁺ and Ag⁺ can be determined as low as 1.33 and 1.01 pM. The paper-based aptasensor can simultaneously detect the ions within about 10 min. The aptasensor is applied prosperously to monitor Hg²⁺ and Ag⁺ in human serum, water, and milk. The designed aptasensor with the main advantages of simplicity and feasibility holds the supreme potential to develop a cost-effective sensing method for environmental monitoring, food control, and human diagnostics.

A fluorescent lateral flow biosensor for the quantitative detection of Vaspin using upconverting nanoparticles

Vaspin is a protein present in human serum that can cause type-2 diabetes, obesity, and other cardiovascular diseases. We report fluorescent upconverting nanoparticles (UCNPs)-based lateral flow biosensor for ultrasensitive detection of Vaspin. A pair (primary and secondary) of cognate aptamers was used that has duo binding with Vaspin. UCNPs with a diameter of around 100 nm were used as a tag to label a detection probe (secondary aptamer). A primary aptamer (capture probe) was immobilized on the test zone. Sandwich type hybridization reactions among the conjugate probe, target Vaspin, and primary aptamer were performed on the lateral flow biosensor. In the presence of target Vaspin, UCNPs were captured on the test zone of the biosensor and the fluorescent intensity of the captured UCNPs was measured through a colorimetric app under NIR. Fluorescence intensity indicates the quantity of Vaspin present in the sample. A range of Vaspin concentration across 0.1-55 ng ml^-1 with a Limit of detection (LOD) 39 pg ml^-1 was tested through this UCNPs based LFSA with high sensitivity, reproducibility and repeatability, whereas it's actual range in human blood is from 0.1 to 7 ng ml^-1. Therefore, this research provides a well-suited lateral flow strip with an ultrasensitive and low-cost approach for the early diagnosis of type-2 diabetes and this could be applied to any targets with a duo of aptamers generated.

Colorimetric aptasensor for the detection of mercury based on signal intensification by rolling circle amplification

Techniques that are sensitive to detect mercury ion (Hg²⁺) are very important, due to its serious threat to public health and food security. In this work, a colorimetric aptasensor was fabricated for the detection of Hg²⁺ based on rolling circle amplification (RCA). The aptamer was immobilized onto the microplate and hybridized with its complementary strand (cDNA₁) which linked with a primer for triggering the RCA reaction of circular template. The successfully RCA process led to the formation of long ssDNA chains on the microplate, which created many hybridized DNA fragments for bio-cDNA₂. The tagged amount of horseradish peroxidase (HRP) was enhanced through the avidin/biotin binding between avi-HRP and bio-cDNA₂. In the addition of TMB-H₂O₂, HRP was catalyzed and generated an optical signal. However, in the presence of target, Hg²⁺ specifically and preferentially bound with aptamer and formed a strong and stable T-Hg²⁺-T complex, which led to the release of cDNA₁ and HRP cluster. Consequently, the optical signal decreased. Our results showed that the limit of detection (LOD) of this system was 1.6 nM with excellent specificity, and that the detection signals were enhanced by up to 18 times under RCA conditions when compared with detections without RCA. This method has been successfully used to detect Hg²⁺ in water samples with a recovery of 98%-105.74%.

Highly sensitive analysis of tetrodotoxin based on free-label fluorescence aptamer sensing system

Tetrodotoxin (TTX) specifically can bind to its nucleic acid aptamer (TTX-aptamer) and cause the conformation of TTX-aptamer to be switched from the single-strand random coiling form to the compact neck ring structure. Based on the microenvironment difference of the fluorescence reporter, berberine in between the single-stranded coil oligonucleotides and the structure of the neck ring, a simple, rapid and sensitive label-free fluorescence aptamer sensing system for detection of TTX was developed. Various factors affecting the analysis of TTX were optimized, including the concentration of berberine, ion strength, pH, reaction time, the concentration of TTX-aptamer. Under the optimal experimental conditions, the fluorescence intensity of the sensing system and the concentration of TTX showed a good linear relationship in the range of 0.1 nM to 500 nM, with the detection limit of 0.074 nM. The standard recovery test result exhibited that the recoveries of TTX in serum samples were 96.54%-106.40%. The established method has the advantages of high specificity, good sensitivity, quickness and convenience, low cost, and can be used for the detection of TTX in serum samples.

Highly sensitive aptasensor based on interferometric reflectance spectroscopy for the determination of amyloid β as an Alzheimer's disease biomarkers using nanoporous anodic alumina

It is well known that Alzheimer's disease is one of the global challenges for the 21st century. Therefore, it is urgent to develop a reliable biosensor for the detection of this disease. Here in, we have developed for the first time, an aptasensor based on interferometric reflectance spectroscopy (IRS) for the determination of amyloid β (Aβ) oligomers that is an Alzheimer's disease biomarker. For this purpose, the nanoporous anodic alumina (NAA) was first fabricated. After that, the pore walls of the NAA were modified with (3-aminopropyl) trimethoxysilane (NAA-NH₂). The amino-terminal aptamers probe were then attached to the pore walls of the NAA-NH₂ by using glutaraldehyde (GA) as the cross-linking agent. Subsequently, methylene blue (MB) was immobilized into the aptamer as the photo-probe, generating the MB/G-quadruplex complex. Since MB has a high absorption coefficient, the intensity of the reflected white light to the charge-coupled device (CCD) detector decreased. In the presence of the Aβ oligomers that have high affinity to the immobilized aptamer, the MB/quadruplex complex broke and MB washed away from the aptasensor. Therefore, the intensity of the reflected white light to the CCD detector increased. The increased signal intensity of the aptasensor has a logarithmic relationship with the concentration of Aβ oligomers. The proposed aptasensor exhibited a good response to the concentration of Aβ oligomers in the range of 0.5-50.0 μg × mL^-1. The experimental detection limit was of 0.02 μg × mL^-1 (at 3σ/S). The proposed optical aptasensor exhibited good selectivity, linear range, and stability.