Sensitive label-free oligonucleotide-based microfluidic detection of mercury (II) ion by using exonuclease I

A facile imine-linked covalent organic framework doped with a carbon dot composite for the detection and removal of Hg2+ in surface water

Hg2+ is one of the most toxic chemical species in the water environment, and thus developing a new fluorescent covalent organic framework for both the detection and removal of Hg2+ is highly desirable. Herein, a fluorescent composite, termed TpPa-1 COF@CDs, was synthesized by inverse emulsion polymerization method using an imine covalent organic framework as the supporting material and carbon dots as the fluorescent sensor element. The crystallinity, porosity, rich functional receptors (hydroxyl and amino groups), thermal stability and fluorescent properties of TpPa-1 COF@CDs were characterized. The results showed that TpPa-1 COF@CDs exhibited a good detection and removal performance for Hg2+, which was evidenced by its high sensitivity (LOD = 0.75 μg L-1), superior selectivity, large adsorption capacity (235 mg g-1), fast adsorption rate (30 min equilibrium time) and good regeneration (at least five cycles). More importantly, the simple functional monomer, short reaction time and metal-free raw material made TpPa-1 COF@CDs reliable, cost effective and eco-friendly. This research demonstrated the facile construction of a functional covalent organic framework composite for water environmental remediation technologies of metal pollution.

Function of Graphene Oxide as the “Nanoquencher” for Hg2+ Detection Using an Exonuclease I-Assisted Biosensor

Graphene oxide is well known for its excellent fluorescence quenching ability. In this study, positively charged graphene oxide (pGO25000) was developed as a fluorescence quencher that is water-soluble and synthesized by grafting polyetherimide onto graphene oxide nanosheets by a carbodiimide reaction. Compared to graphene oxide, the fluorescence quenching ability of pGO25000 is significantly improved by the increase in the affinity between pGO25000 and the DNA strand, which is introduced by the additional electrostatic interaction. The FAM-labeled single-stranded DNA probe can be almost completely quenched at concentrations of pGO25000 as low as 0.1 μg/mL. A simple and novel FAM-labeled single-stranded DNA sensor was designed for Hg²⁺ detection to take advantage of exonuclease I-triggered single-stranded DNA hydrolysis, and pGO25000 acted as a fluorescence quencher. The FAM-labeled single-stranded DNA probe is present as a hairpin structure by the formation of T–Hg²⁺–T when Hg²⁺ is present, and no fluorescence is observed. It is digested by exonuclease I without Hg²⁺, and fluorescence is recovered. The fluorescence intensity of the proposed biosensor was positively correlated with the Hg²⁺ concentration in the range of 0–250 nM (R² = 0.9955), with a seasonable limit of detection (3σ) cal. 3.93 nM. It was successfully applied to real samples of pond water for Hg²⁺ detection, obtaining a recovery rate from 99.6% to 101.1%.

A novel electrochemical insulin aptasensor: From glassy carbon electrodes to disposable, single-use laser-scribed graphene electrodes

Insulin, a peptide hormone secreted by pancreatic β cells, affects the development of diabetes and associated complications. Herein, we propose an electrochemical aptasensor for sensitive and selective detection of insulin using laser-scribed graphene electrodes (LSGEs). Before using disposable LSGEs, the development and proof-of-concept sensing experiments were firstly carried out on research-grade glassy carbon electrode (GCE). The aptasensor is based on using Exonuclease I (Exo I) that catalyses the hydrolysis of single-stranded aptamers attached to the electrode surface; however, the hydrolysis does not occur if the insulin is bound to the aptamer. Therefore, the unbound aptamers are cleaved by Exo I while insulin-bound aptamers remain on the electrode surface. In the next step, the gold nanoparticle - aptamer (AuNPs-Apt) probes are introduced to the electrode surface to form a 'sandwich' structure with the insulin on the surface-attached aptamer. The redox probe, methylene blue (MB), intercalates into the aptamers' guanine bases and the sandwich structure of AuNPs-Apt/insulin/surface-bound aptamer amplifies electrochemical signal from MBs. The signal can be well-correlated to the concentrations of insulin. A limit of detection of 22.7 fM was found for the LSGE-based sensors and 9.8 fM for GCE-based sensors used for comparison and initial sensor development. The results demonstrate successful fabrication of the single-use and sensitive LSGEs-based sensors for insulin detection.

Development of DNA Biosensors Based on DNAzymes and Nucleases

DNA biosensors play important roles in environmental, medical, industrial and agricultural analysis. Many DNA biosensors have been designed based on the enzyme catalytic reaction. Because of the importance of enzymes in biosensors, we present a review on this topic. In this review, the enzymes were divided into DNAzymes and nucleases according to their chemical nature. Firstly, we introduced the DNAzymes with different function inducing cleavage, metalation, peroxidase, ligation and allosterism. In this section, the G-quadruplex DNAzyme, as a hot topic in recent years, was described in detail. Then, the nucleases-assisted signal amplification method was also reviewed in three categories including exonucleases, endonucleases and other nucleases according to the digestion sites in DNA substrates. In exonucleases section, the Exo I and Exo III were selected as examples. Then, the DNase I, BamH I, nicking endonuclease, S1 nuclease, the duplex specific nuclease (DSN) and RNases were chosen to illustrate the application of endonucleases. In other nucleases section, DNA polymerases and DNA ligases were detailed. Last, the challenges and future perspectives in the field were discussed.

Construction of DNA Biosensors for Mercury (II) Ion Detection Based on Enzyme-Driven Signal Amplification Strategy

Mercury ion (Hg²⁺) is a well-known toxic heavy metal ion. It is harmful for human health even at low concentrations in the environment. Therefore, it is very important to measure the level of Hg²⁺. Many methods, reviewed in several papers, have been established on DNA biosensors for detecting Hg²⁺. However, few reviews on the strategy of enzyme-driven signal amplification have been reported. In this paper, we reviewed this topic by dividing the enzymes into nucleases and DNAzymes according to their chemical nature. Initially, we introduce the nucleases including Exo III, Exo I, Nickase, DSN, and DNase I. In this section, the Exo III-driven signal amplification strategy was described in detail. Because Hg²⁺ can help ssDNA fold into dsDNA by T-Hg-T, and the substrate of Exo III is dsDNA, Exo III can be used to design Hg²⁺ biosensor very flexibly. Then, the DNAzyme-assisted signal amplification strategies were reviewed in three categories, including UO₂²⁺-specific DNAzymes, Cu²⁺-specific DNAzymes and Mg²⁺-specific DNAzymes. In this section, the Mg²⁺-specific DNAzyme was introduced in detail, because this DNAzyme has highly catalytic activity, and Mg²⁺ is very common ion which is not harmful to the environment. Finally, the challenges and future perspectives were discussed.

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.

Ultrasensitive Biosensor for Detection of Mercury(II) Ions Based on DNA-Cu Nanoclusters and Exonuclease III-assisted Signal Amplification

This paper describes a novel method for label-free mercury(II) ion detection based on exonuclease III-induced target signal recycling amplification using double-stranded DNA templated copper nanoclusters. The synthesized DNA-Cu nanoclusters were used with exonuclease III loop amplification technology for ultra-high sensitivity detection of mercury(II) ions, which were detected by significantly decreased fluorescence intensity. Under the optimal experimental conditions, there was a clear linear relationship between Hg²⁺ concentration in the range of 0.04 to 8 nM and fluorescence intensity. The detection limit for Hg²⁺ was 4 pM. In addition, the interference of other metal ions on the mercury(II) ion detection was also studied. To confirm the application of the fluorescent sensor, it was applied to determine the concentrations of mercury(II) ions in tap water, and the results showed that the method can be used to detect mercury(II) ions in water samples successfully.

A catalytic cleavage strategy for fluorometric determination of Hg(II) based on the use of a Mg(II)-dependent split DNAzyme and hairpins conjugated to gold nanoparticles

A catalytic cleavage strategy was developed for the fluorometric determination of Hg(II). The method is based on the use of a Mg(II)-dependent split DNAzyme. Fluorophore labeled hairpins were conjugated to gold nanoparticles (AuNPs) upon which fluorescence is quenched. Thymine-Hg(II)-thymine (T-Hg(II)-T) interaction causes the two DNA sequences to form an entire enzyme-strand DNA (E-DNA). The E-DNA bind to the hairpins on the AuNPs to form a Mg(II)-dependent DNAzyme structure. The circular cleavage of hairpins results in a signal amplification and in the recovery of fluorescence. The assay has a limit of detection (LOD) as low as 80 pM of Hg(II). This LOD is comparable to those obtained with other amplification strategies. The method was successfully applied to the determination of Hg(II) in Chinese herbs (Atractylodes macrocephala Koidz). Graphical abstract Schematic of a catalytic cleavage strategy based on Mg(II)-dependent split DNAzyme for fluorometric determination of Hg(II).

New portable smartphone-based PDMS microfluidic kit for the simultaneous colorimetric detection of arsenic and mercury

A smartphone-based microfluidic platform was developed for point-of-care (POC) detection using surface plasmon resonance (SPR) of gold nanoparticles (GNPs). The simultaneous colorimetric detection of trace arsenic and mercury ions (As3+ and Hg2+) was performed using a new image processing application (app). To achieve this goal, a microfluidic kit was fabricated using a polydimethylsiloxane (PDMS) substrate with the configuration of two separated sensing regions for the quantitative measurement of the color changes in GNPs to blue/gray. To fabricate the microfluidic kit, a Plexiglas mold was cut using a laser based on the model obtained from AutoCAD and Comsol outputs. The colorimetric signals originated from the formation of nanoparticle aggregates through the interaction of GNPs with dithiothreitol - 10,12-pentacosadiynoic acid (DTT-PCDA) and lysine (Lys) in the presence of As3+ and Hg2+ ions. This assembly exhibited the advantages of simplicity, low cost, and high portability along with a low volume of reagents and multiplex detection. Heavy Metals Detector (HMD), as a new app for the RGB reader, was programmed for an Android smartphone to quantify colorimetric analyses. Compared with traditional image processing, this app provided significant improvements in sensitivity, time of analysis, and simplicity because the color intensity is measured through a new normalization equation by converting RGB to an Integer system. As a simple, real-time, and portable analytical kit, the fabricated sensor could detect low concentrations of As3+ (710 to 1278 μg L-1) and Hg2+ (10.77 to 53.86 μg L-1) ions in water samples at ambient conditions.

Mercury nanoladders: a new method for DNA amplification, signal identification and their application in the detection of Hg(ii) ions

A biosensor based on Hg(ii) nanoladders integrated with graphene oxide (GO) for Hg(ii) detection was developed.

Development of mercury (II) ion biosensors based on mercury-specific oligonucleotide probes

Mercury (II) ion (Hg(2+)) contamination can be accumulated along the food chain and cause serious threat to the public health. Plenty of research effort thus has been devoted to the development of fast, sensitive and selective biosensors for monitoring Hg(2+). Thymine was demonstrated to specifically combine with Hg(2+) and form a thymine-Hg(2+)-thymine (T-Hg(2+)-T) structure, with binding constant even higher than T-A Watson-Crick pair in DNA duplex. Recently, various novel Hg(2+) biosensors have been developed based on T-rich Mercury-Specific Oligonucleotide (MSO) probes, and exhibited advanced selectivity and excellent sensitivity for Hg(2+) detection. In this review, we explained recent development of MSO-based Hg(2+) biosensors mainly in 3 groups: fluorescent biosensors, colorimetric biosensors and electrochemical biosensors.

Sensitive detection for coralyne and mercury ions based on homo-A/T DNA by exonuclease signal amplification

Based on specific homo-A/T DNA binding properties, a strategy for coralyne and mercury ions detection was realised by exonuclease-aided signal amplification. Coralyne could specifically bind homo-A DNA and protect it from the hydrolysis of exonuclease I. The coralyne-protected DNA was subsequently used as a trigger strand to hydrolyze DNA2 in exonuclease-aided signal amplification process. Thiazole orange was used to quantify the remainder DNA2. Under the optimal condition, the fluorescence intensity was linearly proportional to the concentration of coralyne in the range of 0.2-100 nM with a limit of detection (LOD) of 0.31 nM, which presented the lowest LOD for coralyne among all reported. With homo-T and Hg(2+) taking the place of homo-A DNA and coralyne, respectively, the system could also be used for Hg(2+) detection. The experiments in real samples also showed good results. This method was label-free, low-cost, easy-operating and highly repeatable for the detection of coralyne and mercury ions. It could also be extended to detect various analytes, such as other metal ions, proteins and small molecules by using appropriate aptamers.

Synthesis, spectroscopy studies, and theoretical calculations of new fluorescent probes based on pyrazole containing porphyrins for Zn(II), Cd(II), and Hg(II) optical detection

New pyrazole-porphyrin conjugates were successfully prepared from a reaction of β-porphyrin-chalcone derivatives with phenylhydrazine in acetic acid followed by an oxidative step. This fast and efficient synthetic approach provided the expected compounds in yields up to 82%. The sensing ability of the new porphyrin-pyrazole derivatives to detect the metal ions Ag(+), Na(+), K(+), Mg(2+), Ca(2+), Ni(2+), Cu(2+), Zn(2+), Cd(2+), Hg(2+), Pb(2+), and Cr(3+) was studied by spectrophotometric and spectrofluorimetric titrations. In the presence of Zn(2+), the conjugates exhibit changes in the emission spectra that are desired for a ratiometric-type fluoroionophoric detection probe. The studies were extended to gas phase, where the pyrazole-porphyrin conjugates show ability to sense metal ions with high selectivity toward Cu(2+) and Ag(+), and in poly(methyl methacrylate) doped films with promising results for Zn(2+) detection.

Exonuclease I aided enzyme-linked aptamer assay for small-molecule detection

A novel enzyme-linked aptamer assay (ELAA) with the aid of Exonuclease I (Exo I) for colorimetric detection of small molecules was developed. The fluorescein isothiocyanate (FITC)-labeled aptamer was integrated into a double-stranded DNA (dsDNA). In the presence of target, the binding of aptamer with target protected the aptamer from Exo I degradation, which resulted in the FITC tag remaining on the aptamer. Then, the anti-FITC-HRP conjugate was used to produce an optically observable signal. By monitoring the color change, we were able to detect two model molecules, ATP and L-argininamide, with high selectivity and high sensitivity even in the serum matrix. It is expected to be a simple and general ELAA method with wide applicability.

Highly sensitive and selective chip-based fluorescent sensor for mercuric ion: development and comparison of turn-on and turn-off systems

Miniaturization is currently an important trend in environmental and food monitoring because it holds great promise for on-site monitoring and detection. We report here two ready-to-use chip-based fluorescent sensors, compatible with microarray technology for reagentless, one-step, fast, highly sensitive and selective detection of the mercuric ion (Hg(2+)) in the turn-on and turn-off operation modes. Both operation modes are based on the highly selective T-Hg(2+)-T coordination between two neighboring polythymine (T) strands at a high probe density and its induced displacement of the complementary polyadenine strand labeled with either fluorophore or quencher, which enables the turn-off and turn-on detection of Hg(2+), respectively. The turn-off sensor is slightly more sensitive than the turn-on sensor, and their detection limits are 3.6 and 8.6 nM, respectively, which are both lower than the U.S. Environmental Protection Agency limit of [Hg(2+)] for drinkable water (10 nM, 2 ppb). Compared to the turn-off sensor with the dynamic Hg(2+) detection range from 3.6 nM to 10 μM (R(2) = 0.99), the turn-on sensor has a broader dynamic Hg(2+) detection range, from 8.6 nM to 100 μM (R(2) = 0.996). Both sensors exhibited superior selectivity over other reported sensors using thymine-rich probes for Hg(2+) detection over other common metal ions. In addition, the practical application of the chip-based sensors was demonstrated by detecting spiked Hg(2+) in drinking water and fresh milk. The sensor has great potential for on-site practical applications due to its operational convenience, simplicity, speed, and portability.

Label-free fluorescent detection of ions, proteins, and small molecules using structure-switching aptamers, SYBR Gold, and exonuclease I

We have demonstrated a label-free sensing strategy employing structure-switching aptamers (SSAs), SYBR Gold, and exonuclease I to detect a broad range of targets including inorganic ions, proteins, and small molecules. This nearly universal biosensor approach is based on the observation that SSAs at binding state with their targets, which fold into secondary structures such as quadruplex structure or Y shape structure, show more resistance to nuclease digestion than SSAs at unfolded states. The amount of aptamer left after nuclease reaction is proportional to the concentrations of the targets and in turn is proportional to the fluorescence intensities from SYBR Gold that can only stain nucleic acids but not their digestion products, nucleoside monophosphates (dNMPs). Fluorescent assays employing this mechanism for the detection of potassium ion (K(+)) are sensitive, selective, and convenient. Twenty μM K(+) is readily detected even at the presence of a 500-fold excess of Na(+). Likewise, we have generalized the approach to the specific and convenient detection of proteins (thrombin) and small molecules (cocaine). The assays were then validated by detecting K(+), cocaine, and thrombin in urine and serum or cutting and masking adulterants with good agreements with the true values. Compared to other reported approaches, most limited to G-quadruplex structures, the demonstrated method has less structure requirements of both the SSAs and their complexes with targets, therefore rending its wilder applications for various targets. The detection scheme could be easily modified and extended to detection platforms to further improve the detection sensitivity or for other applications as well as being useful in high-throughput and paralleled analysis of multiple targets.