Impedimetric Immobilized DNA-Based Sensor for Simultaneous Detection of Pb2+, Ag+, and Hg2+

SERS detection and removal of mercury(II)/silver(I) using oligonucleotide-functionalized core/shell magnetic silica sphere@Au nanoparticles

Heavy metal ions, such as Hg(2+) and Ag(+), pose severe risks in human health and the environment. For sensitive detection and selective removal of Hg(2+) and Ag(+) ions, here, we demonstrate a surface-enhanced Raman scattering (SERS)-active platform by employing the oligonucleotide-functionalized magnetic silica sphere (MSS)@Au nanoparticles (NPs). This system exploits mismatched T-Hg-T and C-Ag-C bridges to capture Hg(2+) and Ag(+) ions, exhibiting excellent responses for Hg(2+) ions in the range of 0.1-1000 nM and for Ag(+) in the range of 10-1000 nM. The assay is highly selective for the target ions and does not respond to other metal ions. Additionally, the Hg(2+) and Ag(+) ions in this system can be effectively removed from surrounding solutions by an external magnetic field or through spontaneous precipitation. Moreover, more than 80% of the MSS@Au NPs can be easily recycled with the help of cysteine. We anticipate that the designed strategy could be extended to other analytes that can bind to DNA molecules with a high affinity, and can be used in many potential applications such as environmental renovation, toxin detection, and groundwater analysis.

Dual fluorescence resonance energy transfer assay between tunable upconversion nanoparticles and controlled gold nanoparticles for the simultaneous detection of Pb²⁺ and Hg²⁺

In this work, we presented a novel dual fluorescence resonance energy transfer (FRET) system for the simultaneous detection of Pb(2+) and Hg(2+). This system employed two color upconversion nanoparticles (UCNPs) as the donors, and controlled gold nanoparticles (AuNPs) as the acceptors. The two donor-acceptor pairs were fabricated by hybridizing the aptamers and their corresponding complementary DNA. Thus, the green and red upconversion fluorescence could be quenched because of a good overlap between the UCNPs fluorescence emission and the AuNPs absorption spectrum. In the presence of Pb(2+) and Hg(2+), the aptamers preferred to bind to their corresponding analytes and formed a G-quadruplexes structure for Pb(2+) and the hairpin-like structure for Hg(2+). As a result, the dual FRET was disrupted, and the green and red upconversion fluorescence was restored. Under optimized experimental conditions, the relative fluorescence intensity increased as the metal ion concentrations were increased, allowing for the quantification of Pb(2+) and Hg(2+). The relationships between the fluorescence intensity and plotting logarithms of ion concentrations were linear in the range from 0.1 to 100 nM for Pb(2+) and 0.5 to 500 nM for Hg(2+), and the detection limits of Pb(2+) and Hg(2+) were 50 pM and 150 pM, respectively. As a practical application, the aptasensor was used to monitor Pb(2+) and Hg(2+) levels in naturally contaminated samples and human serum samples. Ultimately, this type of dual FRET could be used to detect other metal ions or contaminants in food safety analysis and environment monitoring.

DNA as sensors and imaging agents for metal ions

Increasing interest in detecting metal ions in many chemical and biomedical fields has created demands for developing sensors and imaging agents for metal ions with high sensitivity and selectivity. This review covers recent progress in DNA-based sensors and imaging agents for metal ions. Through both combinatorial selection and rational design, a number of metal-ion-dependent DNAzymes and metal-ion-binding DNA structures that can selectively recognize specific metal ions have been obtained. By attachment of these DNA molecules with signal reporters such as fluorophores, chromophores, electrochemical tags, and Raman tags, a number of DNA-based sensors for both diamagnetic and paramagnetic metal ions have been developed for fluorescent, colorimetric, electrochemical, and surface Raman detection. These sensors are highly sensitive (with a detection limit down to 11 ppt) and selective (with selectivity up to millions-fold) toward specific metal ions. In addition, through further development to simplify the operation, such as the use of "dipstick tests", portable fluorometers, computer-readable disks, and widely available glucose meters, these sensors have been applied for on-site and real-time environmental monitoring and point-of-care medical diagnostics. The use of these sensors for in situ cellular imaging has also been reported. The generality of the combinatorial selection to obtain DNAzymes for almost any metal ion in any oxidation state and the ease of modification of the DNA with different signal reporters make DNA an emerging and promising class of molecules for metal-ion sensing and imaging in many fields of applications.

A sensitive fluorescence anisotropy method for detection of lead (II) ion by a G-quadruplex-inducible DNA aptamer

Sensitive and selective detection of Pb(2+) is of great importance to both human health and environmental protection. Here we propose a novel fluorescence anisotropy (FA) approach for sensing Pb(2+) in homogeneous solution by a G-rich thrombin binding aptamer (TBA). The TBA labeled with 6-carboxytetramethylrhodamine (TMR) at the seventh thymine nucleotide was used as a fluorescent probe for signaling Pb(2+). It was found that the aptamer probe had a high FA in the absence of Pb(2+). This is because the rotation of TMR is restricted by intramolecular interaction with the adjacent guanine bases, which results in photoinduced electron transfer (PET). When the aptamer probe binds to Pb(2+) to form G-quadruplex, the intramolecular interaction should be eliminated, resulting in faster rotation of the fluorophore TMR in solution. Therefore, FA of aptamer probe is expected to decrease significantly upon binding to Pb(2+). Indeed, we observed a decrease in FA of aptamer probe upon Pb(2+) binding. Circular dichroism, fluorescence spectra, and fluorescence lifetime measurement were used to verify the reliability and reasonability of the sensing mechanism. By monitoring the FA change of the aptamer probe, we were able to real-time detect binding between the TBA probe and Pb(2+). Moreover, the aptamer probe was exploited as a recognition element for quantification of Pb(2+) in homogeneous solution. The change in FA showed a linear response to Pb(2+) from 10 nM to 2.0 μM, with 1.0 nM limit of detection. In addition, this sensing system exhibited good selectivity for Pb(2+) over other metal ions. The method is simple, quick and inherits the advantages of aptamer and FA.

Cu(ii)4L4coordination-driven molecular container: a reusable visual colorimetric sensor for Ag(i) ions

A Cu₄L₄square-like molecular container which can be a reusable visual sensor for Ag⁺is reported. The present results can be a useful stepwise approach for the construction of heterometallic supramolecular complexes with potential applications.

Target-initiated impedimetric proximity ligation assay with DNAzyme design for in situ amplified biocatalytic precipitation

A target-initiated proximity ligation assay protocol with DNAzyme formation was for the first time designed for ultrasensitive impedimetric monitoring of heavy metal ions (silver ions were used in this case) by coupling with an enzymatic biocatalytic precipitation technique.

Electron transport in DNA initiated by diaminonaphthalene donors alternatively bound by non-covalent and covalent association

Non-covalent association can identify active donors for study of charge transfer in DNA but may not establish detailed correlations between donor structure and transfer efficiency.

Electrochemical uranyl cation biosensor with DNA oligonucleotides as receptor layer

The present study aims at the further development of the uranyl oligonucleotide-based voltammetric biosensor, which takes advantage of strong interaction between UO2(2+) and phosphate DNA backbone. Herein we report the optimization of working parameters of previously elaborated electrochemical DNA biosensor. It is shown that the sensor sensitivity is highly dependent on the oligonucleotide probe length and the incubation time of sensor in a sample solution. Consequently, the highest sensitivity was obtained for 10-nucleotide sequence and 60 min incubation time. The lower detection limit towards uranyl cation for developed biosensor was 30 nM. The influence of mixed monolayers and the possibility of developing a non-calibration device were also investigated. The selectivity of the proposed biosensor was significantly improved via elimination of adenine nucleobases from the DNA probe. Moreover, the regeneration procedure was elaborated and tested to prolong the use of the same biosensor for 4 subsequent determinations of UO2(2+).

Photoluminescent graphene oxide microarray for multiplex heavy metal ion analysis

An aptamer-linked graphene oxide (GO) microarray is synthesized for multiplex heavy metal ion detection. Fluorescent nanosized GO sheets are micropatterned, and specific aptamers targeting Ag(+) and Hg(2+) are immobilized on the GO array. Upon capture of the target heavy metal ions, electron transfer occurs between the GO (donors) and the heavy metal ions (acceptors), leading to fluorescence quenching of the GO.

Label-free detection of Cu(2+) and Hg(2+) ions using reconstructed Cu(2+)-specific DNAzyme and G-quadruplex DNAzyme

Label-free metal ion detection methods were developed. To achieve these, a reconstructed Cu(2+)-specific DNA-cleaving DNAzyme (Cu(2+)-specific DNAzyme) with an intramolecular stem-loop structure was used. G-quadruplex-forming G-rich sequence(s), linked at the ends of double-helix stem of an intramolecular stem-loop structure, was partly caged in an intramolecular duplex or formed a split G-quadruplex. Cu(2+)-triggered DNA cleavage at a specific site decreased the stability of the double-helix stem, resulting in the formation or destruction of G-quadruplex DNAzyme that can effectively catalyze the 2,2'-azinobis(3-ethylbenzothiazoline)-6-sulfonic acid (ABTS)-H2O2 reaction. Based on these, two label-free, cost-effective and simple Cu(2+) sensors were designed. These two sensors followed different detection modes: 'turn-on' and 'turn-off'. As for the 'turn-on' sensor, the intramolecular stem-loop structure ensured a low background signal, and the co-amplification of detection signal by dual DNAzymes (Cu(2+)-specific DNAzyme and G-quadruplex DNAzyme) provided a high sensitivity. This sensor enabled the selective detection of aqueous Cu(2+) with a detection limit of 3.9 nM. Visual detection was possible. Although the 'turn-off' sensor gave lower detection sensitivity than the 'turn-on' one, the characteristics of cost-effectiveness and ease of operation made it an important implement to reduce the possibility of pseudo-positive or pseudo-negative results. Combining the ability of Hg(2+) ion to stabilize T-T base mismatch, above dual DNAzymes-based strategy was further used for Hg(2+) sensor design. The proposed sensor allowed the specific detection of Hg(2+) ion with a detection of 4.8 nM. Visual detection was also possible.

Mechanism of the hairpin folding transformation of thymine-cytosine-rich oligonucleotides induced by Hg(II) and Ag(I) ions

The metal-induced folding of thymine-cytosine-rich oligonucleotides into hairpin-like structures was characterised by isothermal titration calorimetry, secondary structure analysis, equilibrium titrations, and fluorescence study. We find that designed thymine-cytosine-rich oligonucleotides can specifically bind with Hg(II) or Ag(I) ions to generate metal-mediated base pairs in a hairpin-like structure from a random coil structure. Isothermal titration calorimetry experiments were performed to reveal the detail of the whole binding process. The thermodynamic result exhibits two possible pathways of significant change upon the addition of Hg(II) ions. Furthermore, this transformation can be enhanced by the presence of Ag(I) ions. The fluorescence decreases through fluorescence resonance energy transfer (FRET) between the fluorophore and quencher confirms the process of formation of the hairpin-like structure. The analysis of optical titration data demonstrates that the saturated binding stoichiometries are 12:1 and 4:1 for Hg(II) and Ag(I) ions, respectively. Our result provides a promising strategy for the investigation of the mechanism of structural transformation of oligonucleotides influenced by metal-mediated base pairs, which may eventually lead to progress in constructing a metal-triggered DNA origami system and metal-containing DNA nanotechnology.

Exploiting the higher specificity of silver amalgamation: selective detection of mercury(II) by forming Ag/Hg amalgam

Heavy metal ion pollution poses severe risks in human health and the environment. Driven by the need to detect trace amounts of mercury, this article demonstrates, for the first time, that silver/mercury amalgamation, combining with DNA-protected silver nanoparticles (AgNPs), can be used for rapid, easy and reliable screening of Hg(2+) ions with high sensitivity and selectivity over competing analytes. In our proposed approach, Hg(2+) detection is achieved by reducing the mercury species to elemental mercury, silver atoms were chosen as the mercury atoms' acceptors by forming Ag/Hg amalgam. To signal fluorescently this silver amalgamation event, a FAM-labeled ssDNA was employed as the signal reporter. AgNPs were grown on the DNA strand that resulted in greatly quenching the FAM fluorescence. Formation of Ag/Hg amalgam suppresses AgNPs growth on the DNA, leading to fluorescence signal increase relative to the fluorescence without Hg(2+) ions, as well as marked by fluorescence quenching. This FAM fluorescence enhancement can be used for detection of Hg(2+) at the a few nanomolar level. Moreover, due to excellent specificity of silver amalgamation with mercury, the sensing system is highly selective for Hg(2+) and does not respond to other metal ions with up to millimolar concentration levels. This sensor is successfully applied to determination of Hg(2+) in tap water, spring water and river water samples. The results shown herein have important implications in the development of new fluorescent sensors for the fast, easy, and selective detection and quantification of Hg(2+) in environmental and biological samples.

Easy design of colorimetric logic gates based on nonnatural base pairing and controlled assembly of gold nanoparticles

Utilizing the principles of metal-ion-mediated base pairs (C-Ag-C and T-Hg-T), the pH-sensitive conformational transition of C-rich DNA strand, and the ligand-exchange process triggered by DL-dithiothreitol (DTT), a system of colorimetric logic gates (YES, AND, INHIBIT, and XOR) can be rationally constructed based on the aggregation of the DNA-modified Au NPs. The proposed logic operation system is simple, which consists of only T-/C-rich DNA-modified Au NPs, and it is unnecessary to exquisitely design and alter the DNA sequence for different multiple molecular logic operations. The nonnatural base pairing combined with unique optical properties of Au NPs promises great potential in multiplexed ion sensing, molecular-scale computers, and other computational logic devices.

Electrochemical detection of the amino-substituted naphthalene compounds based on intercalative interaction with hairpin DNA by electrochemical impedance spectroscopy

The amino-substituted naphthalene compounds, such as 1,8-diaminonaphthalene (1,8-DANAP), 2,3-diaminonaphthalene (2,3-DANAP), 1,5-diaminonaphthalene (1,5-DANAP), 1-naphthylamine (1-NAP) and 2-naphthylamine (2-NAP), were investigated by electrochemical impedance spectroscopy (EIS), which was based on the interaction with hairpin DNA immobilized on the gold electrodes. Upon hairpin DNA interacting with the target chemicals, the charge transfer resistance (RCT) of the hairpin DNA films was significantly decreased and the charge transfer resistance change (ΔR(CT)) decreased in a sequence of ΔR(CT) (1,8-DANAP)>ΔR(CT) (2,3-DANAP)>ΔR(CT) (1,5-DANAP)>ΔR(CT) (1-NAP)>ΔR(CT) (2-NAP). The ΔR(CT) changes were due to the difference in the binding constant (K(SV)) of the target chemicals to DNA. In addition, the interaction mechanism was further explored using 1,8-DANAP as a model analyte by fluorescence spectra, Raman spectroscopy, differential pulse voltammetry (DPV) and EIS, correspondingly. The results demonstrated that the amino-substituted naphthalene compounds intercalated into "stem" appearing in the hairpin DNA. Moreover, the hairpin DNA sensor exhibited high sensitivity to the amino-substituted naphthalene compounds with the detection limit of nano-mole, and maintained high selectivity over other selected environmental pollutants. Finally, the DNA sensor was challenged in natural water sample with a recovery of 96-102%, which offered a platform for prospective future development of a simple, rapid, sensitive and low-cost assay for the detection of target aromatic amine pollutants.

Electrochemical and density functional theory investigation on high selectivity and sensitivity of exfoliated nano-zirconium phosphate toward lead(II)

A new strategy on the understanding of selective and sensitive identification of Pb(II) using combined experimental and theoretical efforts is described. Amorphous phase formation of exfoliated nano-zirconium phosphate (ZrP) has been prepared via a hydrothermal process and subsequent intercalation reaction. Exfoliated ZrP was used as coating on the electrode surface, and it was found to be selective and sensitive for Pb(II) detection due to its selective adsorption ability. To better and scientifically understand the microscopic adsorption mechanism, density functional theory (DFT) calculations about the details of chemical interactions between heavy metal ions and exfoliated ZrP were carried out at an atomistic level. It is verified that the exfoliated ZrP shows the strongest adsorption capability toward Pb(II) among all heavy metal ions, thereby resulting in selective detection consequently. With our combined experimental and theoretical efforts, we are able to provide a new route to realize the improved selectivity in electrochemical sensing of toxic metal ions.

Synthesis and characterization of oligonucleotide conjugates bearing electroactive labels

Oxime bond formation has been applied to the preparation of oligonucleotides labeled with electrochemical ferrocene and viologen labels. Aminooxy functionalized ferrocene and viologen derivatives were prepared by a straightforward route and efficiently conjugated with aldehyde containing oligonucleotides either at 3' or 5' end. Both labels were found to not disturb the recognition properties of the oligonucleotide. The versatility of the method was further demonstrated by preparing bi-functionalized conjugates with a disulfide at 3' end and an electrochemical label at 5' end.

Ultrasensitive detection of toxic cations through changes in the tunnelling current across films of striped nanoparticles

Although multiple methods have been developed to detect metal cations, only a few offer sensitivities below 1 pM, and many require complicated procedures and sophisticated equipment. Here, we describe a class of simple solid-state sensors for the ultrasensitive detection of heavy-metal cations (notably, an unprecedented attomolar limit for the detection of CH(3)Hg(+) in both standardized solutions and environmental samples) through changes in the tunnelling current across films of nanoparticles (NPs) protected with striped monolayers of organic ligands. The sensors are also highly selective because of the ligand-shell organization of the NPs. On binding of metal cations, the electronic structure of the molecular bridges between proximal NPs changes, the tunnelling current increases and highly conductive paths ultimately percolate the entire film. The nanoscale heterogeneity of the structure of the film broadens the range of the cation-binding constants, which leads to wide sensitivity ranges (remarkably, over 18 orders of magnitude in CH(3)Hg(+) concentration).

Fluorescent aptamer-functionalized graphene oxide biosensor for label-free detection of mercury(II)

Label-free fluorescent detection of Hg(2+) has been realized via quenching of fluorescence of graphene oxide (GO). The water-soluble GO sheets, which are functionalized with single-stranded DNA aptamer, exhibit strong fluorescence emission at 600 nm under the excitation of 488 nm in the absence of Hg(2+) ions. When Hg(2+) ions appear in the aqueous solution, Hg(2+) ions are sandwiched between the hairpin-shaped double-stranded DNA due to the formation of the thymine-Hg(2+)-thymine complex, which holds the Hg(2+) ions in proximity to the surface of GO sheets. As a result, the fluorescence emission of GO is quenched. The present GO-based sensor shows a limit of detection as low as 0.92 nM and excellent selectivity toward Hg(2+) over a wide range of metal ions. The present work indicates that GO is a promising fluorescent probe for detection of metal ions and biomolecules.

Three-dimensional paper-based electrochemiluminescence device for simultaneous detection of Pb2+ and Hg2+ based on potential-control technique

In this work, a microfluidic paper-based analytical device (μPADs) has been proposed for simultaneous electrochemiluminescence (ECL) detection of lead ion (Pb(2+)) and mercury ion (Hg(2+)) based on oligonucleotide. The functionalized wax-patterned three-dimensional (3D) paper-based ECL device that can provide fast, cost-effective, simple, and sensitive detection for analysis was dependent on Pb(2+) and Hg(2+)-induced conformational change of DNA strands through the formation of G-quadruplex and T-Hg-T complex, respectively. The carbon nanocrystals (CNCs) capped silica nanoparticles (Si@CNCs) and Ru(bpy)(3)(2+)-gold nanoparticles (AuNPs) aggregates (Ru@AuNPs) were both used as ECL labels in our case. Structure characterization of Si@CNCs and Ru@AuNPs were obtained by the transmission electron microscope (TEM). Due to the different operational potentials of Si@CNCs and Ru@AuNPs, Pb(2+) and Hg(2+) coexisting in one paper working zone can be determined simultaneously with detection limits of 10 pM and 0.2 nM, respectively. Finally, this simple and cost-effective device was successfully applied for simultaneous detection of Pb(2+) and Hg(2+) in lake water and human serum samples, respectively.

Single-step multiplex detection of toxic metal ions by Au nanowires-on-chip sensor using reporter elimination

We have developed a Au nanowires (NWs)-on-chip surface-enhanced Raman scattering (SERS) multiplex sensor that can sensitively detect multiple toxic metal ions. Most importantly, the reporter elimination method simplified the detection procedure to a single step, which has been much desired for remote environmental monitoring. This sensor has several notable features. First, it shows high reproducibility based on well-defined single-crystalline Au NWs. Second, single-NW-sensors that can detect a specific metal ion are combined for multiplex sensing of metal ions. Third, when a sample solution is put onto the NWs-on-chip sensor, a decrease in the SERS signal of a specific NW-sensor identifies the target metal ion. Simple, rapid, sensitive and quantitative detection of metal ions becomes possible through the measurement of the SERS signals. We successfully detected ions of mercury (Hg(2+)), silver (Ag(+)), and lead (Pb(2+)) coexisting in the same solution by using this sensor.

Sensitive dual DNAzymes-based sensors designed by grafting self-blocked G-quadruplex DNAzymes to the substrates of metal ion-triggered DNA/RNA-cleaving DNAzymes

A universal label-free metal ion sensor design strategy was developed on the basis of a metal ion-specific DNA/RNA-cleaving DNAzyme and a G-quadruplex DNAzyme. In this strategy, the substrate strand of the DNA/RNA-cleaving DNAzyme was designed as an intramolecular stem-loop structure, and a G-rich sequence was caged in the double-stranded stem and could not form catalytically active G-quadruplex DNAzyme. The metal ion-triggered cleavage of the substrate strand could result in the release of the G-rich sequence and subsequent formation of a catalytic G-quadruplex DNAzyme. The self-blocking mechanism of the G-quadruplex DNAzyme provided the sensing system with a low background signal. The signal amplifications of both the DNA/RNA-cleaving DNAzyme and the G-quadruplex DNAzyme provided the sensing system with a high level of sensitivity. This sensor design strategy can be used for metal ions with reported specific DNA/RNA-cleaving DNAzymes and extended for metal ions with unique properties. As examples, dual DNAzymes-based Cu(2+), Pb(2+) and Hg(2+) sensors were designed. These "turn-on" colorimetric sensors can simply detect Cu(2+), Pb(2+) and Hg(2+) with high levels of sensitivity and selectivity, with detection limits of 4 nM, 14 nM and 4 nM, respectively.

Label-free sensing of pH and silver nanoparticles using an "OR" logic gate

Many natural phenomena are associated with the presence of two or more separate variables. We report here an "OR" DNA logic gate based on a luminescent platinum(II) switch-on probe for silver nanoparticles and pH, both of which may be considered putative indicators of pollution. The modulation of metal complex/double-stranded DNA complex phosphorescence by Ag(+) and H(+) was used to construct a simple, rapid and label-free method for the label-free detection of pH and nanomolar Ag(+) ions and nanoparticles in aqueous solutions with high selectivity.

Amplified fluorescence detection of mercury(II) ions (Hg2+) using target-induced DNAzyme cascade with catalytic and molecular beacons

In this work, a fluorescent sensing strategy was developed for the detection of mercury(II) ions (Hg(2+)) in aqueous solution with excellent sensitivity and selectivity using a target-induced DNAzyme cascade with catalytic and molecular beacons (CAMB). In order to construct the biosensor, a Mg(2+)-dependent DNAzyme was elaborately designed and artificially split into two separate oligonucleotide fragments. In the presence of Hg(2+), the specific thymine-Hg(2+)-thymine (T-Hg(2+)-T) interaction induced the two fragments to produce the activated Mg(2+)-dependent DNAzyme, which would hybridize with a hairpin-structured MB substrate to form the CAMB system. Eventually, each target-induced activated DNAzyme could catalyze the cleavage of many MB substrates through true enzymatic multiple turnovers. This would significantly enhance the sensitivity of the Hg(2+) sensing system and push the detection limit down to 0.2 nM within a 20 min assay time, much lower than those of most previously reported fluorescence assays. Owning to the strong coordination of Hg(2+) to the T-T mismatched pairs, this proposed sensing system exhibited excellent selectivity for Hg(2+) detection, even in the presence of 100 times of other interferential metal ions. Furthermore, the applicability of the biosensor for Hg(2+) detection in river water samples was demonstrated with satisfactory results. These advantages endow the sensing strategy with a great potential for the simple, rapid, sensitive, and specific detection of Hg(2+) from a wide range of real samples.

Dual polarisation interferometry for real-time, label-free detection of interaction of mercury(II) with mercury-specific oligonucleotides

A real-time, label-free dual polarisation interferometry technique was used to investigate the interaction of Hg(2+) with a 21-mer T-rich oligonucleotide and further construct a Hg(2+) biosensor based on thymine-Hg(2+)-thymine coordination chemistry.