A mini-review on functional nucleic acids-based heavy metal ion detection

Oligonucleotide-induced regulation of the oxidase-mimicking activity of octahedral Mn3O4 nanoparticles for colorimetric detection of heavy metals

A colorimetric assay for the determination of heavy metal ions is presented that is based on the regulation of the oxidase-mimicking activity of Mn₃O₄ nanoparticles (NPs) by oligonucleotides. The chromogenic agent tetramethylbenzidine (TMB) is oxidized by the catalytic action of Mn₃O₄ NPs to generate products that have a yellow color in acidic solution, with a peak at 450 nm. It is found that random oligonucleotides are absorbed on the regular surface of the Mn₃O₄ NPs and temporarily inhibit the oxidation of TMB. This leads to a decrease in absorbance and a light-green coloration of the solution. The results show that the purine bases in oligonucleotides play a key role in their regulation of the activity of the NPs. The regulatory effect is assumed to be of the noncompetitive type. In the presence of heavy metal ions like Hg(II) or Cd(II), the inhibition is canceled due to the binding of heavy metal ions to thymine bases, and the color of the solution changes from light green to yellow. The increase in absorbance at 450 nm is related to the amount of heavy metal ions present. The method allows Hg(II) and Cd(II) to be determined visually in concentrations as low as 20 μg·L^-1. The detection limit of the colorimetric assay is 3.8 and 2.4 μg·L^-1 of Hg(II) and Cd(II), respectively. The assay displays good selectivity over other heavy metal ions. The method was successfully validated by analyzing several water samples. Graphical abstract Schematic representation of the colorimetric assay for Hg(II) and Cd(II) based on the intrinsic oxidase-mimicking activity of Mn₃O₄ nanoparticles that is regulated by oligonucleotides.

Improved performances of catalytic G-quadruplexes (G4-DNAzymes) via the chemical modifications of the DNA backbone to provide G-quadruplexes with double 3'-external G-quartets

Here we report on the design of a new catalytic G-quadruplex-DNA system (G4-DNAzyme) based on the modification of the DNA scaffold to provide the DNA pre-catalyst with two identical 3'-ends, known to be more catalytically proficient than the 5'-ends. To this end, we introduced a 5'-5' inversion of polarity site in the middle of the G4-forming sequences AG₄A and AG₆A to obtain d(^3'AGG^5'-^5'GGA^3') (or AG₂-G₂A) and d(^3'AGGG^5'-^5'GGGA^3') (or AG₃-G₃A) that fold into stable G4 whose tetramolecular nature was confirmed via nuclear magnetic resonance (NMR) and circular dichroism (CD) investigations. Both AG₂-G₂A and AG₃-G₃A display two identical external G-quartets (3'-ends) known to interact with the cofactor hemin with a high efficiency, making the resulting complex competent to perform hemoprotein-like catalysis (G4-DNAzyme). A systematic comparison of the performances of modified and unmodified G4s lends credence to the relevance of the modification exploited here (5'-5' inversion of polarity site), which represents a new chemical opportunity to improve the overall activity of catalytic G4s.

Nanomaterial-based aptamer sensors for arsenic detection

Arsenic (As) is a highly toxic contaminant in the environment and a serious carcinogen for the human being. The toxicity of arsenic significantly threatens environmental and human health. The effective removing technology for arsenic remains challenging, and one of the reasons is due to the lack of powerful detection method in the complex environmental matrix. There is thus an urgent need to develop novel analytical methods for arsenic, preferably with the potential for the field-testing. To combat arsenic pollution and maintain a healthy environment and eco-system, many analytical methods have been developed for arsenic detection in various samples. Among these strategies, biosensors hold great promise for rapid detection of arsenic, in particular, nanomaterials-based aptamer sensors have attracted significant attention due to their simplicity, high sensitivity and rapidness. In this paper, we reviewed the recent development and applications of aptamer sensors (aptasensors) based-on nanomaterial for arsenic detection, in particular with emphasis on the works using optical and electrochemical technologies. We also discussed the recent novel technology in aptasensors development for arsenic detection, including nucleic acid amplification for signal enhancement and device integration for the portability of arsenic sensors. We are hoping this review could inspire further researches in developing novel nanotechnologies based aptasensors for possible on-site detection of arsenic.

Recent advances in the development of electrochemical aptasensors for detection of heavy metals in food

Heavy metal contamination in environment and food has attracted intensive attention from the public since it poses serious threats to ecological system and human health. Traditional detection methods for heavy metals such as atomic absorption spectrometry have a fairly low detection limit, but the methods have many limitations and disadvantages. Therefore, it is of significance to develop a rapid technology for real-time and online detection of heavy metals. The electrochemical aptasensor-based technology is promising in the detection of heavy metals with advantages of high sensitivity, specificity, and accuracy. Although its development is rapid, more researches should be carried out before this technology can be used for on-site detection. In this review, the origin, basic principles and development of electrochemical aptasensors are introduced. The applications of nanomaterials and electrochemical aptasensors for the detection of heavy metals (mainly mercury, lead, cadmium, and arsenic) are summarized. The research and application tendency of electrochemical aptasensors for detection of heavy metals are prospected.

Heavy Metal/Toxins Detection Using Electronic Tongues

The growing concern for sustainability and environmental preservation has increased the demand for reliable, fast response, and low-cost devices to monitor the existence of heavy metals and toxins in water resources. An electronic tongue (e-tongue) is a multisensory array mostly based on electroanalytical methods and multivariate statistical techniques to facilitate information visualization in a qualitative and/or quantitative way. E-tongues are promising analytical devices having simple operation, fast response, low cost, easy integration with other systems (microfluidic, optical, etc) to enable miniaturization and provide a high sensitivity for measurements in complex liquid media, providing an interesting alternative to address many of the existing environmental monitoring challenges, specifically relevant emerging pollutants such as heavy metals and toxins.

Bio-Recognition in Spectroscopy-Based Biosensors for *Heavy Metals-Water and Waterborne Contamination Analysis

: Microsystems and biomolecules integration as well multiplexing determinations are key aspects of sensing devices in the field of heavy metal contamination monitoring. The present review collects the most relevant information about optical biosensors development in the last decade. Focus is put on analytical characteristics and applications that are dependent on: (i) Signal transduction method (luminescence, colorimetry, evanescent wave (EW), surface-enhanced Raman spectroscopy (SERS), Förster resonance energy transfer (FRET), surface plasmon resonance (SPR)); (ii) biorecognition molecules employed (proteins, nucleic acids, aptamers, and enzymes). The biosensing systems applied (or applicable) to water and milk samples will be considered for a comparative analysis, with an emphasis on water as the primary source of possible contamination along the food chain.

Detection of coralyne and heparin by polymerase extension reaction using SYBR Green I

Polydeoxyadenosine (poly (dA)) has been extensively applied for detecting many drug molecules. Herein, we developed a sensitive method for detecting coralyne and heparin using a modified DNA probe with poly (dA) at one end. In the absence of coralyne, the DNA probe was digested by the Exonuclease I (Exo I), and therefore the SYBR Green I (SG I) emitted an extremely low fluorescent signal. While coralyne specifically binding to poly (dA) with strong propensity could remarkably restrain the disintegration of the DNA probe, through which as a template the second strand of DNA sequence was formed with the introduction of DNA polymerase. Therefore, the fluorescent signal of SG I was intensified to quantify coralyne. Based on this method, heparin can be determined due to its strong affinity towards coralyne. This method showed a linear range from 2 to 500 nM for coralyne with a low detection limit of 0.98 nM, and the linear range of heparin was from 1 to 100 nM when 1.25 nm was the detection limit. The proposed method was also implemented successfully in biological samples and showed a potential application for screening potential therapeutic molecules.

DNAzyme-Functionalized R-Phycoerythrin as a Cost-Effective and Environment-Friendly Fluorescent Biosensor for Aqueous Pb2+ Detection

The sensitive detection of Pb²⁺ is of significant importance for food safety, environmental monitoring, and human health care. To this end, a novel fluorescent biosensor, DNAzyme-functionalized R-phycoerythrin (DNAzyme-R-PE), was presented for Pb²⁺ analysis. The biosensor was prepared via the immobilization of Iowa Black^® FQ-modified DNAzyme–substrate complex onto the surface of SPDP-functionalized R-PE. The biosensor produced a minimal fluorescence signal in the absence of Pb²⁺. However, Pb²⁺ recognition can induce the cleavage of substrate, resulting in a fluorescence restoration of R-PE. The fluorescence changes were used to measure sensitively Pb²⁺ and the limit of detection was 0.16 nM with a linear range from 0.5–75 nM. Furthermore, the proposed biosensor showed excellent selectivity towards Pb²⁺ even in the presence of other metal ions interferences and was demonstrated to successfully determine Pb²⁺ in spiked lake water samples.

Binding of metal ions and water molecules to nucleic acid bases: the influence of water molecule coordination to a metal ion on water-nucleic acid base hydrogen bonds

The interactions of nucleic acid bases with non-coordinated and coordinated water molecules were studied by analyzing data in the Protein Data Bank (PDB) and by quantum chemical calculations. The analysis of the data in the crystal structures from the PDB indicates that hydrogen bonds involving oxygen or nitrogen atoms of nucleic acid bases and water molecules are shorter when water is bonded to a metal ion. These results are in agreement with the quantum chemical calculations on geometries and interaction energies of hydrogen bonds; the calculations on model systems show that hydrogen bonds of nucleic acid bases with water bonded to a metal ion are stronger than hydrogen bonds with non-coordinated water. These calculated values are similar to the strength of hydrogen bonds between nucleic acid bases. The results presented in this paper may be relevant to understand the role of water molecules and metal ions in the process of replication and stabilization of nucleic acids and also to understand the possible toxicity of metal ion interactions with nucleic acids.

Coordination-induced structural changes of DNA-based optical and electrochemical sensors for metal ions detection

Metal ions play a critical role in human health and abnormal levels are closely related to various diseases. Therefore, the detection of metal ions with high selectivity, sensitivity and accuracy is particularly important. This article highlights and comments on the coordination-induced structural changes of DNA-based optical, electrochemical and optical-electrochemical-combined sensors for metal ions detection. Challenges and potential solutions of DNA-based sensors for the simultaneous detection of multiple metal ions are also discussed for further development and exploitation.

One-Pot Synthesis of Nucleoside-Templated Fluorescent Silver Nanoparticles and Gold Nanoparticles

In this study, a simple one-pot method was proposed to synthesize water-soluble nucleoside-templated fluorescent silver nanoparticles (Ag NPs) and gold nanoparticles (Au NPs). The nucleoside-templated fluorescent Ag NPs and Au NPs were further characterized by transmission electron microscopy (TEM), Fourier transform infrared spectroscopy (FTIR), and fluorescence spectroscopy (FLS). The effects of the molar ratio of reactants, reaction environment, and nucleotides on the synthesis of Ag NPs and Au NPs were also discussed. The results showed that nucleoside and ascorbic acid acted as a stabilizer and reductant, respectively, in the synthesis of Ag NPs and Au NPs, while citrate buffer acted as both a pH regulator and reductant. The synthesized nucleoside-templated fluorescent Ag NPs and Au NPs have good fluorescence stability and easy water solubility. In this study, a simple one-pot method was proposed to synthesize water-soluble nucleoside-templated fluorescent silver nanoparticles (Ag NPs) and gold nanoparticles (Au NPs).

A simple paper-based aptasensor for ultrasensitive detection of lead (II) ion

In this study, a simple paper-based aptasensor has been developed for the ultrasensitive detection of lead (Pb²⁺) ion within about 10 min. The aptasensor has been successfully designed by taking advantages of the Förster Resonance Energy Transfer (FRET) process and the super fluorescence quenching property of graphene oxide (GO) sheet. The sensing mechanism of the aptasensor is based on the conformational switch of the Pb²⁺-specific aptamer from a random coil to a G-quadruplex structure. An injection of Pb²⁺ on the paper-based platform induces the release of the specific aptamer from the GO surface that recovers the fluorescence emission. Under the optimal experimental conditions, there is a good linear relationship between the fluorescence recovery and the Pb²⁺concentration in the ranges of 5-70 pM and 0.07-20 nM. Moreover, the aptasensing array exhibits a high sensitivity to Pb²⁺ with an ultra-low detection limit of 0.5 pM. The developed aptasensor has been successfully applied to determine Pb²⁺ in tap water, lake water, milk, and human blood serum. The paper-based aptasensor can be efficiently utilized to detect other metal ions and biological molecules by substituting target specific aptamer.

Microfluidic Technology for Nucleic Acid Aptamer Evolution and Application

The intersection of microfluidics and aptamer technologies holds particular promise for rapid progress in a plethora of applications across biomedical science and other areas. Here, the influence of microfluidics on the field of aptamers, from traditional capillary electrophoresis approaches through innovative modern-day approaches using micromagnetic beads and emulsion droplets, is reviewed. Miniaturizing aptamer-based bioassays through microfluidics has the potential to transform diagnostics and embedded biosensing in the coming years.

Facile detection of melamine by a FAM-aptamer-G-quadruplex construct

The development of a novel method for melamine detection that uses a FAM-aptamer-G-quadruplex construct due to the efficient quenching ability of an aptamer-linked G-quadruplex is reported herein. The construct, which is labeled with the fluorescent dye 6-carboxyfluorescein (FAM), consists of two parts: a melamine-binding aptamer and a G-rich sequence that can form a G-quadruplex structure. Because of the specific recognition of melamine by the T-rich aptamer, this aptamer folds into a hairpin structure in the presence of melamine, which draws the G-quadruplex closer to the FAM fluorophore, leading to the quenching of the fluorescence of FAM. Thus, a highly sensitive and selective fluorescence strategy for assaying melamine was established. Under optimal conditions, the fluorescence quenching is proportional to the concentration of melamine within the range 10-90 nM, and the method has a detection limit of 6.32 nM. Further application of the method to plastic cup samples suggested that it permitted recoveries of between 97.15% ± 1.02 and 101.92% ± 2.07. The detected amounts of melamine spiked into the plastic cup samples and the corresponding amounts measured by HPLC were in good accordance, indicating that this fluorescent method is reliable and practical. Owing to its high sensitivity, excellent selectivity, and convenient procedure, this strategy represents a promising alternative method of melamine screening. Graphical abstract.

Label-free biosensing using a microring resonator integrated with poly-(dimethylsiloxane) microfluidic channels

Microring resonators have shown promising potential for highly sensitive, label-free, real-time detection of biomolecules. Accurate quantitative detection of target molecules through use of photonic integrated circuits has been demonstrated for environmental monitoring and medical diagnostics. Here, we described the design, fabrication, and characterization of a highly sensitive, label-free microring optical resonator integrated with poly-(dimethylsiloxane) microfluidic channels, which consumes only 30 µl of sample solution. The resonance wavelength shifts resulting from the change in the effective refraction index can be measured in situ, and thus the binding events on the resonator surface, including antibody immobilization, blocking of the resonator surface, and the specific binding of antibody and antigen, can be recorded throughout the entire experimental process in real time. We measured the binding events for the detection of human immunoglobulin G. The system had a detection limit of 0.5 µg/ml, a value substantially (14 times) lower than that of a previously reported microring resonator. To verify the usefulness and adaptability of this technique, human epidermal growth factor receptor 2 was used for the detection. The microring optical resonator was able to monitor reactions between biological molecules in real time and thus can be used in quantitative detection and biological sensing with little sample consumption.

Heavy Metal Ion Detection Platforms Based on a Glutathione Probe: A Mini Review

Globally, heavy metal ion (HMI) contamination is on the rise, posing an ever-increasing risk to ecological and human health. In recent years, great research effort has been devoted to the sensitive detection and quantitative analysis of HMIs. Low cost, sensitive, selective, and rapid methods for HMI detection are of growing demand, and HMI biosensors have great potential in meeting this need due to their timeliness, cost-effectiveness and convenience in operation. Glutathione is known for its strong ability to bind with toxic heavy metal ions, in addition to its water solubility, stable activity and ready availability. As a result, glutathione is becoming a molecular probe of choice in the preparation of sensors for sensitive, affordable, and accessible HMI detection. This review summarizes the results from various glutathione-based HMI detection strategies reported in recent years, which are categorized according to their signal transduction methods. Their operation and implementation, along with figures of merit such as limit of detection, selectivity, and response time, are discussed and compared. Based on the review, both individual HMI detection and simultaneous detection of multiple HMIs can be realized under specific reaction conditions, showing the great potential of glutathione-based detection to realize various types of practical HMI detection.

Electrochemical aptasensor for ampicillin detection based on the protective effect of aptamer-antibiotic conjugate towards DpnII and Exo III digestion

A simple and sensitive electrochemical method was developed for ampicillin detection based on the protective effect of aptamer-antibiotic conjugate towards endonuclease DpnII activity. Without ampicillin, DNA aptamer firstly hybridizes with the capture probe to form double strand DNA (dsDNA) structure. Then, dsDNA is cleaved by DpnII restriction endonuclease to form two dsDNA fragments. In which, one fragment is released from electrode surface and the other fragment is kept on electrode surface. Then, the dsDNA fragment kept on electrode surface is further digested by Exo III, which leads to the release of the dsDNA fragment from electrode surface. Thus, the electrochemical signal increases due to the decrease of the interface electron transfer resistance causing by the release of dsDNA from electrode surface. However, the formation of dsDNA is blocked when forming aptamer-ampicillin conjugate, which makes the obstruction of the digestion of DpnII and Exo III towards capture probe. Thus, a weak electrochemical signal is achieved due to the increase of the interface electron transfer resistance causing by the dsDNA on the electrode surface. Based on the relationship between ampicillin concentration and the decrease of the electrochemical signal, antibiotic is detected with low detection limit of 32 pM under optimal conditions, which is lower than the mandated maximum residue limit of European Union (9.93 nM). The developed method also presents good detection selectivity. Moreover, the applicability is confirmed by detecting antibiotic in milk and water samples with satisfactory results.

Experimental and computational investigation of a DNA-shielded 3D metal–organic framework for the prompt dual sensing of Ag+ and S2−

We herein report an efficient Ag⁺ and S²⁻ dual sensing scenario by a three-dimensional (3D) Cu-based metal–organic framework [Cu(Cdcbp)(bpea)]_n (MOF 1, H₃CdcbpBr = 3-carboxyl-(3,5-dicarboxybenzyl)-pyridinium bromide, bpea = 1,2-di(4-pyridinyl)ethane) shielded with a 5-carboxytetramethylrhodamine (TAMRA)-labeled C-rich single-stranded DNA (ss-probe DNA, P-DNA) as a fluorescent probe. The formed MOF-DNA probe, denoted as P-DNA@1, is able to sequentially detect Ag⁺ and S²⁻ in one pot, with detection limits of 3.8 nM (for Ag⁺) and 5.5 nM (for S²⁻), which are much more lower than the allowable Ag⁺ (0.5 μM) and S²⁻ (0.6 μM) concentration in drinking water as regulated by World Health Organization (WHO). The detection method has been successfully applied to sense Ag⁺ and S²⁻ in domestic, lake, and mineral water with satisfactory recoveries ranging from 98.2 to 107.3%. The detection mechanism was further confirmed by molecular simulation studies.

We herein report an efficient Ag⁺ and S²⁻ dual sensing scenario by a three-dimensional Cu-based metal–organic framework shielded with a 5-carboxytetramethylrhodamine-labeled C-rich single-stranded DNA as a fluorescent probe.

A colorimetric assay system for dopamine using microfluidic paper-based analytical devices

We report the colorimetric detection of dopamine (DA) on microfluidic paper-based analytical devices (μPADs) using an oxidation-reduction method. Here, dopamine reacts with ferric chloride forming reduced Fe²⁺ that subsequently reacts with phenanthroline to form the red tris(1,10-phenanthroline)iron(II) complex. The devices were fabricated by wax printing and changes in color intensity were recorded using a common cell phone. Subsequent analysis using Photoshop software, yielded a limit of detection (LOD) for DA of 0.37 μmol/L with a linear range of 0.527-4.75 μmol/L and relative standard deviation of 0.11% (inter-day) and 0.15% (intra-day) for n = 15 paper chips. The effects of detection conditions have been investigated and are discussed. Cow serum samples and human blood serum and plasma samples were detected. The work, herein, demonstrates the potential of this method as a low cost and rapid colorimetric technique to detect DA in real samples.

An aptamer-based fluorescence bio-sensor for chiral recognition of arginine enantiomers

In this study, a novel aptamer - based fluorescence bio-sensor (aptamer-AuNps) was developed for chiral recognition of arginine (Arg) enantiomers based on aptamer and gold nanoparticles (AuNps). Carboxyfluorescein (FAM) labeled aptamers (Apt) were absorbed on AuNps and their fluorescence intensity could be significantly quenched by AuNps based on fluorescence resonance energy transfer (FRET). Once d-Arg or l-Arg were added into the above solution, the aptamer specifically bind to Arg enantiomers and released from AuNps, so the fluorescence intensity of d-Arg system and l-Arg system were all enhanced. The affinity of Apt to l-Arg is tighter to d-Arg, so the enhanced fluorescence signals of l-Arg system was stronger than d-Arg system. What's more, the enhanced fluorescence were directly proportional to the concentration of d-Arg and l-Arg ranging from 0-300 nM and 0-400 nM with related coefficients of 0.9939 and 0.9952, respectively. Furthermore, the method was successfully applied to detection l-Arg in human urine samples with satisfactory results. Eventually, a simple "OR" logic gate with d-Arg &l-Arg as inputs and AuNps aggregation state as outputs was fabricated, which can help us understand the chiral recognition process deeply.

Simultaneous detection and determination of mercury (II) and lead (II) ions through the achievement of novel functional nucleic acid-based biosensors

The serious threats of mercury (Hg²⁺) and lead (Pb²⁺) ions for the public health makes it important to achieve the detection methods of the ions with high affinity and specificity. Metal ions usually coexist in some environment and foodstuff or clinical samples. Therefore, it is very necessary to develop a fast and simple method for simultaneous monitoring the amount of metal ions, especially when Hg²⁺ and Pb²⁺ coexist. DNAzyme-based biosensors and aptasensors have been highly regarded for this purpose as two main groups of the functional nucleic acid (FNA)-based biosensors. In this review, we summarize the recent achievements of functional nucleic acid-based biosensors for the simultaneous detection of Hg²⁺ and Pb²⁺ ions in two main optical and electrochemical groups. The tremendous interest in utilizing the various nanomaterials is also highlighted in the fabrication of the FNA-based biosensors. Finally, some results are presented based on the advantages and disadvantages of the studied FNA-based biosensors to compare their validation.

Paper-Based Sensor Chip for Heavy Metal Ion Detection by SWSV

Heavy metal ion pollution problems have had a terrible influence on human health and the environment. Therefore, the monitoring of heavy metal ions is of great practical significance. In this paper, an electrochemical three-electrode system was fabricated and integrated on nitrocellulose membrane (NC) by the use of magnetron sputtering technology, which exhibited a uniform arrangement of porous structure without further film modification. This paper-based sensor chip was used for Cu²⁺ detection by square-wave stripping voltammetry (SWSV). Within the ranges of 5–200 μg·L⁻¹ and 200–1000 μg·L⁻¹, it showed good linearity of 99.58% and 98.87%, respectively. The limit of detection was 2 μg·L⁻¹. On the basis of satisfying the detection requirements (10 μg·L⁻¹), the integrated sensor was small in size and inexpensive in cost. Zn²⁺, Cd²⁺, Pb²⁺ and Bi³⁺ were also detected by this paper-based sensor chip with good linearity.

Highly selective apo-arginase based method for sensitive enzymatic assay of manganese (II) and cobalt (II) ions

A novel enzymatic method of manganese (II) and cobalt (II) ions assay, based on using apo-enzyme of Mn²⁺-dependent recombinant arginase I (arginase) and 2,3-butanedione monoxime (DMO) as a chemical reagent is proposed. The principle of the method is the evaluation of the activity of L-arginine-hydrolyzing of arginase holoenzyme after the specific binding of Mn²⁺ or Co²⁺ with apo-arginase. Urea, which is the product of enzymatic hydrolysis of L-arginine (Arg), reacts with DMO and the resulted compound is detected by both fluorometry and visual spectrophotometry. Thus, the content of metal ions in the tested samples can be determined by measuring the level of urea generated after enzymatic hydrolysis of Arg by reconstructed arginase holoenzyme in the presence of tested metal ions. The linearity range of the fluorometric apo-arginase-DMO method in the case of Mn²⁺ assay is from 4pM to 1.10nM with a limit of detection of 1pM Mn²⁺, whereas the linearity range of the present method in the case of Co²⁺ assay is from 8pM to 45nM with a limit of detection of 2.5pM Co²⁺. The proposed method being highly sensitive, selective, valid and low-cost, may be useful to monitor Mn²⁺ and Co²⁺ content in clinical laboratories, food industry and environmental control service.

Quantifying the Degree of Aggregation from Fluorescent Dye-Conjugated DNA Probe by Single Molecule Photobleaching Technology for the Ultrasensitive Detection of Adenosine

In this work, we demonstrated a single molecule photobleaching-based strategy for the ultrasensitive detection of adenosine. A modified split aptamer was designed to specifically recognize individual adenosine molecules in solution. The specific binding of dye-labeled short strand DNA probes onto the elongated aptamer strand in the presence of adenosine resulted in a concentration-dependent self-aggregation process. The degree-of-aggregation (DOA) of the short DNA probes on the elongated aptamer strand could then be accurately determined based on the single molecule photobleaching measurement. Through statistically analyzing the DOA under different target concentrations, a well-defined curvilinear relationship between the DOA and target molecule concentration (e.g., adenosine) was established. The limit-of-detection (LOD) is down to 44.5 pM, which is lower than those recently reported results with fluorescence-based analysis. Owing to the high sensitivity and excellent selectivity, the sensing strategy described herein would find broad applications in biomolecule analysis under complicated surroundings.

Practical Application of Aptamer-Based Biosensors in Detection of Low Molecular Weight Pollutants in Water Sources

Water pollution has become one of the leading causes of human health problems. Low molecular weight pollutants, even at trace concentrations in water sources, have aroused global attention due to their toxicity after long-time exposure. There is an increased demand for appropriate methods to detect these pollutants in aquatic systems. Aptamers, single-stranded DNA or RNA, have high affinity and specificity to each of their target molecule, similar to antigen-antibody interaction. Aptamers can be selected using a method called Systematic Evolution of Ligands by EXponential enrichment (SELEX). Recent years we have witnessed great progress in developing aptamer selection and aptamer-based sensors for low molecular weight pollutants in water sources, such as tap water, seawater, lake water, river water, as well as wastewater and its effluents. This review provides an overview of aptamer-based methods as a novel approach for detecting low molecular weight pollutants in water sources.

Interband transitions in closed-shell vacancy containing graphene quantum dots complexed with heavy metals

High-performance optical detection of toxic heavy metals by using graphene quantum dots (GQDs) requires a strong interaction between the metals and GQDs, which can be reached through artificial creation of vacancy-type defects in GQDs.

Cascaded signal amplification via target-triggered formation of aptazyme for sensitive electrochemical detection of ATP

The construction of reliable sensors for adenosine triphosphate (ATP) detection gains increasing interest because of its important roles in various enzymatic activities and biological processes. Based on a cascaded, significant signal amplification approach by the integration of the aptazymes and catalytic hairpin assembly (CHA), we have developed a sensitive electrochemical sensor for the detection of ATP. The target ATP leads to the conformational change of the aptazyme sequences and their association with the hairpin substrates to form active aptazymes, in which the hairpin substrates are cyclically cleaved by the metal ion cofactors in buffer to release the enzymatic sequences that can also bind the hairpin substrates to generate active DNAzymes. The catalytic cleavage of the hairpin substrates in the aptazymes/DNAzymes thus results in the generation of a large number of intermediate sequences. Subsequently, these intermediate sequences trigger catalytic capture of many methylene blue-tagged signal sequences on the electrode surface through CHA, producing significantly amplified current response for sensitive detection of ATP at 0.6nM. Besides, the developed sensor can discriminate ATP from analogous interference molecules and be applied to human serum samples, making the sensor a useful addition to the arena for sensitive detection of small molecules.

Design of Research on Performance of a New Iridium Coordination Compound for the Detection of Hg2

Heavy metal pollution has become one of the most significant pollution problems encountered by our country in terms of environment protection. In addition to the significant effects of heavy metals on the human body and other organisms through water, food chain enrichment and other routes, heavy metals involved in daily necessities beyond the level limit could also affect people’s lives, so the detection of heavy metals is extremely important. Ir (III) coordination compound, considered to be one of the best phosphorescent sensing materials, is characterized by high luminous efficiency, easy modification of the ligand and so on, and it has potential applications in the field of heavy metal detection. This project aims to product a new Ir (III) functional coordination compound by designing a new auxiliary ligand and a main ligand with a sulfur identification unit, in order to systematically investigate the application of iridium coordination compound in the detection of the heavy metal Hg²⁺. With the introduction of the sulfur identification unit, selective sensing of Hg²⁺ could be achieved. Additionally, a new auxiliary ligand is also introduced to produce a functional iridium coordination compound with high quantum efficiency, and to diversify the application of iridium coordination compound in this field.

Selective Heavy Element Sensing with a Simple Host-Guest Fluorescent Array

A simple three component array of host-fluorophore complexes is capable of sensitive and selective discrimination of heavy metal ions, including lanthanide and actinide salts in aqueous solution. Instead of applying optical sensors that only use "single-mode" detection, i.e., coordination of the metal to a specific ligand and monitoring the change in emission of an appended fluorophore, we exploit a series of host-fluorophore complexes that are affected by the presence of small amounts of metal ions in aqueous solution in different ways. Variable host-metal and host-guest-metal interactions lead to both turn-on and turn-off fluorescence sensing mechanisms, enhancing the discriminatory properties of the array. The limit of detection for certain metals is as low as 70 nM, and highly similar metals such as lanthanides and actinides can be easily distinguished at low micromolar concentrations in complex salt mixtures.

DNAzyme sensors for detection of metal ions in the environment and imaging them in living cells

The on-site and real-time detection of metal ions is important for environmental monitoring and for understanding the impact of metal ions on human health. However, developing sensors selective for a wide range of metal ions that can work in the complex matrices of untreated samples and cells presents significant challenges. To meet these challenges, DNAzymes, an emerging class of metal ion-dependent enzymes selective for almost any metal ion, have been functionalized with fluorophores, nanoparticles and other imaging agents and incorporated into sensors for the detection of metal ions in environmental samples and for imaging metal ions in living cells. Herein, we highlight the recent developments of DNAzyme-based fluorescent, colorimetric, SERS, electrochemical and electrochemiluminscent sensors for metal ions for these applications.

Fe(III)-based metal-organic framework-derived core-shell nanostructure: Sensitive electrochemical platform for high trace determination of heavy metal ions

A new core-shell nanostructured composite composed of Fe(III)-based metal-organic framework (Fe-MOF) and mesoporous Fe₃O₄@C nanocapsules (denoted as Fe-MOF@mFe₃O₄@mC) was synthesized and developed as a platform for determining trace heavy metal ions in aqueous solution. Herein, the mFe₃O₄@mC nanocapsules were prepared by calcining the hollow Fe₃O₄@C that was obtained using the SiO₂ nanoparticles as the template, followed by composing the Fe-MOF. The Fe-MOF@mFe₃O₄@mC nanocomposite demonstrated excellent electrochemical activity, water stability and high specific surface area, consequently resulting in the strong biobinding with heavy-metal-ion-targeted aptamer strands. Furthermore, by combining the conformational transition interaction, which is caused by the formation of the G-quadruplex between a single-stranded aptamer and high adsorbed amounts of heavy metal ions, the developed aptasensor exhibited a good linear relationship with the logarithm of heavy metal ion (Pb²⁺ and As³⁺) concentration over the broad range from 0.01 to 10.0nM. The detection limits were estimated to be 2.27 and 6.73 pM toward detecting Pb²⁺ and As³⁺, respectively. The proposed aptasensor showed good regenerability, excellent selectivity, and acceptable reproducibility, suggesting promising applications in environment monitoring and biomedical fields.

The Effect of Adenine Repeats on G-quadruplex/hemin Peroxidase Mimicking DNAzyme Activity

The catalytic activity of G-quadruplex/hemin is much lower than that of proteinous enzymes, so it is very important to increase its activity. Very recently, flanking sequences, which can be regarded as an external part of G-quadruplexes, were found to enhance the activity of G-quadruplex/hemin DNAzyme. However, little is known about the effect of internal parts, such as loop sequences and linkers, on the activity. In the present study, adenine repeats were incorporated into several designed G-quadruplex structures either in the loops, bulges, or linkers, and the constructed G-quadruplex/hemin DNAzyme exhibit about fivefold improvement in peroxidase-mimicking activity in some cases. The enhancement effect may result from the formation of compound I, protoporphyrin⋅Fe^IV =O^.+ , accelerated by dA repeats, which was demonstrated by H₂ O₂ decay kinetics and pH dependency analysis. The novel enhancement methods described here may help in the development of high-activity DNAzymes, illustrated by a dimer G-quadruplex with flanking adenine at one end, a relatively long adenine run in one loop, and another adenine run in the linker.

Fluorescent aptasensor for 17β-estradiol determination based on gold nanoparticles quenching the fluorescence of Rhodamine B

In this paper, we developed a fluorescent aptasensor for 17β-estradiol (E2) determination in aqueous solution using label-free E2-specific aptamer, gold nanoparticles (AuNPs) and Rhodamine B (RhoB) as sensing probe, fluorescent quencher and fluorescent indicator respectively. In the absence of E2, AuNPs were wrapped by E2 aptamer and maintained dispersed in NaCl solution basically. These dispersed AuNPs could effectively impair the originally high fluorescence of RhoB. Contrarily, in the presence of E2, E2 aptamer could specifically combine with E2 to form E2-aptamer complex, so the AuNPs were released by E2 aptamer and aggregated under the influence of NaCl. The aggregated AuNPs have a weak influence on RhoB fluorescence. Therefore, the E2 concentration can be determined by the change of fluorescence intensity of RhoB. This fluorescent assay has a detection limit as low as 0.48 nM, a linear range from 0.48 to 200 nM, and high selectivity over other disrupting chemicals. It was applied to determine E2 in water samples with recoveries in the range of 94.3-111.7%. The fluorescent aptasensor holds great potential for E2 detection in environmental water samples.

Local conformational changes in the 8–17 deoxyribozyme core induced by activating and inactivating divalent metal ions

Placing 2-aminopurine at position 15 of the 8–17 DNAzyme allows the detection of a specific metal-induced conformational change, apparently coupled to the activation of catalysis.

Specificity of SNP detection with molecular beacons is improved by stem and loop separation with spacers

Dissection of stem and loop regions in molecular beacons by nucleotide or non-nucleotide linkers minimizes nonspecific recognition in SNP discrimination.

Colorimetric aptasensor for progesterone detection based on surfactant-induced aggregation of gold nanoparticles

This paper proposes an aptasensor for progesterone (P4) detection in human serum and urine based on the aggregating behavior of gold nanoparticles (AuNPs) controlled by the interactions among P4-binding aptamer, target P4 and cationic surfactant hexadecyltrimethylammonium bromide (CTAB). The aptamer can form an aptamer-P4 complex with P4, leaving CTAB free to aggregate AuNPs in this aptasensor. Thus, the sensing solution will turn from red (520 nm) to blue (650 nm) in the presence of P4 because P4 aptamers are used up firstly owing to the formation of an aptamer-P4 complex, leaving CTAB free to aggregate AuNPs. However, in the absence of P4, CTAB combines with aptamers so that AuNPs still remain dispersed. Therefore, this assay makes it possible to detect P4 not only by absorbance measurement but also through naked eyes. By monitoring the variation of absorbance and color, a CTAB-induced colorimetric assay for P4 detection was established with a detection limit of 0.89 nM. Besides, the absorbance ratio A650/A520 has a linear correlation with the P4 concentration of 0.89-500 nM. Due to the excellent recoveries in serum and urine, this biosensor has great potential with respect to the visual and instrumental detection of P4 in biological fluids.

2-Aminopurine-modified DNA homopolymers for robust and sensitive detection of mercury and silver

Heavy metal detection is a key topic in analytical chemistry. DNA-based metal recognition has advanced significantly producing many specific metal ligands, such as thymine for Hg²⁺ and cytosine for Ag⁺. For practical applications, however, robust sensors that can work in a diverse range of salt concentrations need to be developed, while most current sensing strategies cannot meet this requirement. In this work, 2-aminopurine (2AP) is used as a fluorescence label embedded in the middle of four 10-mer DNA homopolymers. 2AP can be quenched up to 98% in these DNA without an external quencher. The interaction between 2AP and all common metal ions is studied systematically for both free 2AP base and 2AP embedded DNA homopolymers. With such low background, Hg²⁺ induces up to 14-fold signal enhancement for the poly-T DNA, and Ag⁺ enhances up to 10-fold for the poly-C DNA. A detection limit of 3nM is achieved for both metals. With these four probes, silver and mercury can be readily discriminated from the rest. A comparison with other signaling methods was made using fluorescence resonance energy transfer, graphene oxide, and SYBR Green I staining, respectively, confirming the robustness of the 2AP label. Detection of Hg²⁺ in Lake Huron water was also achieved with a similar sensitivity. This work has provided a comprehensive fundamental understanding of using 2AP as a label for metal detection, and has achieved the highest fluorescence enhancement for non-protein targets.