Progress in biosensor based on DNA-templated copper nanoparticles

DNA-templated fluorescent metal nanoclusters and their illuminating applications

After the discovery of DNA during the mid-20th century, a multitude of novel methodologies have surfaced which exploit DNA for its various properties. One such recently developed application of DNA is as a template in metal nanocluster formation. In the early years of the new millennium, a group of researchers found that DNA can be adopted as a template for the binding of metal nanoparticles that ultimately form nanoclusters. Three metal nanoclusters have been studied so far, including silver, gold, and copper, which have a plethora of biological applications. This review focuses on the synthesis, mechanisms, and novel applications of DNA-templated metal nanoclusters, including the therapies that have employed them for their wide range of fluorescent properties, and the future perspectives related to their development by exploiting machine learning algorithms and molecular dynamics simulation studies.

A sequential dual-locked luminescent copper nanocluster probe for tumor cell imaging and killing

A sequential dual-locked luminescent copper nanoclusters (CuNCs) probe was designed and synthesized for the specific imaging and selective killing of tumor cells. This nanoprobe was prepared by first forming a Fe3+-coupled tannic acid (TA)-stabilized CuNCs (CuNCs-FeIII), which is in quenching state due to the electron transfer between CuNCs and Fe3+, and then coating a protectable layer of hyaluronic acid (HA) on the surface of CuNCs-FeIII to form the final dual-locked nanoprobe (CuNCs-FeIII@HA). When the nanoprobe of CuNCs-FeIII@HA target enter the tumor cells through CD44-HA receptor, HAase will first digest the HA layer of the nanoprobes, and then, GSH over-expressed in tumor cells will reduce Fe3+ to Fe2+, thus restoring the fluorescence emission of CuNCs and at the same time killing the tumor cells with the hydroxyl free radicals (∙OH) produced by the Fenton reaction between Fe2+ and H2O2. This sequential dual-locked luminescent nanoprobe of CuNCs-FeIII@HA has been successfully used for the specific imaging and selective killing of tumor cells.

Electrochemical aptasensor based on DNA-templated copper nanoparticles and RecJf exonuclease-assisted target recycling for lipopolysaccharide detection

An electrochemical aptasensor for detecting lipopolysaccharides (LPS) was fabricated based on DNA-templated copper nanoparticles (DNA-CuNPs) and RecJf exonuclease-assisted target recycling. The DNA-CuNPs were synthesized on a double-stranded DNA template generated through the hybridization of the LPS aptamer and its complementary chain (cDNA). In the absence of LPS, the CuNPs were synthesized on DNA double-strands, and a strong readout corresponding to the CuNPs was achieved at 0.10 V (vs. SCE). In the presence of LPS, the fabricated aptamer could detach from the DNA double-strand to form a complex with LPS, disrupting the template for the synthesis of CuNPs on the electrode. Meanwhile, RecJf exonuclease could hydrolyze the cDNA together with this single-stranded aptamer, releasing the LPS for the next round of aptamer binding, thereby enabling target recycling amplification. As a result, the electrochemical signal decreased and could be used to indicate the LPS content. The fabricated electrochemical aptasensor exhibited an extensive dynamic working range of 0.01 pg mL-1 to 100 ng mL-1, and its detection limit was 6.8 fg mL-1. The aptasensor also exhibited high selectivity and excellent reproducibility. Moreover, the proposed aptasensor could be used in practical applications for the detection of LPS in human serum samples.

A highly sensitive colorimetric DNA sensor for MicroRNA-155 detection: leveraging the peroxidase-like activity of copper nanoparticles in a double amplification strategy

A novel and highly sensitive colorimetric DNA sensor for determination of miRNA-155 at attomolar levelsis presented that combines the peroxidase-like activity of copper nanoparticles (CuNPs) with the hybridization chain reaction (HCR) . The utilization of CuNPs offers advantages such as strong interaction with double-stranded DNA, excellent molecular recognition, and mimic catalytic activity. Herein, a capture probe DNA (P1) was immobilized on carboxylated magnetic beads (MBs), allowing for amplified immobilization due to the 3D surface. Subsequently, the presence of the target microRNA-155 led to the formation of a sandwich structure (P2/microRNA-155/P1/MBs) when P2 was introduced to the modified P1/MBs. The HCR reaction was then triggered by adding H1 and H2 to create a super sandwich (H1/H2)n. Following this, Cu2+ ions were attracted to the negatively charged phosphate groups of the (H1/H2)n and reduced by ascorbic acid, resulting in the formation of CuNPs, which were embedded into the grooves of the (H1/H2)n. The peroxidase-like activity of CuNPs catalyzed the oxidation reaction of 3,3',5,5'-Tetramethylbenzidine (TMB), resulting in a distinct blue color measured at 630 nm. Under optimal conditions, the colorimetric biosensor exhibited a linear response to microRNA-155 concentrations ranging from 80 to 500 aM, with a detection limit of 22 aM, and discriminate against other microRNAs. It was also successfully applied to the determination of microRNA-155 levels in spiked human serum.

Highly Stable Fluorescent-Traffic-Light Sensor for Point-of-Care Detection of Tetracycline

Fluorescent point-of-care (POC) sensors have found great utility in fields like clinical diagnosis, food testing, and environmental monitoring. Herein, we developed a highly stable POC sensor that enabled the visual detection of tetracycline (TC) in a distinct fluorescent-traffic-light manner. In the sensor, a composite material of copper nanoclusters and metal-organic framework (CuNCs@MOF-5) prepared with a facile one-pot synthetic strategy was employed as the core element for target recognition and signal transduction. As evidenced by experiments, the as-prepared CuNCs@MOF-5 exhibited significantly improved fluorescence properties in terms of emission enhancement (about 28-fold) and stability improvement (over 110 days) compared to the CuNCs without confining and protection by MOF-5. More importantly, it was found that TC could uniquely interact with Zn(II) to trigger the disassembly of CuNCs@MOF-5, resulting in green fluorescence emission from the TC-Zn(II) complex and red fluorescence weakening of CuNCs. On the basis of this finding, a simple and stable sensor was proposed for POC detection of TC, which demonstrated high sensitivity, selectivity, and reproducibility. In addition to homogeneous visual detection in a 96-well plate, a CuNCs@MOF-5-contained agarose gel array was easily fabricated to achieve direct detection of TC in milk without any pretreatment, thanks to the size-sieving effect of the gel. Moreover, a test paper array was also put forward for low-cost TC detection, which indicates the extensibility and practicability of this sensing strategy.

A Sensitive Fluorescence Sensor for Tetracycline Determination Based on Adenine Thymine-Rich Single-Stranded DNA-Templated Copper Nanoclusters

A sensitive fluorescent sensor has been developed for the determination of tetracycline (TC) using adenine thymine (AT)-rich single-stranded DNA (ssDNA) templated copper nanoclusters (CuNCs) as a fluorescent probe. Fluorescent ssDNA-CuNCs were synthesized by employing AT-rich ssDNA as templates and ascorbic acid as reducing agents through a facile one-step method. The as-prepared ssDNA-CuNCs exhibited strong fluorescence with a large Stokes shift (240 nm) and stable fluorescence emission. In the presence of TC, the fluorescent intensity of ssDNA-CuNCs was obviously decreased through the inner filter effect, due to the spectral overlapping between ssDNA-CuNCs and TC. Under the optimal conditions, the strategy exhibited sensitive detection of TC with a linear range from 2 nM to 30 μM and with a limit of detection of 0.5 nM. Furthermore, the sensor was successfully applied for the detection of TC in milk samples. Therefore, it provided a simple, rapid, and label-free fluorescent method for TC detection.

Cyclodextrin Host-Guest Recognition in Glucose-Monitoring Sensors

Diabetes mellitus is a prevalent chronic health condition that has caused millions of deaths worldwide. Monitoring blood glucose levels is crucial in diabetes management, aiding in clinical decision making and reducing the incidence of hypoglycemic episodes, thereby decreasing morbidity and mortality rates. Despite advancements in glucose monitoring (GM), the development of noninvasive, rapid, accurate, sensitive, selective, and stable systems for continuous monitoring remains a challenge. Addressing these challenges is critical to improving the clinical utility of GM technologies in diabetes management. In this concept, cyclodextrins (CDs) can be instrumental in the development of GM systems due to their high supramolecular recognition capabilities based on the host-guest interaction. The introduction of CDs into GM systems not only impacts the sensitivity, selectivity, and detection limit of the monitoring process but also improves biocompatibility and stability. These findings motivated the current review to provide a comprehensive summary of CD-based blood glucose sensors and their chemistry of glucose detection, efficiency, and accuracy. We categorize CD-based sensors into four groups based on their modification strategies, including CD-modified boronic acid, CD-modified mediators, CD-modified nanoparticles, and CD-modified functionalized polymers. These findings shed light on the potential of CD-based sensors as a promising tool for continuous GM in diabetes mellitus management.

Label-Free, High-Throughput, Sensitive, and Logical Analysis Using Biomimetic Array Based on Stable Luminescent Copper Nanoclusters and Entropy-Driven Nanomachine

The development of an array for high-throughput and logical analysis of biomarkers is significant for disease diagnosis. DNA-templated copper nanoclusters (CuNCs) have a strong potential to serve as a label-free photoluminescence source in array platforms, but their luminescent stability and sensitivity need to be improved. Herein, we report a facile, sensitive, and robust biomimetic array assay by integrating with stable luminescent CuNCs and entropy-driven nanomachine (EDN). In this strategy, the luminescent stability of CuNCs was improved by adding fructose in CuNCs synthesis to offer a reliable label-free signal. Meanwhile, the DNA template for CuNCs synthesis was introduced into EDN with excellent signal amplification ability, in which the reaction triggered by target miRNA would cause the blunt/protruding conformation change of 3'-terminus accompanied by the production or loss of luminescence. In addition, a biomimetic array fabricated by photonic crystals (PCs) physically enhanced the emitted luminescent signal of CuNCs and achieved high-throughput signal readout by a microplate reader. The proposed assay can isothermally detect as low as 4.5 pM of miR-21. Moreover, the logical EDN was constructed to achieve logical analysis of multiple miRNAs by "AND" or "OR" logic gate operation. Therefore, the proposed assay has the advantages of label-free property, high sensitivity, flexible design, and high-throughput analysis, which provides ideas for developing a new generation of facile and smart platforms in the fields of biological analysis and clinical application.

Fluorescence enhancement of organic dyes by femtosecond laser-induced cavitation bubbles for crystal imaging

Fluorescence from organic dyes can be applied in many research fields such as imaging, bio-sensing and diagnosis. One shortcoming of fluorescence imaging is the limitation in emission intensity. Amplification of fluorescence signals can be achieved by the enhancement of localized electromagnetic fields. Metallic nanoparticles are widely applied to produce plasmon resonance, but they cause thermal damage to fragile bio-materials. In this study, we propose a method for nanoparticle-free fluorescence enhancement by ultrafast laser-induced cavitation bubbles in organic dye solutions. Fluorescence enhancement without the use of nanoparticles prevents potential hazards including thermal effects and biotoxicity. In order to achieve fluorescence enhancement in neat dye solution, cavitation bubbles were induced by focusing an 800 nm ultrafast laser beam. Another 400 nm laser beam was used to pump the gain medium. Fluorescence enhancement was observed in various dye solutions. The intensity and spectra of the fluorescence emission can be controlled by changing the power and focus of the excitation laser. According to time-resolved microscopy and simulation results, the cavity formed by the laser-induced bubbles results in the enhancement of the localized electromagnetic field and induces the amplification of the fluorescence signal. The bubble-enhanced fluorescence emission was used for imaging of protein crystals without causing thermal damage to the samples. This study provides an effective method for bio-compatible fluorescence enhancement and has application prospects in fields such as bio-imaging.

A universal approach for synthesis of copper nanoclusters templated by G-rich oligonucleotide sequences and their applications in sensing

Herein, five common G4 sequences have been selected, including three different length of telomere DNA, hemin aptamer, and thrombin aptamer, to synthesize Cu nanoclusters (Cu NCs) in-situ. All G4s are proper templates for Cu NCs with low temperature treatment. The particles (G4-Cu NCs) smaller than 3 nm in diameter were obtained and showed light green fluorescence. This is the first report of metal clusters templated by G4s in-situ. As proof of the concept, hemin and alkaline phosphatase (ALP) were used as the targets to test whether the system can monitor the interaction between G4s and its substrate. The results suggest that G4-Cu NCs can indicate the behavior of G4 and its interaction with hemin, and sensing ALP is achieved with the aid of ATP. The linear ranges of hemin and ALP are 300-4000 nM and 10-500 U/L, respectively, and the corresponding limits of detection as low as 97 nM for hemin and 2.8 U/L for ALP. Moreover, this present system has been successfully applied for the detection of ALP in human serum samples with satisfactory recoveries. This synthesis approach is universal, and it can be easily extended to evaluating the formation of G4, or monitoring the interaction between G4 and its substrate, or selective targeting individual G4, or sensitive detection of other important biomarkers by changing template G4 sequence.

Label-free and low-background FEN1 sensing based on cleavage-induced ligation of bifunctional dumbbell DNA and in-situ signal readout

Flap endonuclease 1 (FEN1) is overexpressed in various types of human tumor cells and has been recognized as a promising biomarker for cancer diagnosis in recent years. In this work, a label-free fluorescent nanosensor for FEN1 detection was developed based on cleavage-induced ligation of bifunctional dumbbell DNA and in-situ signal readout by copper nanoparticles (CuNPs). The dumbbell DNA was rationally designed with a FEN1 cleavable 5' flap for target recognition and AT-riched stem-loop template for CuNPs formation. In the presence of FEN1, 5' overhanging DNA flap of dumbbell DNA was effectively removed to form a linkable nick site. After the ligation by T4 DNA ligase, the dumbbell DNA changed to exonuclease-resisted closed structure which enabled in-situ generation of fluorescent CuNPs that served as signal source for target quantification. The low background attributed to synergic digestion by exonucleases facilitated the highly sensitive detection of FEN1 with limit of detection of 0.007 U/mL. Additionally, the sensor was extended to the assay of FEN1 inhibitor (aurintricarboxylic acid) with reasonable results. Last but not least, the normal cells and tumor cells were distinguished unambiguously by this sensor according to the detected concentration difference of cellular FEN1, which indicates the robustness and practicability of this nanosensor.

Determination of trypsin using protamine mediated fluorescent enhancement of DNA templated Au nanoclusters

A fluorescent method is described for trypsin determination through the strong electrostatic interactions between cationic polyelectrolytes and single-stranded DNA (ssDNA) templated Au nanoclusters (AuNCs). The ssDNA-AuNCs display improved fluorescence emission with excitation/emission maxima at 280/475 nm after being incorporated with poly(diallyldimethylammonium chloride) (PDDA). Fluorescent enhancement is mainly attributed to the electrostatic interactions occurring  between PDDA and ssDNA templates. This can make the conformation of the ssDNA templates to change. Thus, it offers a better microenvironment for stabilizing and protecting ssDNA-AuNCs, and results in fluorescence emission enhancement. By using protamine as a model, the method is employed for the determination of trypsin. The assay enables trypsin to be determined with good sensitivity and a linear response ranging from 5 ng⋅mL^-1 to 60 ng⋅mL^-1 with a 1.5 ng⋅mL^-1 limit of detection. It is also extended to determine  the trypsin contents in human's serum samples with recoveries between 98.7% and 103.5% with relative standard deviations (RSDs) between 3.5% and 4.8%. A novel fluorescent strategy has been developed for of trypsin determination by using protamine mediated fluorescent enhancement of DNA templated Au nanoclusters.

In situ imaging miRNAs using multifunctional linear DNA nanostructure

The microRNAs (miRNAs) play a critical role in many biological processes and are essential biomarkers for diagnosing disease. However, the sensitive and specific quantification of microRNAs (miRNAs) expression in living cells still faces a huge challenge. Our study designed a multifunctional linear DNA nanostructure (MLN) as a carrier of molecular beacons (MB-21) for detecting and intracellular imaging miRNA-21. The MLN-MB consists of three parts: aptamer, MLN, and MB-21. The aptamer (AS1411) could media MLN-MB enter live cells without additional transfection reagents. Once inside the cells, the intracellular miRNA-21 could hybridize the MB-21s, resulting in significantly enhanced fluorescence signals. The whole process was enzyme-free, autonomous, and continuous, which avoided the necessity of adding external fuel strands or enzymes. We demonstrated that the MLN-MB could be used to screen the miRNA-21 with a detection limit of 320 pM in a short time (10 min) and show high specificity toward miRNA-21 against other miRNAs. Moreover, the proposed MLN-MB could detect the miRNA-21 in complex matrixes stably. With its outstanding stability, dual recognition, and biocompatibility, MLN-MB is capable of delivering into living cells to identify specific cancer cells. Therefore, our sensing approach, with high sensitivity, specificity, and simplicity advantages, holds great potential for early cancer diagnosis.

Potential Environmental and Health Implications from the Scaled-Up Production and Disposal of Nanomaterials Used in Biosensors

Biosensors often combine biological recognition elements with nanomaterials of varying compositions and dimensions to facilitate or enhance the operating mechanism of the device. While incorporating nanomaterials is beneficial to developing high-performance biosensors, at the stages of scale-up and disposal, it may lead to the unmanaged release of toxic nanomaterials. Here we attempt to foster connections between the domains of biosensors development and human and environmental toxicology to encourage a holistic approach to the development and scale-up of biosensors. We begin by exploring the toxicity of nanomaterials commonly used in biosensor design. From our analysis, we introduce five factors with a role in nanotoxicity that should be considered at the biosensor development stages to better manage toxicity. Finally, we contextualize the discussion by presenting the relevant stages and routes of exposure in the biosensor life cycle. Our review found little consensus on how the factors presented govern nanomaterial toxicity, especially in composite and alloyed nanomaterials. To bridge the current gap in understanding and mitigate the risks of uncontrolled nanomaterial release, we advocate for greater collaboration through a precautionary One Health approach to future development and a movement towards a circular approach to biosensor use and disposal.

High Fructose Concentration Increases the Fluorescence Stability of DNA-Templated Copper Nanoclusters by Several Thousand Times

DNA-templated copper nanoclusters (CuNCs) have limited applications because of their low fluorescence stability (several tens of minutes). In this study, we prepared CuNCs with improved temporal fluorescence stability by introducing fructose into the CuNC synthesis process and optimizing the reaction conditions. The inclusion of fructose increased the operating lifetime of CuNCs by approximately 5200-fold from 30 min to 108 days and improved their stability against heat, acids, and bases compared to CuNCs synthesized under original conditions. In addition, the fluorescence signal of CuNCs was maintained for a significantly longer time when stored at refrigeration (4 °C) and freezing (-20 °C) temperatures. Importantly, this method did not require the addition of substances other than fructose or any additional physicochemical treatment to maintain the fluorescence of DNA-templated CuNCs for more than several tens of days. As such, this study could serve as a basis to improve the stability of CuNCs for various applications.

Rolling Circle Amplification-based Copper Nanoparticle Synthesis on Cyclic Olefin Copolymer Substrate and Its Application in Aptasensor

This study aimed to develop a label-free fluorescent aptasensor for the detection of diazinon (DZN) on a cyclic olefin copolymer (COC) substrate. The aptasensor design was based on rolling circle amplification (RCA) technology and the use of self-assembled copper nanoparticles (CuNPs). A dual-function (DF) probe, capable of binding to circular DNA and an aptamer, was designed and immobilized on a COC-bottom 96-well plate. An aptamer was used for selective recognition of DZN, and the specific site of the aptamer that strongly reacted with DZN was successfully identified using circular dichroism (CD) analysis. In presence of DZN, the aptamer and DZN formed a strong complex, thus providing an opportunity for hybridization of the DF probe and circular DNA, thereby initiating an RCA reaction. Repetitive poly thymine (T) sequence with a length of 30-mer, generated in the RCA reaction, served as a template for the synthesis of fluorescent copper nanoparticles, emitting an orange fluorescence signal (at approximately 620 nm) proportional to the amount of RCA product, within 10 min under UV irradiation. The CuNP fluorescence was imaged and quantified using an image analysis software. A linear correlation of the fluorescence signal was confirmed in the DZN concentration range of 0.1–3 ppm, with a detection limit of 0.15 ppm. Adoption of a label-free detection method, utilizing RCA and fluorescent CuNPs on COC substrates, reduced the need for complex equipment and requirements for DZN analysis, thereby representing a simple and rapid sensing method circumventing the limitations of current complex and labor-intensive methods.

Advancement in Nanoparticle-Based Biosensors for Point-of-Care In Vitro Diagnostics

Abstract:

Recently, there has been great progress in the field of extremely sensitive and precise detection of bioanalytes. The importance of the utilization of nanoparticles in biosensors has been recognized due to their unique properties. Specifically, nanoparticles of gold, silver, and magnetic plus graphene, quantum dots, and nanotubes of carbon are being keenly considered for utilizations within biosensors to detect nucleic acids, glucose, or pathogens (bacteria as well as a virus). Taking advantage of nanoparticles, faster and sensitive biosensors can be developed. Here we review the nanoparticles' contribution to the biosensors field and their potential applications.

Fluorescence determination of glyphosate based on a DNA-templated copper nanoparticle biosensor

A rapid and convenient fluorescence glyphosate (GLYP) biosensor was developed based on DNA-templated copper nanoparticles (DNA-CuNPs). In the absence of GLYP, the DNA-CuNPs were formed through the reduction of Cu2+ by vitamin C (Vc). The DNA-CuNPs emitted intense fluorescence at 615 nm when being excited at 340 nm. In the presence of GLYP, GLYP can strongly chelate with Cu2+ by the phosphate and carboxyl groups to decrease the amount of free Cu2+. Due to the lack of free Cu2+, DNA-CuNPs cannot be formed, which caused the fluorescence to decrease. The whole detection process of this proposed GLYP biosensor can be completed within 14 min. Titration experiments showed that this biosensor had a linear relationship for GLYP in the range 1 to 18 µM with a limit of detection (LOD) of 0.47 µM. This biosensor showed obvious selectivity among other pesticides, even between GLYP and organophosphorus pesticides. This biosensor performed well for GLYP detection in real samples with recoveries of 88.0-104.0%.

An Effective Label-Free Electrochemical Aptasensor Based on Gold Nanoparticles for Gluten Detection

Nanomaterials can be used to modify electrodes and improve the conductivity and the performance of electrochemical sensors. Among various nanomaterials, gold-based nanostructures have been used as an anchoring platform for the functionalization of biosensor surfaces. One of the main advantages of using gold for the modification of electrodes is its great affinity for thiol-containing molecules, such as proteins, forming a strong Au-S bond. In this work, we present an impedimetric biosensor based on gold nanoparticles and a truncated aptamer for the quantification of gluten in hydrolyzed matrices such as beer and soy sauce. A good relationship between the R_ct values and PWG-Gliadin concentration was found in the range between 0.1–1 mg L⁻¹ of gliadin (corresponding to 0.2–2 mg L⁻¹ of gluten) with a limit of detection of 0.05 mg L⁻¹ of gliadin (corresponding to 0.1 mg L⁻¹ of gluten). The label-free assay was also successfully applied for the determination of real food samples.

RNA polymerization actuating nucleic acid membrane (RANAM)-based biosensing for universal RNA virus detection

The coronavirus disease (COVID-19) pandemic has shown the importance of early disease diagnosis in preventing further infection and mortality. Despite major advances in the development of highly precise and rapid detection approaches, the time-consuming process of designing a virus-specific diagnostic kit has been a limiting factor in the early management of the pandemic. Here, we propose an RNA polymerase activity-sensing strategy utilizing an RNA polymerization actuating nucleic acid membrane (RANAM) partially metallized with gold for colorimetric RNA virus detection. Following RANAM-templated amplification of newly synthesized RNA, the presence of the RNA polymerase was determined by visualization of the inhibition of an oxidation/reduction (redox) reaction between 3,3',5,5'-tetramethylbenzidine (TMB) and blocked Au3+. As a proof of concept, a viral RNA-dependent RNA polymerase (RdRP), which is found in various RNA virus-infected cells, was chosen as a target molecule. With this novel RANAM biosensor, as little as 10 min of RdRP incubation could significantly reduce the colorimetric signal. Further development into an easy-to-use prototype kit in viral infection diagnosis detected RdRP present at levels even as low as 100 aM. Color formation based on the presence of RdRP could be simply and clearly confirmed through smartphone-assisted color imaging of the prototype kit. This study provides a non-PCR-based RNA virus detection including its variants using RdRP-mediated polymerization.

Application of Nanomaterials in Isothermal Nucleic Acid Amplification

Because of high sensitivity and specificity, isothermal nucleic acid amplification are widely applied in many fields. To facilitate and improve their performance, various nanomaterials, like nanoparticles, nanowires, nanosheets, nanotubes, and nanoporous films are introduced in isothermal nucleic acid amplification. However, the specific application, roles, and prospect of nanomaterials in isothermal nucleic acid amplification have not been comprehensively reviewed. Here, the application of different nanomaterials (0D, 1D, 2D, and 3D) in isothermal nucleic acid amplification is comprehensively discussed and recent progress in the field is summarized. The nanomaterials are mainly used for reaction enhancer, signal generation/amplification, or surface loading carriers. In addition, 3D nanomaterials can be also functioned as isolated chambers for digital nucleic acid amplification and the tools for DNA sequencing of amplified products. Challenges and future recommendations are also proposed to be better used for recent covid-19 detection, point-of-care diagnostic, food safety, and other fields.

Photoluminescent nanocluster-based probes for bioimaging applications

In the continuous search for versatile and better performing probes for optical bioimaging and biosensing applications, many research efforts have focused on the design and optimization of photoluminescent metal nanoclusters. They consist of a metal core composed by a small number of atoms (diameter < 2-3 nm), usually coated by a shell of stabilizing ligands of different nature, and are characterized by molecule-like quantization of electronic states, resulting in discrete and tunable optical transitions in the UV-Vis and NIR spectral regions. Recent advances in their size-selective synthesis and tailored surface functionalization have allowed the effective combination of nanoclusters and biologically relevant molecules into hybrid platforms, that hold a large potential for bioimaging purposes, as well as for the detection and tracking of specific markers of biological processes or diseases. Here, we will present an overview of the latest combined imaging or sensing nanocluster-based systems reported in the literature, classified according to the different families of coating ligands (namely, peptides, proteins, nucleic acids, and biocompatible polymers), highlighting for each of them the possible applications in the biomedical field.

Nanomaterials for electrochemical detection of pollutants in water: A review

The survival of living beings, including humanity, depends on a continuous supply of clean water. However, due to the development of industry, agriculture, and population growth, an increasing number of wastewaters is discarded, and the negative effects of such actions are clear. The first step in solving this situation is the collection and monitoring of pollutants in water bodies to subsequently facilitate their treatment. Nonetheless, traditional sensing techniques are typically laboratory-based, leading to potential diminishment in analysis quality. In this paper, the most recent developments in micro- and nano-electrochemical devices for pollutant detection in wastewater are reviewed. The devices reviewed are based on a variety of electrodes and the sensing of three different categories of pollutants: nutrients and phenolic compounds, heavy metals, and organic matter. From these electrodes, Cu, Co, and Bi showed promise as versatile materials to detect a grand variety of contaminants. Also, the most commonly used material is glassy carbon, present in the detection of all reviewed analytes.

A versatile fluorescent nanobeacon lighted by DNA-templated copper nanoparticles and the application in isothermal amplification detection

In this work, an environmentally-friendly and versatile nanobeacon was constructed by utilizing DNA-templated copper nanoparticles (CuNPs) as fluorescence signal source. As the key component of the nanobeacon, a hairpin DNA was designed to contain four segments: two segments for CuNPs template sequence, a target recognition segment and a blocking segment. At room temperature, the target recognition segment partly hybridizes with the blocking segment and thus prohibits the formation of double stranded DNA template, so that no CuNPs can be generated on the hairpin DNA. While a target is introduced, the specific binding of target with recognition sequence triggers off the conformational transformation of the hairpin DNA, which contributes to the formation of the CuNPs template. As a result, the in-situ generation of CuNPs gives birth to the fluorescence signal readout that can be used to identify the target. By reasonably varying the recognition sequence within hairpin DNA, a series of nanobeacons in response to corresponding targets, such as DNA, microRNA, thrombin, and ATP, were put forward with satisfactory sensitivity and selectivity. Moreover, this nanobeacon was also integrated with the strategy of enzyme-assisted target-recycling to realize signal amplification and ultrasensitive detection, which further demonstrated the versatility of the nanobeacon. This novel nanobeacon is expected to be a promising alternative to classical dye-labeled molecular beacon and provide new perspective on ultrasensitive fluorescence sensing.

Copper nanocluster composites for analytical (bio)-sensing and imaging: a review

As an ideal substitute for traditional organic fluorescent dyes or up-conversion nanomaterials, copper nanoclusters (CuNCs) have developed rapidly and have been involved in exciting achievements in versatile applications. The emergence of novel CuNCs composites improves the poor stability and fluorescence intensity of CuNCs. With this in mind, great efforts have been made to develop a wide variety of CuNCs composites, and impressive progress has been made in the past few years. In this review, we systematically summarize absorption, fluorescence, electrochemiluminescence, and catalytic properties and focus on the multiple factors that affect the fluorescence properties of CuNCs. The fluorescence properties of CuNCs are discussed from the point of view of core size, surface ligands, self-assembly, metal defects, pH, solvent, ions, metal doping, and confinement effect. Especially, we illustrate the research progress and representative applications of CuNCs composites in bio-related fields, which have received considerable interests in the past years. Additionally, the sensing mechanism of CuNCs composites is highlighted. Finally, we summarize current challenges and look forward to the future development of CuNCs composites. Schematic diagram of the categories, possible sensing mechanisms, and bio-related applications of copper nanoclusters composites.

Ultrasensitive and turn-on homogeneous Hg2+ sensing based on a target-triggered isothermal cycling reaction and dsDNA-templated copper nanoparticles

In this work, an ultrasensitive and turn-on sensor for homogeneous Hg2+ detection has been constructed based on a target-triggered isothermal cycling reaction and rapid label-free signal output with dsDNA-templated copper nanoparticles (CuNPs). As the key component of the sensor, a hairpin DNA without any labels was designed to contain different functional sequence segments and to resist digestion by exonuclease due to the protruding 3'-terminus. In the presence of Hg2+, the formation of a T-Hg2+-T structure turned the protruding 3'-terminus of the hairpin DNA to a blunt end that could be efficiently digested by Exo III, accompanied by Hg2+ release, followed by another digestion cycle. Hence, the Hg2+-triggered isothermal cycling reaction accumulated numerous dsDNA templates that facilitated fluorescent CuNP generation and finally output an amplified signal used to identify the target. This protocol is capable of Hg2+ sensing in a concentration range of 5 orders of magnitude with a detection limit down to 3.9 pM. The as-constructed sensor also revealed high selectivity, as well as satisfactory results in recovery experiments of Hg2+ detection in real water samples.

L-Histidine-DNA interaction: a strategy for the improvement of the fluorescence signal of poly(adenine) DNA-templated gold nanoclusters

An interesting phenomenon is described that the fluorescence signal of poly(adenine) (A) DNA-templated gold nanoclusters (AuNCs) is greatly improved in the presence of L-histidine by means of L-histidine-DNA interaction. The modified nanoclusters display strong fluorescence emission with excitation/emission maxima at 290/475 nm. The fluorescence quantum yield (QY) is improved from 1.9 to 6.5%. Fluorescence enhancement is mainly ascribed to the L-histidine-DNA interaction leading to conformational changes of the poly(A) DNA template, which offer a better microenvironment to protect AuNCs. The assay enables L-histidine to be determined with good sensitivity and a linear response that covers the 1 to 50 nM L-histidine concentration range with a 0.3 nM limit of detection. The proposed method has been applied to the determination of imidazole-containing drugs in pharmaceutical samples. A turn-on fluorescent method has been designed for the sensitive detection of L-histidine as well as imidazole-containing drugs on the basis of the L-histidine-DNA interaction.

Copper nanoclusters: designed synthesis, structural diversity, and multiplatform applications

Atomically precise metal nanoclusters (MNCs) have gained tremendous research interest in recent years due to their extraordinary properties. The molecular-like properties that originate from the quantized electronic states provide novel opportunities for the construction of unique nanomaterials possessing rich molecular-like absorption, luminescence, and magnetic properties. The field of monolayer-protected metal nanoclusters, especially copper, with well-defined molecular structures and compositions, is relatively new, about two to three decades old. Nevertheless, the massive progress in the field illustrates the importance of such nanoobjects as promising materials for various applications. In this respect, nanocluster-based catalysts have become very popular, showing high efficiencies and activities for the catalytic conversion of chemical compounds. Biomedical applications of clusters are an active research field aimed at finding better fluorescent contrast agents, therapeutic pharmaceuticals for the treatment and prevention of diseases, the early diagnosis of cancers and other potent diseases, especially at early stages. A huge library of structures and the compositions of copper nanoclusters (CuNCs) with atomic precisions have already been discovered during last few decades; however, there are many concerns to be addressed and questions to be answered. Hopefully, in future, with the combined efforts of material scientists, inorganic chemists, and computational scientists, a thorough understanding of the unique molecular-like properties of metal nanoclusters will be achieved. This, on the other hand, will allow the interdisciplinary researchers to design novel catalysts, biosensors, or therapeutic agents using highly structured, atomically precise, and stable CuNCs. Thus, we hope this review will guide the reader through the field of CuNCs, while discussing the main achievements and improvements, along with challenges and drawbacks that one needs to face and overcome.

Biomarker sensing platforms based on fluorescent metal nanoclusters

Metal nanoclusters (NCs) and their unique properties are increasing in importance and their applications are covering a wide range of areas. Their remarkable fluorescence properties and easy synthesis procedure and the possibility of functionalizing them for the detection of specific targets, such as biomarkers, make them a very interesting biosensing tool. Nowadays the detection of biomarkers related to different diseases is critical. In this context, NCs scaffolded within an appropriate molecule can be used to detect and quantify biomarkers through specific interactions and fluorescence properties of the NCs. These methods include analytical detection and biolocalization using imaging techniques. This review covers a selection of recent strategies to detect biomarkers related to diverse diseases (from infectious, inflammatory, or tumour origin) using fluorescent nanoclusters.

Label-Free DNA Biosensor Using Modified Reduced Graphene Oxide Platform as a DNA Methylation Assay

This work reports the use of modified reduced graphene oxide (rGO) as a platform for a label-free DNA-based electrochemical biosensor as a possible diagnostic tool for a DNA methylation assay. The biosensor sensitivity was enhanced by variously modified rGO. The rGO decorated with three nanoparticles (NPs)—gold (AuNPs), silver (AgNPs), and copper (CuNPs)—was implemented to increase the electrode surface area. Subsequently, the thiolated DNA probe (single-stranded DNA, ssDNA−1) was hybridized with the target DNA sequence (ssDNA-2). After the hybridization, the double-stranded DNA (dsDNA) was methylated by M.SssI methyltransferase (MTase) and then digested via a HpaII endonuclease specific site sequence of CpG (5′-CCGG-3′) islands. For monitoring the MTase activity, differential pulse voltammetry (DPV) was used, whereas the best results were obtained by rGO-AuNPs. This assay is rapid, cost-effective, sensitive, selective, highly specific, and displays a low limit of detection (LOD) of 0.06 U·mL⁻¹. Lastly, this study was enriched with the real serum sample, where a 0.19 U·mL⁻¹ LOD was achieved. Moreover, the developed biosensor offers excellent potential in future applications in clinical diagnostics, as this approach can be used in the design of other biosensors.

Synthesis of FeO@SiO2-DNA core-shell engineered nanostructures for rapid adsorption of heavy metals in aqueous solutions

Creating novel and innovative nanostructures is a challenge, aiming to discover nanomaterials with promising properties for environmental remediation. In this study, the physicochemical and adsorption properties of a heterogeneous nanostructure are evaluated for the rapid removal of heavy metal ions from aqueous solutions. Core–shell nanostructures are prepared using iron oxide cores and silica dioxide shells. The core is synthesized via the co-precipitation method and modified in situ with citric acid to grow a carboxyl layer. The shell was hydrolyzed/condensed and then functionalized with amine groups for ds-DNA condensation via electrostatic interaction. The characterization techniques revealed functional FeO@SiO₂–DNA nanostructures with good crystallinity and superparamagnetic response (31.5 emu g⁻¹). The predominant superparamagnetic nature is attributed to the citric acid coating. This improves the dispersion and stability of the magnetic cores through the reduction of the dipolar–dipolar interaction and the enhancement of the spin coordination. The rapid adsorption mechanism of FeO@SiO₂–DNA was evaluated through the removal of Pb(ii), As(iii), and Hg(ii). A rapid adsorption rate is observed in the first 15 min, attributed to a heterogeneous chemisorption mechanism based on electrostatic interactions. FeO@SiO₂–DNA shows higher adsorption efficiency of 69% for Pb(ii) removal compared to As(iii) (51%) and Hg(ii) (41%). The selectivity towards Pb(ii) is attributed to the similar acid nature to ds-DNA, where the ionic strength interaction provides good affinity and stability. The facile synthesis and rapid adsorption suggest a promising nanostructure for the remediation of water sources contaminated with heavy metal ions and can be extended to other complex molecules.

Facile synthesis of well-dispersed and magnetic FeO@SiO₂–DNA nanostructures with electrostatic active sites for interaction and rapid adsorption of heavy metals.

Graphene biosensors for bacterial and viral pathogens

The infection and spread of pathogens (e.g., COVID-19) pose an enormous threat to the safety of human beings and animals all over the world. The rapid and accurate monitoring and determination of pathogens are of great significance to clinical diagnosis, food safety and environmental evaluation. In recent years, with the evolution of nanotechnology, nano-sized graphene and graphene derivatives have been frequently introduced into the construction of biosensors due to their unique physicochemical properties and biocompatibility. The combination of biomolecules with specific recognition capabilities and graphene materials provides a promising strategy to construct more stable and sensitive biosensors for the detection of pathogens. This review tracks the development of graphene biosensors for the detection of bacterial and viral pathogens, mainly including the preparation of graphene biosensors and their working mechanism. The challenges involved in this field have been discussed, and the perspective for further development has been put forward, aiming to promote the development of pathogens sensing and the contribution to epidemic prevention.

Bright fluorescent nucleic acid detection with CRISPR-Cas12a and poly(thymine) templated copper nanoparticles

Fluorescence-based diagnostic tools are attractive and versatile tests with multiple advantages: ease of use, sensitivity and rapid results. The advent of CRISPR-Cas technology has created new avenues for the development of diagnostic testing tools. In this study, by effectively combining the specific functions of two enzymes, CRISPR-Cas12a and terminal deoxynucleotidyl transferase (TdT), we developed a DNA detection assay that generates copper nanoparticles (CuNPs) that are easily visible to the naked eye under UV-light; we named this detection assay Cas12a Activated Nuclease poly-T Reporter Illuminating Particles (CANTRIP). Upon specific target DNA recognition by Cas12a, single-stranded DNA (ssDNA) reporter oligos with blocked 3'-ends are cut into smaller ssDNA fragments, thereby generating neo 3'-hydroxyl moieties. TdT subsequently elongates these newly formed ssDNA fragments, incorporating only dTTP nucleotides, and these poly(thymine)-tails subsequently function as scaffolds for the formation of CuNPs. These CuNPs produce a bright fluorescent signal upon UV excitation, and thus, this bright orange signal indicates the presence of target DNA, which in this proof-of-concept study consisted of anthrax lethal factor plasmid DNA. CANTRIP, which combines two detection platforms consisting of CRISPR-Cas12a and fluorescent CuNPs into a single reaction, appears to be a robust, low-cost and simple diagnostic tool.

Sensitive detection of microRNA using a label-free copper nanoparticle system with polymerase-based signal amplification

The abnormal expression of microRNAs (miRNAs) has been reported in many diseases, so it is of great interest to develop simple and accurate methods for the detection and analysis of miRNA expression. We have developed a novel biosensor to detect miRNAs. This method is based on a polymeric double-stranded DNA (dsDNA) copper nanoparticle (CuNP) template that is synthesised by a polymerase. When Cu²⁺ and ascorbic acid are added to the system, the dsDNA template (which is rich in A-T bases) promotes the formation of CuNPs, resulting in high fluorescence intensity. This system provides sensitive analysis of miRNA expression with a limit of detection down to 17.8 pmol/L, due to significant changes in the fluorescence signal of the system before and after the addition of the target. The linear range between F₀-F and concentration of miR-122 is 80.0 pmol/L to 4.50 nmol/L, and the recovery rate in spiked HepG2 cell lysates is 93.33-102.53%. This method expands the applications of fluorescent DNA-CuNPs in the field of biosensor analysis, and can be used to detect and analyse any miRNA marker by changing the target recognition sequence. Graphical abstract A label-free dsDNA-CuNP-based and enzyme-assisted signal amplification method for microRNA is constructed.

Developing fluorescent copper nanoclusters: Synthesis, properties, and applications

Metal nanoclusters exhibit strong fluorescence emission, providing immense potential for developments in biological labeling and imaging. Copper nanoclusters in particular, due to their unique optical properties such as molecular-like absorption and strong luminescence, represent a novel fluorescent nanomaterial for sensing and bioimaging applications. This review describes research progress on Cu nanoclusters in recent years, investigating the synthesis techniques, their properties, and their promising applications. A concluding summary provides an outlook on the future research challenges for Cu nanoclusters and their corresponding synthesis techniques.

Quantitative Analysis of Salmonella typhimurium Based on Elemental-Tags Laser-Induced Breakdown Spectroscopy

Current rapid bacterial detection methods are dedicated to the classification and identification of bacteria. However, there is still a lack of a method for specific quantitative analysis of certain bacteria. In this work, a method based on elemental-tags laser-induced breakdown spectroscopy (ETLIBS) was developed for the rapid and specific quantitative analysis of Salmonella typhimurium (S. ty). Elemental tags were first synthesized by assembling copper nanoparticles (CuNPs) with poly(thymine) (poly-T) template that linked with the aptamer sequence. Under the specific recognition of the aptamer, S. ty can be fully combined with the elemental tags within 30 min to achieve labeling. Afterward, the silicon nanowires (SiNWs) array modified with Au@Ag nanoparticles (SiNWs-Au@Ag) was employed to capture S. ty in 30 min. Attributed to the rapid analysis superiority of ETLIBS mapping, 100 spectra of SiNWs-Au@Ag/S. ty/CuNPs can be obtained in 5 min. It was found that the peak area of the Cu(I) atomic emission line at 324.75 nm fitted by the Voigt profile was linearly related to the bacterial concentration in the range of 10²-10⁶ CFU/mL(R² = 0.978). Furthermore, ETLIBS mapping achieved a low limit of detection (LOD) of 61 CFU/mL and showed good selectivity to S. ty compared with other bacteria. Besides, the method exhibited preeminent detection performance in spiked samples with the recoveries of 87-113%. With the advantages of rapidity, high efficiency, and specificity, the proposed method is expected to be a powerful tool for bacterial detection.