Fluorescence Regulation of Copper Nanoclusters via DNA Template Manipulation toward Design of a High Signal-to-Noise Ratio Biosensor

Recent Advances of DNA-Templated Metal Nanoclusters for Food Safety Detection: From Synthesis, Applications, Challenges, and Beyond

Food safety concerns have become a significant threat to human health and well-being, catching global attention in recent years. As a result, it is imperative to research conceptually novel biosensing and effective techniques for food matrices detection. Currently, DNA-templated metal nanoclusters (DNA-MNCs) are considered as one of the most promising nanomaterials due to their excellent properties in biosensing. While DNA-MNCs have garnered increasing interest, the reviews of design strategies, applications, and futuristic prospects for biosensing have been hardly found especially in food safety. The synthesis of DNA-MNCs and their use as biosensing materials in food contamination detection, including pathogenic bacteria, toxins, heavy metals, residues of pesticides, and others were comprehensively reviewed. In addition, we summarize the properties of DNA-MNCs briefly and discuss the challenges and future trends. The application of DNA-MNCs powered biosensing has been demonstrated and actively studied, which is a promising paradigm for food safety testing that can supplement or even replace current existing methods. Despite the challenges of difficulty regulating accurately, poor stability, low quantum yield, and difficult commercial transformation, the application prospects of DNA-MNCs biosensors are promising. This review aims to provide insights and directions for the future development of DNA-MNCs based food detection technology.

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.

C-doped ZnO nanocomposites molecularly imprinted photoelectrochemical sensor for ultrasensitive and selective detection of oxytetracycline in milk

Antibiotic monitoring remains vital to ensure human health and safety in the environment and foods. As the most popular detection method, photoelectrochemical (PEC) sensor can achieve rapid and accurate detection of antibiotics with the advantages of high sensitivity, easy-to-preparation process, as well as high selectivity. Herein, an extremely-efficient visible-light responsible ZnO/C nanocomposite was prepared and combined with acetylene black (as an enhanced conductive matrix), and the electron migration efficiency was greatly accelerated. Meanwhile, a molecularly imprinted polymer obtained by electrical agglomeration was conjugated as a specific recognizing site for target. Furthermore, the as-prepared rMIP-PEC sensor showed a low detection limit (8.75 pmol L^-1, S/N = 3) in a wide linear detection range of 0.01-1000 nmol L^-1 for oxytetracycline (OTC), with excellent selectivity and long-term stability. Our work shed light on applying C-doped ZnO semiconductor and molecularly imprinted polymer as photoelectric active sensing materials for rapid and accurate analysis of antibiotics in foods and environment.

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.

A novel electrochemical biosensor based on signal amplification of Au HFGNs/PnBA-MXene nanocomposite for the detection of miRNA-122 as a biomarker of breast cancer

Cancer is one of the leading causes of death worldwide and a crisis for global health. Breast cancer is the second most common cancer globally. In the perusal, a novel electrochemical biosensor amplified with hierarchical flower-like gold, poly (n-butyl acrylate), and MXene (AuHFGNs/PnBA-MXene) nanocomposite and activated by highly special antisense ssDNA (single-stranded DNA) provide a promising alternative for miRNA-122 detection as a biomarker of breast cancer. The biosensor presented a detection limit of 0.0035 aM (S/N = 3) with a linear range from 0.01 aM to 10 nM. The platform was tried on 20 breast cancer miRNAs extracted from actual serum specimens (10 positives and 10 negatives). Founded on the quantitatively obtained outcomes and statistic analysis (t-test, box-graph, receiver performance characteristic curve, and cut-off amount), the biosensor showed a meaningful discrepancy between the native and positive groups with 100% specificity and 100% sensitivity. While, RT-qPCR showed less specificity and sensitivity (70% specificity, 100% sensitivity) than the proposed biosensor. To assess the quantitative capacity and biosensor detection limit for clinical tests, the biosensor diagnosis performance for continually diluted miRNA extracted from patients was compared to that gained by RT-qPCR results, indicating that the biosensor detection limit was lower than RT-qPCR. ssDNA/AuHFGN/PnBA-MXene/GCE displayed little cross-reaction with other sequences and also showed desirable stability, reproducibility, and specificity and stayed stable until 32 days. As a result, the designed biosensor can perform as a hopeful method for diagnosis applications.

ZnO/C nanocomposite grafted molecularly imprinted polymers as photoelectrochemical sensing interface for ultrasensitive and selective detection of chloramphenicol

Nanomaterials-based photoelectrochemical (PEC) detection is becoming a rapidly-developing analytical technique in chemical and biological assays due to its unique advantages of easy miniaturization, high sensitivity, and rapid turnaround time. Herein, a molecularly imprinted polymer-assisted PEC sensor based on ZnO/C nanocomposite was successfully fabricated for the highly sensitive and selective determination of chloramphenicol (CAP). Benefiting from the hydrophilic functional groups (-OH, -COOH) and large surface area of bio-templated ZnO/C nanocomposite, the tight grafting of MIP with excellent recognition ability on substrate is easier and more stable than traditional PEC sensor, thus significantly increasing the performance. Under optimal conditions, the PEC sensor exhibited significant CAP detection performance in the range of 0.01-5000 ng mL^-1 with a detection LOD of 5.08 pg mL^-1 (S/N = 3) and successfully applied to the detection of CAP in milk sample. Our results show that ZnO/C nanocomposite and MIP can act as an efficient photo-responsible matrix to fabricate PEC sensor, providing important application potentials for pollutants control in food and environment.

DNA-Based Biosensors for the Biochemical Analysis: A Review

In recent years, DNA-based biosensors have shown great potential as the candidate of the next generation biomedical detection device due to their robust chemical properties and customizable biosensing functions. Compared with the conventional biosensors, the DNA-based biosensors have advantages such as wider detection targets, more durable lifetime, and lower production cost. Additionally, the ingenious DNA structures can control the signal conduction near the biosensor surface, which could significantly improve the performance of biosensors. In order to show a big picture of the DNA biosensor's advantages, this article reviews the background knowledge and recent advances of DNA-based biosensors, including the functional DNA strands-based biosensors, DNA hybridization-based biosensors, and DNA templated biosensors. Then, the challenges and future directions of DNA-based biosensors are discussed and proposed.

Synthesis of metal nanoclusters and their application in Hg2+ ions detection: A review

Mercuric (Hg²⁺) ions released from human activities, natural phenomena, and industrial sources are regarded as the global pollutant of world's water. Hg²⁺ ions contaminated water has several adverse effects on human health and the environment even at low concentrations. Therefore, rapid and cost-effective method is urgently required for the detection of Hg²⁺ ions in water. Although, the current analytical methods applied for the detection of Hg²⁺ ions provide low detection limit, they are time consuming, require expensive equipment, and are not suitable for in-situ analysis. Metal nanoclusters (MNCs) consisting of several to ten metal atoms are important transition missing between single atoms and plasmonic metal nanoparticles. In addition, sub-nanometer sized MNCs possess unique electronic structures and the subsequent unusual optical, physical, and chemical properties. Because of these novel properties, MNCs as a promising material have attracted considerable attention for the construction of selective and sensitive sensors to monitor water quality. Hence this review is focused on recent advances on synthesis strategies, and optical and chemical properties of various MNCs including their applications to develop optical assay for Hg²⁺ ions in aqueous solutions.

Ultrafast Ratiometric Detection of Aflatoxin B1 Based on Fluorescent β-CD@Cu Nanoparticles and Pt2+ Ions

Rapid detection of aflatoxin B1 (AFB1) is a very important task in food safety monitoring. However, it is still challenging to achieve highly sensitive detection without antibody or aptamer biomolecules. In this work, a rapid detection of aflatoxin B1 was achieved using a ratiometric fluorescence probe without antibody or aptamer for the first time. In the ratiometric fluorescence system, the fluorescence emission of AFB1 at 433 nm was significantly enhanced due to the β-cyclodextrin-AFB1 host-guest interaction and the complexation of AFB1 and Pt²⁺. Meanwhile, the inclusion of aflatoxin B1 also quenched the fluorescence emission of β-CD@Cu nanoparticles (NPs) at 650 nm based on inner filter effect mechanism. On the basis of the above effects, the ratiometric detection of aflatoxin B1 was achieved in the range of 0.03-10 ng/mL with a low detection limit of 0.012 ng/mL (3σ/s). In addition, the β-CD@Cu NPs based nanoprobe could achieve stable response within 1 min to AFB1. The above ratiometric detection also demonstrated excellent application potential in the rapid on-site detection of AFB1 in food due to the advantages of convenience, rapidness, and high accuracy.

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.

Synthesis of Copper Nanocluster and Its Application in Pollutant Analysis

Copper nanoclusters (Cu NCs) with their inherent optical and chemical advantages have gained increasing attention as a kind of novel material that possesses great potential, primarily in the use of contaminants sensing and bio-imaging. With a focus on environmental safety, this article comprehensively reviews the recent advances of Cu NCs in the application of various contaminants, including pesticide residues, heavy metal ions, sulfide ions and nitroaromatics. The common preparation methods and sensing mechanisms are summarized. The typical high-quality sensing probes based on Cu NCs towards various target contaminants are presented; additionally, the challenges and future perspectives in the development and application of Cu NCs in monitoring and analyzing environmental pollutants are discussed.

DNA dendrimer-templated copper nanoparticles: self-assembly, aggregation-induced emission enhancement and sensing of lead ions

Copper nanomaterials based on DNA scaffold (DNA-Cu NMs) are becoming a novel fluorescent material, but it is still challenging to obtain highly fluorescent DNA-Cu NMs with excellent stability. In this work, we report a kind of copper nano-assemblies (Cu NASs) with aggregation-induced emission enhancement (AIEE) property using DNA dendrimers with sticky end as template. The sticky end of the DNA dendrimers induced the formation of much bigger Cu NASs with average size ranging from 131 to 264 nm, depending on the length of the DNA dendrimer sticky end from 6 bases to 27 bases. Compared with complete complementary DNA dendrimer, nearly 6-fold fluorescence enhancement was achieved using DNA dendrimer with 27 bases sticky end. Moreover, the DNA dendrimer-Cu NASs demonstrated excellent stability in serum and could be rapidly quenched by Pb²⁺ ions. Based on the above property, highly sensitive and selective fluorescent detection of Pb²⁺ ions was possible with a linear range of 2.0-100 nM and a detection limit of 0.75 nM. Due to the sensitive and rapid response to Pb²⁺ as well as excellent stability in complex matrix, the proposed fluorescent Cu NASs demonstrated high potential as an excellent fluorescent probe for Pb²⁺ in complex matrix.

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.

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.

Recent advances in templated synthesis of metal nanoclusters and their applications in biosensing, bioimaging and theranostics

As a kind of promising nanomaterials, metal nanoclusters (MNCs) generally composed of several to hundreds of metal atoms have received increasing interest owing to their unique properties, such as ultrasmall size (<2 nm), fascinating physical and chemical properties, and so on. Recently, template-assisted synthesis of MNCs (e.g., Au, Ag, Cu, Pt and Cd) has attracted extensive attention in biological fields. Up to now, various templates (e.g., dendrimers, polymers, DNAs, proteins and peptides) with different configurations and spaces have been applied to prepare MNCs with the advantages of facile preparation, controllable size, good water-solubility and biocompatibility. Herein, we focus on the recent advances in the template-assisted synthesis of MNCs, including the templates used to synthesize MNCs, and their applications in biosensing, bioimaging, and disease theranostics. Finally, the challenges and future perspectives of template-assisted synthesized MNCs are highlighted. We believe that this review could not only arouse more interest in MNCs but also promote their further development and applications by presenting the recent advances in this area to researchers from various fields, such as chemistry, material science, physiology, biomedicine, and so on.

DNA functionalized metal and metal oxide nanoparticles: principles and recent advances in food safety detection

The frequent occurrence of food safety incidents has given rise to unprecedented concern about food contamination issues for both consumers and the industry. Various contaminations in food pose serious threats to food safety and human health. Many detection methods were studied to address the challenge. Recently, biosensors relying on deoxyribonucleic acid (DNA)-functionalized nanoparticles have been developed as an efficient and effective detection method. In the current review, the strategies for DNA assembly metal and metal oxide nanoparticles are elaborated, recent applications of the sensors based on DNA-functionalized nanoparticles in food contaminant detection are discussed. Pathogenic bacteria, heavy metal ions, mycotoxins, antibiotics, and pesticides are covered as food contaminants. Additionally, limitations and future trends of functionalized nanoparticles-based technology are also presented. The current review indicates that DNA-functionalized metal and metal oxide nanoparticles are a novel nanomaterial with unique biological and physical properties for developing electrochemical, fluorescent, colourimetric and surface-enhanced Raman spectroscopy (SERS) sensors, etc. Compared with conventional detection techniques, DNA-functionalized metal and metal oxide nanoparticles have considerable advantages with high accuracy, high specificity, micro-intelligence, and low cost. Nevertheless, the stability of these sensors and the limitations of real-time detection are still under discussion. Therefore, more tolerant, portable, and rapid DNA sensors should be developed to better the real-time monitoring of harmful contaminants.

Construction of a Novel Biosensor Based on the Self-assembly of Dual-Enzyme Cascade Amplification-Induced Copper Nanoparticles for Ultrasensitive Detection of MicroRNA153

MicroRNAs (miRNAs) have received extensive attention because of their potential as biomarkers for cancer diagnosis and monitoring, and their effective detection is very significant. Here, a specific, one-pot, rapid, femtomolar sensitive miRNAs detection biosensor was developed based on the target-triggered three-way junction (3-WJ) and terminal deoxynucleotide transferase (TDT)/Nt.BspQI in combination with activated copper nanoparticles (CuNPs) self-assembly. To this end, a 3-WJ hairpin probe and helper probe were designed to selectively identify the target miRNA, so as to form a stable 3-WJ structure that further triggered the double-enzyme cycling to produce poly T to activate the self-assembly of CuNPs. Based on the simplicity of CuNPs generation, the poly T template fluorescence CuNPs can detect the minimum detection limit of 1 fm within 1.75 h. In addition, the applicability of this method in complex samples was demonstrated by analyzing the whole-blood RNA extraction from Parkinson patients, consisting of the results of commercial miRNA kits. The developed strategy performs powerful implications for miRNA detection, which may be beneficial for the effective diagnostic assays and biological research of Parkinson's disease.

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.

Ultrasensitive Electrochemical DNA Biosensor Fabrication by Coupling an Integral Multifunctional Zirconia-Reduced Graphene Oxide-Thionine Nanocomposite and Exonuclease I-Assisted Cleavage

In this work, a simple but sensitive electrochemical DNA biosensor for nucleic acid detection was developed by taking advantage of exonuclease (Exo) I-assisted cleavage for background reduction and zirconia-reduced graphene oxide-thionine (ZrO2-rGO-Thi) nanocomposite for integral DNA recognition, signal amplification, and reporting. The ZrO2-rGO nanocomposite was obtained by a one-step hydrothermal synthesis method. Then, thionine was adsorbed onto the rGO surface, via π-π stacking, as an excellent electrochemical probe. The biosensor fabrication is very simple, with probe DNA immobilization and hybridization recognition with the target nucleic acid. Then, the ZrO2-rGO-Thi nanocomposite was captured onto an electrode via the multicoordinative interaction of ZrO2 with the phosphate group on the DNA skeleton. The adsorbed abundant thionine molecules onto the ZrO2-rGO nanocomposite facilitated an amplified electrochemical response related with the target DNA. Since upon the interaction of the ZrO2-rGO-Thi nanocomposite with the probe DNA an immobilized electrode may also occur, an Exo I-assisted cleavage was combined to remove the unhybridized probe DNA for background reduction. With the current proposed strategy, the target DNA related with P53 gene could be sensitively assayed, with a wide linear detection range from 100 fM to 10 nM and an attractive low detection limit of 24 fM. Also, the developed DNA biosensor could differentiate the mismatched targets from complementary target DNA. Therefore, it offers a simple but effective biosensor fabrication strategy and is anticipated to show potential for applications in bioanalysis and medical diagnosis.

Ratiometric assay of mercury ion based on nitrogen-doped carbon dots with two different optical signals: second-order scattering and fluorescence

Ratiometric assays, which can effectively surmount external interference, have attracted extensive research interests. Herein, a novel ratiometric sensing platform for Hg²⁺ is designed based on nitrogen-doped carbon dots (N-CDs) with two different optical signals. Under a single excitation, N-CDs have two emission peaks around 668 nm and 412 nm, which are second-order scattering and fluorescence, respectively. Upon the addition of Hg²⁺, the weak scattering emission at 668 nm can be increased apparently, while the strong fluorescence intensity at 412 nm is weakened. Moreover, the ratio of scattering intensity to fluorescence intensity is linearly dependent on Hg²⁺ concentration (0.1-10 μM and 10-30 μM, respectively), and the detection limit is 66 nM. In addition, the ratiometric sensing mechanism is investigated in detail, which is due to the combined effect of aggregation-induced fluorescence quenching and scattering enhancement. Furthermore, the developed sensing approach holds a promising application for Hg²⁺ detection in actual samples. Graphical abstract.

Structure-dependent luminescent copper nanoclusters: self-assembly and morphological evolution

Highly ordered metal nanoclusters (NCs) have attracted much attention due to their controllability and regularity.

DNA-Templated Fluorescent Nanoclusters for Metal Ions Detection

DNA-templated fluorescent nanoclusters (NCs) have attracted increasing research interest on account of their prominent features, such as DNA sequence-dependent fluorescence, easy functionalization, wide availability, water solubility, and excellent biocompatibility. Coupling DNA templates with complementary DNA, aptamers, G-quadruplex, and so on has generated a large number of sensors. Additionally, the preparation and applications of DNA-templated fluorescent NCs in these sensing have been widely studied. This review firstly focuses on the properties of DNA-templated fluorescent NCs, and the synthesis of DNA-templated fluorescent NCs with different metals is then discussed. In the third part, we mainly introduce the applications of DNA-templated fluorescent NCs for sensing metal ions. At last, we further discuss the future perspectives of DNA-templated fluorescent NCs in the synthesis and sensing metal ions in the environmental and biological fields.

Recyclable DNA-Derived Polymeric Sensor: Ultrasensitive Detection of Hg(II) Ions Modulated by Morphological Changes

Going beyond organic solvent as the solubilizer for small-molecular organic probes motivates exploration of water-soluble polymeric sensors. In this respect, dye-derived thermal-responsive polymeric sensors are an attractive direction, but for its practical application, it is limited by sensor recycling because only irreversible change in the structure of the recognition unit for many sensors can trigger the appearance of the detection signal. Here, we established the oligonucleotide-derived thermal-responsive polymeric sensor, TBC-P1, which overcame this fundamental limitation. The TBC-P1 sensor was based on reversible binding between oligonucleotides and Hg²⁺ ions, and easy sensor separation via tuning temperature, achieving the Hg²⁺ detection in a cost-effective and green manner. The TBC-P1 sensor displayed specific and rapid sensing properties toward Hg²⁺ ions in pure aqueous media via turn-off fluorescence emission, with a limit of detection as low as 0.65 nM (much lower than the presently reported dye-derived polymeric sensors). This high detection sensitivity was further enhanced (with LOD = 0.17 nM) via warming to yield spherical micelles, in which the oligonucleotide-containing thermoresponsive PNIPAM block forming a hydrophobic core amplified the fluorescence signals. Treating the Hg²⁺-trapped micelles with cysteine (Cys) led to competition-induced release of these combined Hg²⁺ ions and then thermally precipitating and recycling polymeric sensor TBC-P1. This oligonucleotide-derived thermalresponsive polymeric sensor will open a universal avenue for sensor recycling, which will achieve the goal of reducing cost and improving detection sensitivity of sensors.

Recent progress in copper nanocluster-based fluorescent probing: a review

Copper nanoclusters (CuNCs) are an attractive alternative to other metal nanoclusters. The synthesis of CuNCs is highly efficient and fast, with low-cost and without any complicated manipulation. Because of their tunable fluorescence and low toxicity, CuNCs have been highly exploited for biochemical sensing. This review (with 172 refs.) summarizes the progress that has been made in the field in the past years. Following an introduction into the fundamentals of CuNCs, the review first focuses on synthetic methods and the fluorescence properties of CuNCs (with subsections on the use of proteins, peptides, DNA and other molecules as templates). This is followed by a section on the use of CuNCs in fluorometric assays, with subsections on the detection of small molecules, proteins, nucleic acids, various other biomolecules including drugs, and of pH values. A further large chapter summarizes the work related to environmental analyses, specifically on determination of metal ions, anions and pollutants. Graphical abstract Schematic representation of the synthesis and potential applications of copper nanocluster (CuNCs) in biochemical analysis, emphatically reflected in some vital areas such as small molecule analysis, biomacromolecule monitoring, cell imaging, ions detection, toxic pollutant, etc.

Substrate specificity-enabled terminal protection for direct quantification of circulating MicroRNA in patient serums

Currently, reported affinity pairings still lack in diversity, and thus terminal protection relying on steric hindrance is restricted in designing nucleic acid-based analytical systems. In this work, resistance to exonuclease is testified by group modification or backbone replacement, and the 3'-phosphate group (P) reveals the strongest exonuclease I-resistant capability. Due to the substrate specificity of enzymatic catalysis, this 3'-P protection works in a "direct mode". By introducing DNA templated copper nanoparticles, an alkaline phosphatase assay is performed to confirm the 3'-P protection. To display the application of this novel terminal protection, a multifunctional DNA is designed to quantify the model circulating microRNA (hsa-miR-21-5p) in serums from different cancer patients. According to our data, hsa-miR-21-5p-correlated cancers can be evidently distinguished from non-correlated cancers. Meanwhile, the effect of chemotherapy and radiotherapy on breast cancer is evaluated from the perspective of hsa-miR-21-5p residue in serums. Since greatly reducing the limitations of DNA design, this P-induced terminal protection can be facilely integrated with other DNA manipulations, thereby constructing more advanced biosensors with improved analytical performances for clinical applications.

Progress in biosensor based on DNA-templated copper nanoparticles

During the last decades, by virtue of their unique physicochemical properties and potential application in microelectronics, biosensing and biomedicine, metal nanomaterials (MNs) have attracted great research interest and been highly developed. Deoxyribonucleic acid (DNA) is a particularly interesting ligand for templating bottom-up nanopreparation, by virtue of its excellent properties including nanosized geometry structure, programmable and artificial synthesis, DNA-metal ion interaction and powerful molecular recognition. DNA-templated copper nanoparticles (DNA-CuNPs) has been developed in recent years. Because of its advantages including simple and rapid preparation, high efficiency, MegaStokes shifting and low biological toxicity, DNA-CuNPs has been highly exploited for biochemical sensing from 2010, especially as a label-free detection manner, holding advantages in multiple analytical technologies including fluorescence, electrochemistry, surface plasmon resonance, inductively coupled plasma mass spectrometry and surface enhanced Raman spectroscopy. This review comprehensively tracks the preparation of DNA-CuNPs and its application in biosensing, and highlights the potential development and challenges regarding this field, aiming to promote the advance of this fertile research area.

A Fluorescence Strategy for Silver Ion Assay via Cation Exchange Reaction and Formation of Poly(thymine)-templated Copper Nanoclusters

The detection of Ag⁺ ions in the environment and biological systems is important to both environmental monitoring and modern medicine. Herein, a novel and label-free method was developed for Ag⁺ detection, which utilizes a florescence strategy combining DNA-templated copper nanoclusters (Cu NCs) with cation exchange reactions. The method is primarily based on the effective detection of an Ag⁺-triggered cation exchange reaction and the release of free Cu²⁺ from CuS nanoparticles (CuS NPs), while the probe T30 serves as an effective template for the formation of fluorescence-inducing Cu NCs. Under optimal conditions, this sensing system displays high sensitivity with a 50 nM limit of detection and a range from 0 - 100 μM. In addition, the proposed method exhibits high selectivity and, therefore, was successfully applied to the analysis of real samples. Overall, these results demonstrate that our established method has advantages of design and operation simplicity, as well as cost-effectiveness.

Recent advances in the synthesis and application of copper nanomaterials based on various DNA scaffolds

Fluorescent copper nanomaterials (CuNMs), including copper nanoparticles (CuNPs) and copper nanoclusters (CuNCs), become more and more popular with the abundant raw materials and low cost. A wide range of applications has been explored due to their fascinating properties such as low toxicity, remarkable water solubility, facile synthesis, large Stokes shifts, and good biocompatibility. As a kind of genetic material, DNA exhibits its molecular recognition function and diversity. The marriage between CuNMs and DNA endows DNA-templated CuNMs (DNA-CuNMs) with unique properties such as fluorescence, electrochemiluminescence and catalytic features. In this review, we summarize the synthesis and recent applications of DNA-CuNMs. Fluorescent CuNMs can be grown on various DNA scaffolds with special sequence design. T base plays an important role in the formation of CuNMs on DNA templates. These fluorescent DNA-CuNMs hold great prospect in logic gate construction, staining and biosensing of DNAs and RNAs, ions, proteins and enzymes, small molecules and so on.

Target-inspired Zn2+-dependent DNAzyme for ultrasensitive impedimetric aptasensor based on polyacrylic acid nanogel as amplifier

In general, the traditional impedimetric aptasensor for detecting protein is based on its high molecular weight and low dielectric constant. Yet, the efficiency of these aptasensors is hindered by the slight resistance change in the trace concentration range because of the high initial resistance (the electrostatic repulsion between the compact negatively charged DNA on the electrode and [Fe(CN)₆]^3-/4-). To effectively and simply circumvent this issue and improve the detection sensitivity, we design an impedimetric aptasensor by reducing the substrate DNA's density on the electrode through the target-inspired recycling DNA cleavage. In order to enlarge the differences in resistance, the polyacrylic acid (PAA) nanogel is implemented as amplifier due to its poor conduction and negative charge that can hinder electron transfer and repulse the mediator [Fe(CN)₆]^3-/4-, respectively. Based on the target-inspired DNAzyme and PAA nanogel as amplifier, the ultrasensitive impedimetric aptasensor of carcinoembryonic antigen (CEA) in the buffer solution possesses a wide dynamic range of 10 fg mL^-1 to 10 ng mL^-1 and ultra-low detection limit of 7.9 fg mL^-1 (10-fold relative to equivalent aptasensors). When tested in human serum, the proposed aptasensor exhibits good performance with an ultra-low detection limit of 1.4 fg mL^-1, which is slightly higher than that in buffer solution.