Ratio fluorescence analysis of T4 polynucleotide kinase activity based on the formation of a graphene quantum dot-copper nanocluster nanohybrid

Fluorescent metal nanoclusters: From luminescence mechanism to applications in enzyme activity assays

Metal nanoclusters (MNCs) have outstanding fluorescence property and biocompatibility, which show widespread applications in biological analysis. Particularly, evaluation of enzyme activity with the fluorescent MNCs has been developed rapidly within the past several years. In this review, we first introduced the fluorescent mechanism of mono- and bi-metallic nanoclusters, respectively, whose interesting luminescence properties are mainly resulted from electron transfer between the lowest unoccupied molecular orbital (LUMO) and highest occupied molecular orbital (HOMO) energy levels. Meanwhile, the charge migration within the structure occurs through ligand-metal charge transfer (LMCT) or ligand-metal-metal charge transfer (LMMCT). On such foundation, diverse enzyme activities were rigorously evaluated, including three transferases and nine hydrolases, in turn harvesting rapid research progresses within past 5 years. Finally, we summarized the design strategies for evaluating enzyme activity with the MNCs, presented the major issues and challenges remained in the relevant research, coupled by showing some improvement measures. This review will attract researchers dedicated to the studies of the MNCs and provide some constructive insights for their further applications in enzyme analysis.

Ultrasensitive detection of the H5N1 nucleic acid fragment by ICP-MS using DNA dendrimer-carried silver nanoparticle labeling

The importance of avian influenza virus (AIV) detection in clinical diagnosis and prognosis has been deeply recognized. In this study, the ultrasensitive detection of AIV subtype H5N1 was achieved by ICP-MS combined with DNA dendrimer-carried silver nanoparticle (AgNP) labeling. First, a magnetic control system was constructed by anchoring double-strand DNAs (dsDNAs) which contained a complementary sequence of H5N1 and two locked triggers on the surface of magnetic beads (MBs). When H5N1 was present, the two triggers were released and initiated dendrimer hybridization chain reactions which led to the generation of DNA dendrimer-carried AgNPs on the surface of the MBs. Finally, the AgNPs were collected via magnetic separation, digested by nitric acid, and tested using ICP-MS. The signal intensities of 107Ag were positively correlated with the concentrations of H5N1. Notably, the DNA dendrimer assembly contributed to significant signal amplification and good sensitivity with the limit of detection as low as 2.0 × 10-11 mol L-1. Moreover, the method displayed favorable selectivity against mismatched H5N1 and good recoveries in human serum samples. It is a promising analytical tool for the H5N1 virus and other subtypes of AIV, and has potential value in clinical diagnosis and prognosis of infectious diseases.

Large-scale assembly of geometrically diverse metal nanoparticles-based 3D plasmonic DNA nanostructures for SERS detection of PNK in cancer cells

The organization of geometrically diverse metal nanoparticles into a core/satellite structure at a large scale is a promising strategy for improve SERS performance due to hot spots localized enrichment and signal increase. However, due to the lack of extensional frames and strong electrostatic repulsion between plasma NPs, the fabrication of such 3D architectures with a high-density periodic hotspot in the focus volume has proven exceedingly difficult. Herein, we demonstrate a facile large-scale assembly of geometrically diverse metal nanoparticles strategy for constructing spatially extended 3D plasmonic nanostructures resembling "signal towers" based on RCA-mediated periodic organization of gold nanospheres (GNS) surrounding gold nanorods (GNRs). Using cancer cell T4 PNK as a model, a padlock probe with 5'- hydroxyl (P-circle) was designed as the T4 PNK substrate. The center Au nanorod was coated with P1 and served as a "pedestal" to allow substantial loading of P-circle after target phosphorylation to initiate the rolling ring amplification reaction (RCA). The resultant DNA nanowire serves as an "antenna" to successively lock numerous Raman reporter P2 (Cy3-P2-SH) through base pairing at regular intervals. Finally, the 3D plasma DNA nanostructures that resemble "signal towers" could be obtained by placing a large number of GNS with a strong affinity for Au-S. The proposed 3D SERS sensor exhibited a sensitivity of LOD as low as 0.274 mU/mL, which was attributed to a substantial electromagnetic field enhancement at the inter-nanoparticle gaps between the adjacent pedestal and antenna. Moreover, by exploiting the synergistic effect of the periodically extended DNA scaffold generated by RCA amplification and the co-assembly of thiol ligand, the loaded GNS can be extended to three-dimensional space, forming a high-density periodic hotspot in the focal volume, thereby ensuring high enhancement and high reproducibility of Raman signals. In addition, this method can be used to quantify T4 PNK in HeLa cells, demonstrating its applicability in diagnosing and estimating PNK-related diseases in complex fluids.

A fluorescent biosensor based on carbon quantum dots and single-stranded DNA for the detection of Escherichia coli

To detect E. coli in food, a simple fluorescent biosensor based on single-stranded DNA (ssDNA) and carbon quantum dots (CQDs) was developed. The carbon quantum dots were synthesized using a superhydrothermal method with carrot juice as a carbon source. The fluorescence intensity of the CQDs was decreased by induced ssDNA attachment. In the presence of E. coli, ssDNA preferentially binds to E. coli through hydrogen bonding and its fluorescence is greater than that in the absence of E. coli. The results showed that the linear range of the sensor was 1 × 102-1 × 108 CFU mL-1 with a coefficient of determination (R2) of 0.9870. The detection limit for E. coli was 60 CFU mL-1.

A label-free fluorescent biosensor for amplified detection of T4 polynucleotide kinase activity based on rolling circle amplification and catalytic hairpin assembly

T4 polynucleotide kinase (PNK) plays a key role in maintaining genome integrity and repairing DNA damage. In this paper, we proposed a label-free fluorescent biosensor for amplified detection of T4 PNK activity based on rolling circle amplification (RCA) and catalytic hairpin assembly (CHA). Firstly, we designed a padlock probe with a 5'-hydroxyl terminus for phosphorylation reaction, a complementary sequence of the primer for initiating RCA, and a complementary sequence of the trigger for triggering CHA. T4 PNK catalyzed the phosphorylation reaction by adding a phosphate group to the 5'-hydroxyl terminus of padlock probe, generating a phosphorylated padlock probe. Then it hybridized with the primer to generate a circular probe under the action of ligase. Subsequently, the primer initiated an RCA reaction along the circular probe to synthesize a large molecular weight product with repetitive trigger sequences. The triggers then triggered the cyclic assembly reactions between hairpin probe 1 and hairpin probe 2 to generate a large amount of complexes with free G-rich sequences. The free G-rich sequences folded into G-quadruplex structures, and the N-methylmesoporphyrin IXs were inserted into them to produce an amplified fluorescent signal. Benefiting from high amplification efficiency of RCA and CHA, this fluorescent biosensor could detect T4 PNK as low as 6.63 × 10^-4 U mL^-1, and was successfully applied to detect its activity in HeLa cell lysates. Moreover, this fluorescent biosensor could effectively distinguish T4 PNK from other alternatives and evaluate the inhibitory effect of inhibitor, indicating that it had great potential in drug screening and disease treatment.

Genetic Algorithm-Assisted Design of Sandwiched One-Dimensional Photonic Crystals for Efficient Fluorescence Enhancement of 3.18-μm-Thick Layer of the Fluorescent Solution

One-dimensional photonic crystal structures have been widely used to enhance fluorescence. However, its fluorescence enhancement is low-fold because of a weak excitation field region. In this paper, we used a genetic algorithm to assist in the design of two photonic crystals based on Al₂O₃ and TiO₂ materials. One of them has a defect consisting of SiO₂. The Fabry-Perot cavity (FP cavity) formed by the sandwiched photonic crystal achieves up to 14-fold enhancement of the excitation electric field. We modulate the electric field radiation distribution of the fluorescent material by using photonic forbidden bands. For a 3.18 μm thick layer of the fluorescent solution, the structure achieves up to 60-fold fluorescence enhancement. We also discussed that the reason for the different enhancement abilities in different places is the phase change caused by the optical path difference. This design is expected to have applications in display, imaging, etc.

Sensitive Autocatalytic Hybridization Circuit for Reliable In Situ Intracellular Polynucleotide Kinase Imaging

Exploring the characteristic functions of polynucleotide kinase (PNK) could substantially promote the elucidation of PNK-related mechanistic pathways. Yet, the sensitive and reliable detection of intracellular PNK still presents a challenging goal. Herein, we propose a simple autocatalytic hybridization circuit (AHC) for in situ intracellular imaging of PNK with high reliability. The AHC amplifier consists of two mutually activated hybridization chain reaction (HCR) modules for magnified signal transduction. The PNK is transduced into initiator I by phosphorylation and cleavage of mediator H_p. Initiator I activates the initial HCR-1 module, leading to the formation of long dsDNA nanowires that carry numerous initiator T. Then, T-initiated feedback HCR-2 module generates branched products that contain plentiful initiator I, thus realizing an autocatalytic HCR amplification reaction. Simultaneously, the HCR-2 module is also assembled as a versatile signal transduction unit for generating the amplified readout. Based on the mutually sustained accumulation of two initiators for the reciprocal activation of two reaction modules, continuous signal amplification and assembly of high-molecular-weight copolymers endow the AHC system with high sensitivity and robustness for the PNK assay. Moreover, the PNK-sensing AHC system achieves reliable imaging of intracellular PNK, thus showing great potential to decipher the correlation between PNK and related diseases.

A label-free T4 polynucleotide kinase fluorescence sensor based on split dimeric G-quadruplex and ligation-induced dimeric G-quadruplex/thioflavin T conformation

The phosphorylation process of DNA by T4 polynucleotide kinase (T4 PNK) plays a crucial role in DNA recombination, DNA replication, and DNA repair. Traditional monomeric G-quadruplex (G4) systems are always activated by single cation such as K⁺ or Na⁺. The conformation transformation caused by the coexistence of multiple cations may interfere with the signal readout and limit their applications in physiological system. In view of the stability of dimeric G4 in multiple cation solution, we reported a label-free T4 PNK fluorescence sensor based on split dimeric G4 and ligation-induced dimeric G4/thioflavin T (ThT) conformation. The dimeric G4 was divided into two independent pieces of one normal monomeric G4 and the other monomeric G4 fragment phosphorylated by T4 PNK in order to decrease the background signal. With the introduction of template DNA, DNA ligase, and invasive DNA, the dimeric G4 could be generated and liberated to combine with ThT to show obvious fluorescence signal. Using our strategy, the linear range from 0.005 to 0.5 U mL^-1, and the detection limit of 0.0021 U mL^-1 could be achieved without the consideration of interference caused by the coexistence of multiple cations. Additionally, research in real sample determination and inhibition effect investigations indicated its further potential application value in biochemical process research and clinic diagnostics.

Combining metal nanoclusters and carbon nanomaterials: Opportunities and challenges in advanced nanohybrids

The development of functional materials with uniquely advanced properties lies at the core of nanoscience and nanotechnology. From the myriad possible combinations of organic and/or inorganic blocks, hybrids combining metal nanoclusters and carbon nanomaterials have emerged as highly attractive colloidal materials for imaging, sensing (optical and electrochemical) and catalysis, among other applications. While the metal nanoclusters provide extraordinary luminescent and electronic properties, the carbon nanomaterials (of zero, one or two dimensions) convey versatility, as well as unique interfacial, electronic, thermal, optical, and mechanical properties, which altogether can be put to use for the desired application. Herein, we present an overview of the field, for experts and non-experts, encompassing the basic properties of the building blocks, a systematic view of the chemical preparation routes and physicochemical properties of the hybrids, and a critical analysis of their ongoing and emerging applications. Challenges and opportunities, including directions towards green chemistry approaches, are also discussed.

Phosphorothioated and phosphate-terminal dumbbell (PP-TD) probe-based rapid detection of polynucleotide kinase activity

A primer-free, sensitive assay has been developed to detect polynucleotide kinase (PNK) activity. This proposed method provides a promising platform for PNK activity monitoring and inhibition screening for drug discovery and clinical treatment.

Primer-template conversion-based cascade signal amplification strategy for sensitive and accurate detection of polynucleotide kinase activity

Here, a primer-template conversion-based cascade signal amplification strategy is described for the sensitive detection of polynucleotide kinase (PNK) activity. This strategy integrated rolling circle amplification (RCA) and multiple-repeated-strand displacement amplification (MRSDA) with G-quadruplex based fluorescence lighting-up assay. A delicate dumbbell-shaped DNA probe with 5'-hydroxyl terminus was designed, in which G-quadruplex and half recognition site of nicking enzyme Nb.BbvCI were encoded in two loops respectively. Under the action of PNK, the 5' terminus on dumbbell probe was firstly phosphorylated, and then the dumbbell was cyclized with the catalyzation of T4 ligase to become the RCA template. The RCA process produced multiple copies of the prolonged primer. After that, under the assistance of nicking enzyme Nb.BbvCI, a primer-template conversion occurred, which converted the primer and template of RCA into the template and primer of the subsequent MRSDA, respectively. The MRSDA generated multiple repeated ssDNA sequences which possessed G-quadruplexes for outputting signal by lighting-up fluorescence of thioflavin T (ThT). The cascade signal amplification of RCA and MRSDA provided high detection sensitivity, and the target-dependence of template in cascade signal amplification led to a low background. The method showed excellent detection limit of 0.2 × 10^-6 U μL^-1 in buffer and 5 cells in cell lysate sample. Moreover, this method displayed favorable selectivity when interfering proteins were present. The developed strategy has good practical potential for PNK activity detection in clinical diagnosis and medical research.

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.

A fluorescence biosensor based on single-stranded DNA and carbon quantum dots for acrylamide detection

As a potential carcinogen produced in food thermal processing, acrylamide (AM) can cause irreversible harm to human health. For the detection of AM in food products, a simple fluorescent biosensor based on single-stranded DNA (ssDNA) and carbon quantum dots (CQDs) was developed. Reduced fluorescence intensity of CQDs at 445 nm (excitation at 350 nm) was induced by the attachment of ssDNA. In the presence of AM, ssDNA was preferentially bound to AM by hydrogen bonding and the degree of fluorescence reduction was smaller than that without AM. Under optimized conditions, results showed that the sensing approach for detecting AM had a low detection limit of 2.41 × 10^-8 M in the standard solution, and a linear relationship ranging from 5 × 10^-3 to 1 × 10^-7 M with the determination coefficient (R²) of 0.9895 was obtained. Furthermore, a good recovery percentage (91.36-98.11%) in bread crust showed the potential for practical applications of this proposed biosensor.

Metal-DNA coordination based bioinspired hybrid nanospheres for in situ amplification and sensing of microRNA

Sufficient delivery of biomolecules into cells with high loading efficiency and easy cleavability would be significant for the visualization of biomolecules in living cells. Herein, a facile approach based on nano-wire balls (NWs) for efficient loading, intracellular delivery of nucleic acids and in situ targeted miRNA bioimaging is proposed, by feeding of Zn ions for generating DNA-inorganic hybrid structures with large surface areas and good stability. Given that the versatile and robust hybridization chain reaction (HCR) amplification strategy combines DNA assembly with intracellular assay, the resulting NWs without any complicated modification are capable of enhanced signals for the targeted imaging of cancer cells. This method realized a linear detection range of 100 fM to 10 nM, with a low detection limit of 83.6 fM in vitro, and could be used to effectively differentiate the expression levels of miRNA-21 in living cells. Due to its high loading efficiency, excellent biocompatibility and low toxicity, this system can be used to construct a coordination-based delivery nanoplatform for in situ enzyme-free amplified imaging of miRNAs, expanding the application of DNA-based nanomaterials for cellular delivery and intracellular molecule analysis.

Electrochemical DNA Sensors Based on MoS2-AuNPs for Polynucleotide Kinase Activity and Inhibition Assay

The determination of T4 polynucleotide kinase (PNK) activity and the screening of PNK inhibitors are critical to disease diagnosis and drug discovery. Numerous electrochemical strategies have been developed for the sensitive measurement of PNK activity and inhibition. However, they often suffer from additional labels and multiple steps of the detection process for the electrochemical readout. Herein, we have demonstrated an electrochemical DNA (E-DNA) sensor for the one-step detection of PNK with "signal-on" readout with no need for additional labels. In our design, the highly switchable double-stranded DNA (dsDNA) probes are immobilized on the gold nanoparticle-decorated molybdenum disulfide nanomaterial (MoS₂-AuNPs), which possesses large surface area and high conductivity for elevating the signal gain in the PNK detection. This signal-on E-DNA sensor integrated with MoS₂-AuNPs exhibits a much higher sensitivity than that without MoS₂-AuNPs, showing a detection limit of 2.18 × 10^-4 U/mL. Furthermore, this assay shows high selectivity, with the ability to discriminate PNK from other enzymes and proteins, and can be utilized to screen inhibitors. The proposed sensor is easy to operate with one-step readout and robust for PNK detection in the biological matrix and shows great potential for point-of-care in clinical diagnostics and drug screening.