Aptamer-based fluorometric determination of ATP by using target-cycling strand displacement amplification and copper nanoclusters

A multifunctional fluorescent sensor for Ag+ and Hg2+ detection in seawater

In order to detect Ag+ and Hg2+ in seawater, we explored a multifunctional fluorescence sensor. A multifunctional Ag+ and Hg2+ sensor was designed by using gold nanoparticles (AuNPs) as quenching agent, PicoGreen dye as fluorescent probe of base pairing double-stranded deoxyribonucleic acid (DNA), and combining the characteristics of Ag+ making C base mismatch and Hg2+ making T base mismatch. Meanwhile, the DNA logic gate was constructed by establishing logic circuit, truth table, and logic formula. The relevant performances of the sensor were investigated. The results revealed that the sensor can detect Ag+ in the range of 100 to 700 nM with R2 = 0.98129, and its detection limit is 16.88 nM (3σ/slope). The detection range of Hg2+is 100-900 nM with R2 = 0.99725, and the detection limit is 5.59 nM (3σ/slope). An AND-AND-NOR-AND molecular logic gate has been successfully designed. With the characteristics of high sensitivity, multifunction, and low cost, the recommended detection method has the potential to be applied to the detection of Ag+ and Hg2+ in seawater.

Fluorescent Sensor Based on Magnetic Separation and Strand Displacement Amplification for the Sensitive Detection of Ochratoxin A

Ochratoxin A (OTA) is a common mycotoxin, and it is a significant threat to human health throughout the food chain. In this study, a sensitive and specific fluorescent sensor based on magnetic separation technology combined with chain displacement amplification was developed for fast and easy detection of OTA in food. The designed strand displacement amplification can improve the sensitivity for the detection, and the magnetic nanomaterials can provide a large surface area, thus enhancing the capture efficiency of the target from the sample. Based on those designs, the experimental results showed that the proposed method displayed excellent performance. The linearity range was 0.5-128.0 ng/mL. The detection limit was 0.125 ng/mL; the relative standard deviations were 3.92-7.71%. Additionally, the developed method was satisfactorily applied to determine OTA in wheat, corn, and red wine samples at three spiked levels (1.0, 8.0, and 64.0 ng/mL). The recoveries ranged from 85.45 to 107.8% for wheat flour, 101.34 to 108.35% for corn flour, and 91.15 to 93.80% for red wine, respectively. Compared with high-performance liquid chromatography, the proposed method showed a lower limit of detection and equal recovery. Hence, the designed method is a potential and good detecting tool for OTA residue analysis in complex matrix samples.

Integrating CRISPR/Cas12a with strand displacement amplification for the ultrasensitive aptasensing of cadmium(II)

Cadmium ion (Cd(II)) is a pernicious environmental pollutant that has been shown to contaminate agricultural lands, accumulate through the food chain, and seriously threaten human health. At present, Cd(II) monitoring is dependent on centralized instruments, necessitating the development of rapid and on-site detection platforms. Against this backdrop, the present study reports on the development of a fluorometric aptasensor designed to target Cd(II), which is achieved through the integration of strand displacement amplification (SDA) and CRISPR/Cas12a. In the absence of Cd(II), the aptamer initiates SDA, resulting in the generation of a profusion of ssDNA that activates Cas12a, leading to a substantial increase in fluorescence output. Conversely, the presence of Cd(II) curtails the SDA efficiency, culminating in a significant reduction in fluorescence output. The proposed approach has been demonstrated to enable the selective detection of Cd(II) at concentrations of 60 pM, with the performance of the aptasensor validated in real water and rice samples. The proposed platform based on aptamer-target interaction holds immense promise as a signal-amplified and precise method for the detection of Cd(II) and has the potential to transform current hazard detection practices in food samples.

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.

Application of tetrahedral -deoxyribonucleic acid electrochemistry platform coupling aptazymes and hybridized hairpin reactions for the measurement of extracellular adenosine triphosphate in plants

Extracellular ATP (eATP) is an important biological signal transduction molecule. Although a variety of detection methods have been extensively used in ATP sensing and analysis, accurate detection of eATP remains difficult due to its extremely low concentration and spatiotemporal distribution. Here, an eATP measurement strategy based on tetrahedral DNA (T-DNA)-modified electrode sensing platform and hybridization chain reaction (HCR) combined with G-quadruplex/Hemin (G4/Hemin) DNAzyme dual signal amplification is proposed. In this strategy, ATP aptamer and RNA-cleaving DNAzyme were combined to form a split aptazyme. In the presence of ATP, this aptazyme hydrolyzes the cleaving substrate strand with high selectivity, releasing cleaved ssDNA, which are captured by the T-DNA assembled on the electrode surface, triggering an HCR on the electrode surface to form numerous linker sequences of the HCR dsDNA product. When G-quadruplex@AuNPs (G4) spherical nucleic acid enzymes (SNAzymes) with other linkers are used as nanocatalyst tags, they are captured by HCR dsDNA through sticky linkers present on the electrode surface. An amplified electrochemical redox current signal is generated through SNAzyme-mediated catalysis of H₂O₂, enabling easy detection of picomole amounts of ATP. Using this strategy, eATP levels released by tobacco suspension cells were accurately measured and the distribution and concentration of eATP released on the surface of an Arabidopsis leaf was determined.

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.

A label-free logic gate hairpin aptasensor for sensitive detection of ATP based on graphene oxide and PicoGreen dye

Background

In this paper, a simple, enzyme-free, label-free fluorescence, high sensitivity logic gate hairpin aptasensor was developed for adenosine triphosphate (ATP) detection based on graphene oxide (GO) and PicoGreen dye.

Methods

Using single-strand deoxyribonucleic acid (DNA) and adenosine triphosphate (ATP) as input signal and fluorescence signal as output signal, if single-strand DNA (DNA-L), single-strand DNA (DNA-S), and ATP were present at the same time, one segment of DNA-L formed a hairpin ring with ATP, and the other segment of DNA-L formed a completely complementary hairpin stem with DNA-S. The hairpin DNA was detached from the GO surface, and PicoGreen dye was embedded into the hairpin stem, and the fluorescence signal was enhanced. The molecular logic gate was constructed through the establishment of logic histogram, logic circuit, truth table, and logic formula. The biosensor-related performances including sensitivity, selectivity, and linearity were investigated, respectively.

Results

We have successfully constructed a AND logic gate. The detection limit of ATP is 138.0 pmol/L (3σ/slope) with detection range of 50–500 nmol/L (R2 = 0.98951), and its sensitivity is 4.748 × 106–6.875 × 108 a.u. (mol/L)−1.

Conclusions

The logic gate hairpin aptamer sensor has the advantages of high sensitivity, low detection limit, and low cost, and can be successfully applied to the detection of adenosine triphosphate (ATP) in actual human urine samples.

One-step and ultrasensitive ATP detection by using positively charged nano-gold@graphene oxide as a versatile nanocomposite

A versatile nanocomposite was simply prepared based upon the electrostatic adsorption of positively charged gold nanoparticles with negatively charged graphene oxide (nano-gold@GO), and utilized as a novel fluorescence quenching platform for ultrasensitive detection of adenosine triphosphate (ATP). In the designed system, DNA-stabilized Ag nanoclusters (DNA/AgNCs) were used as fluorescent probes, DNA duplex was formed in the presence of ATP, and they can electrostatically adsorb onto the surface of nano-gold@GO to quench the fluorescence signal. Upon the addition of exonuclease III (Exo III), the DNA duplex would be hydrolyzed into DNA fragments and resulted in the recovery of the fluorescence signals due to the diffusion of AgNCs away from nano-gold@GO. Based on these, sensitive detection of ATP was realized with a detection range of 5.0 pM-20 nM. Notably, a good recovery in the range of 94-104% was obtained when detecting ATP in human serum samples, indicating a promising application value in early disease diagnosis. Graphical abstract A functional positively charged nano-gold@graphene oxide was fabricated and utilized as an enhanced fluorescence quenching platform for the detection of ATP, coupled with exonuclease III-assisted signal amplification.

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.

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 label-free fluorescent probe for the detection of adenosine 5'‑triphosphate via inhibiting the aggregation-induced emission enhancement of glutathione modified silver nanoclusters triggered by zinc ion

It is important to establish sensitive and simple analysis methods for adenosine 5'‑triphosphate (ATP). A label-free fluorescent probe for the determination of ATP was constructed based on glutathione modified silver nanoclusters (AgNCs/GSH). AgNCs/GSH showed aggregation-induced emission enhancement (AIEE) property in the organic solvent. The effects of metal ions on the fluorescence of AgNCs/GSH were also studied. Only zinc ion enhanced the fluorescence of AgNCs/GSH obviously. This was because Zn²⁺ coordinated with AgNCs/GSH to cause the aggregation of AgNCs/GSH, which was sufficiently proved by TEM. With the addition of ATP, Zn²⁺ bound with ATP through ZnOP bond and the binding between Zn²⁺ and AgNCs/GSH was inhibited. Hence the fluorescence of AgNCs/GSH was decreased with increasing the ATP concentration. The fluorescence response was linear in the ATP concentration range of 1-110 μM, and the detection limit was 0.8 μM. Then this method was successfully applied for determining ATP in the samples of human urine and rat serum, the recoveries were in the range of 97.6%-103%.

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.

A Label-Free Fluorescent AND Logic Gate Aptasensor for Sensitive ATP Detection

In this study, a label-free fluorescent, enzyme-free, simple, highly sensitive AND logic gate aptasensor was developed for the detection of adenosine triphosphate (ATP). Double-stranded deoxyribonucleic acid (DNA) with cohesive ends was attached to graphene oxide (GO) to form an aptasensor probe. ATP and single-stranded DNA were used as input signals. Fluorescence intensity of PicoGreen dye was used as an output signal. The biosensor-related performances, including the logic gate construction, reaction time, linearity, sensitivity, and specificity, were investigated and the results showed that an AND logic gate was successfully constructed. The ATP detection range was found to be 20 to 400 nM (R² = 0.9943) with limit of detection (LOD) of 142.6 pM, and the sensitivity range was 1.846 × 10⁶ to 2.988 × 10⁶ M^-1. This method for the detection of ATP has the characteristics of being simple, low cost, and highly sensitive.

Nanosensing of ATP by fluorescence recovery after surface energy transfer between rhodamine B and curcubit[7]uril-capped gold nanoparticles

The authors describe a method for functionalization of gold nanoparticles (AuNPs) with the supramolecular host molecule, curcubit[7]uril (CB[7]) which can bind rhodamine B (RhB). The fluorescence of RhB is quenched by the AuNPs via surface energy transfer. On addition of ATP, a dimeric RhB-ATP complex is formed and RhB is pushed out of CB[7]. Hence, fluorescence increases by a factor of 8. This fluorescence recovery effect has been utilized to develop a new detection scheme for ATP. The assay, measured at fluorescence excitation and emission wavelengths of 500 nm and 574 nm respectively, works in the 0.5-10 μM concentration range and has a 100 nM detection limit. The method is not interfered by UTP, GTP, CTP, TTP, ascorbic acid and glutathione. Graphical abstract Schematic of a method for determination of ATP in the 500 nM to 10 μM concentration range by using fluorescence recovery after surface energy transfer (SET) between rhodamine B (RhB) and gold nanoparticles capped with curcubit[7]uril (CB[7]).

Bimetallic NiFe oxide structures derived from hollow NiFe Prussian blue nanobox for label-free electrochemical biosensing adenosine triphosphate

We designed and constructed a novel aptasensor based on the porous nanostructured bimetallic NiFe-oxides embedded with the mesoporous carbon (represented by NiO_xFeO_y@mC) for sensitively detecting adenosine triphosphate (ATP), of which the porous NiO_xFeO_y@mC was derived from the hollow NiFe Prussian blue analogue (hollow NiFe PBA) by calcinating under high temperature. Owning to the excellent electrochemical activity originated from the metal oxides and mesoporous carbon and the strong binding interaction between the aptamer strands and the nanostructure hybrid, the formed porous NiO_xFeO_y@mC composite calcinated at 900 °C exhibited superior sensitivity toward ATP determination in comparison with other porous nanocubes obtained at 500 and 700 °C. The proposed aptasensor not only revealed a wide linear range from 5.0 fg·mL^-1 to 5.0 ng mL^-1 with a extremely low detection limit of 0.98 fg·mL^-1 (1.62 fM) (S/N = 3), but also displayed high selectivity towards other interferences, good stability and reproducibility, and acceptable applicability. Therefore, this proposed approach provides a promising platform for ultra-sensitive detection of ATP, further having the potential applications on diagnosis of ATP-related diseases.

Aptamer based fluorometric sulfamethazine assay based on the use of graphene oxide quantum dots

The authors have developed a homogeneous "off-on" fluorometric method for the determination of the antibiotic sulfamethazine (SMZ). Aptamer against SMZ was labeled with graphene oxide quantum dots upon which the Graphene oxide quenched the blue fluorescence of the GOQDs. On addition of SMZ, the aptamers will bind SMZ and this will cause the release of GOQDs. As a result, fluorescence will be regenerated. Fluorescence, best measured at excitation/emission wavelengths of 365/455 nm, increases linearly in the 8 pg·mL^-1 to 60 ng·mL^-1 SMZ concentration range, with a 5 pg·mL^-1 detection limit. The method is reliable and was successfully applied to the determination of SMZ in spiked milk samples, with recoveries ranging from 89 to 96% depending on analyte concentration. Graphical abstract Graphene oxide quantum dots (GOQDs) were covalently bound to the aptamer (apt) against sulfamethazine (SMZ) and adsorbed on the surface of graphene oxide (GO). This results in quenching of the fluorescence of GOQDs. On addition of SMZ, fluorescence is restored due to the release of GOQD@apt from GO.