Label-free detection of exonuclease III by using dsDNA–templated copper nanoparticles as fluorescent probe

CRISPR/Cas12a Collateral Cleavage Activity for Sensitive 3'-5' Exonuclease Assay

This study presents a technique for detecting 3'-5' exonuclease activity through the use of CRISPR/Cas12a. These enzymes, including 3'-5' exonuclease (Exo III), perform crucial roles in various cellular processes and are associated with life expectancy. However, imbalances in their expression can increase susceptibility to diseases such as cancer, particularly under prolonged stress. In this study, an activator sequence of CRISPR/Cas12a was constructed on the 5'-end of a hairpin probe (HP), forming a blunt end. When the 3'-end of the HP was hydrolyzed with Exo III activity, the activator sequence of Cas12a was exposed, which led to collateral cleavage of the DNA signal probe and generated a fluorescent signal, allowing sensitive and highly specific Exo III detection. This detection principle relied on the fact that Exo III exclusively cleaves the 3'-end mononucleotide of dsDNA and does not affect ssDNA. Based on this strategy, Exo III activity was successfully assayed at 0.0073 U/mL, demonstrating high sensitivity. In addition, this technique was used to screen candidate inhibitors of Exo III activity.

Peroxidase-Mimicking Activity of Nanoceria for Label-Free Colorimetric Assay for Exonuclease III Activity

We present a novel label-free colorimetric method for detecting exonuclease III (Exo III) activity using the peroxidase-mimicking activity of cerium oxide nanoparticles (nanoceria). Exo III, an enzyme that specifically catalyzes the stepwise removal of mononucleotides from the 3'-OH termini of double-stranded DNA, plays a significant role in various cellular and physiological processes, including DNA proofreading and repair. Malfunctions of Exo III have been associated with increased cancer risks. To assay the activity of Exo III, we applied the previous reports in that the peroxidase-mimicking activity of nanoceria is inhibited due to the aggregation induced by the electrostatic attraction between DNA and nanoceria. In the presence of Exo III, the substrate DNA (subDNA), which inhibits nanoceria's activity, is degraded, thereby restoring the peroxidase-mimicking activity of nanoceria. Consequently, the 3,3',5,5'-tetramethylbenzidine (TMB) substrate is oxidized, leading to a color change from colorless to blue, along with an increase in the absorbance intensity. This approach enabled us to reliably detect Exo III at a limit of detection (LOD) of 0.263 units/mL across a broad dynamic range from 3.1 to 400 units/mL, respectively, with an outstanding specificity. Since this approach does not require radiolabels, complex DNA design, or sophisticated experimental techniques, it provides a simpler and more feasible alternative to standard methods.

Enzyme activity termination by titanium carbide nanosheet and its application for the detection of deoxyribonuclease I

Deoxyribonuclease I (DNase I) is a typical nuclease that plays key roles in many physiological processes and the development of a novel biosensing strategy for DNase I detection is of fundamental significance. In this study, a fluorescence biosensing nanoplatform based on a two-dimensional (2D) titanium carbide (Ti₃C₂) nanosheet for sensitive and specific detection of DNase I was reported. Fluorophore-labeled single-stranded DNA (ssDNA) can be spontaneously and selectively adsorbed on Ti₃C₂ nanosheet through the hydrogen bond and metal chelate interaction between phosphate groups of ssDNA and titanium of Ti₃C₂ nanosheet, resulting in effective quenching of the fluorescence emitted by fluorophore. Notably, it was found the enzyme activity of DNase I will be terminated by the Ti₃C₂ nanosheet. Therefore, the fluorophore-labeled ssDNA was firstly digested by DNase I and the "post-mixing" strategy of Ti₃C₂ nanosheet was chosen to evaluate the enzyme activity of DNase I, which provided the possibility of improving the accuracy of the biosensing method. Experimental results demonstrated that this method can be utilized for quantitative analysis of DNase I activity and exhibited a low detection limit of 0.16 U/ml. Additionally, the evaluation of DNase I activity in human serum samples and the screening of inhibitors with this developed biosensing strategy were successfully realized, implying that it has high potential as a promising nanoplatform for nuclease analysis in bioanalytical and biomedical fields.

Fluorescent Biosensor Based on Hairpin DNA Stabilized Copper Nanoclusters for Chlamydia trachomatis Detection

Chlamydia trachomatis (C. trachomatis) is a kind of intracellular parasitic microorganism, which can causes many diseases such as trachoma. In this strategy, a specific hairpin DNA with the probe loop as specific regions to recognize C. trachomatis DNA with strong affinity was designed, and its stem consisted of 24 AT base pairs as an effective template for hairpin DNA-CuNCs formation. In the absence of C. trachomatis DNA, the detection system showed strong orange fluorescence emission peaks at 606 nm. In the presence of C. trachomatis DNA, the conformation of DNA probe changed after hybridizing with C. trachomatis DNA. Then, the amount of hairpin DNA-CuNCs was reduced and resulted in low fluorescence emission. C. trachomatis DNA displayed a significant inhibitory effect on the synthesis of fluorescent hairpin DNA-CuNCs due to the competition between C. trachomatis DNA and the specific hairpin DNA. Under the optimal experimental conditions, different concentrations of C. trachomatis were tested and the results showed a good linear relationship in the range of 50 nM to 950 nM. Moreover, the detection limit was 18.5 nM and this detection method possessed good selectivity. Finally, the fluorescent biosensor had been successfully applied to the detection of C. trachomatis target sequence in HeLa cell lysate, providing a new strategy for the detection of C. trachomatis.

Functional nucleic acids in glycobiology: A versatile tool in the analysis of disease-related carbohydrates and glycoconjugates

As significant components of the organism, carbohydrates and glycoconjugates play indispensable roles in energy supply, cell signaling, immune modulation, and tumor cell invasion, and function as biomarkers since aberrance of them has been proved to be associated with the emergence and development of certain diseases. Functional nucleic acids (FNAs) have properties including easy-to-synthesize, good stability, good biocompatibility, low cost, and high programmability, they have attracted significant research attention and been incorporated into biosensors for detecting disease-related carbohydrates and glycoconjugates. This review summarizes the construction strategies and biosensing applications of FNAs-based biosensors in glycobiology in terms of target recognition and signal transduction. By illustrating the mechanisms and comparing the performances, the challenges and development opportunities in this area have been critically elaborated. We believe that this review will provide a better understanding of the role of FNAs in the analysis of disease-related carbohydrates and glycoconjugates, and inspire further discovery in fields that include glycobiology, chemical biology, clinical diagnosis, and drug development.

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.

dsDNA-templated fluorescent copper nanoparticles for the detection of lipopolysaccharides

The introduction of lipopolysaccharides (LPS) or endotoxins that originate from Gram-negative bacteria into the human blood stream induces a severe immune response that can lead to septic shock, and even death. Hence, the accurate detection of LPS is of great importance in the medical and pharmaceutical sectors. This paper proposes a novel label-free fluorescence assay for the detection of LPS utilizing aptamers and the interference synthesis of dsDNA-templated copper nanoparticles. The assay can be performed at room temperature and does not require expensive reagents. The proposed assay has a limit of detection of 0.95 ng ml-1 of LPS, and the fluorescence emission from the copper nanoparticles was found to vary linearly with the concentration of LPS over a wide range (1 to 105 ng ml-1) with R2 = 0.9877.

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.

Handheld fluorometer for in-situ melamine detection via interference synthesis of dsDNA-templated copper nanoparticles

Fluorescent copper nanoparticles templated by dsDNA have gained significant research interest as they are inexpensive and easy to synthesize, and have found applications in the detection of a wide range of analytes. The presence of the analyte in the reaction mixture interferes with the synthesis of the copper nanoparticles and the subsequent drop in fluorescence can be correlated to the concentration of the analyte present in the solution. Analyte detection using copper nanoparticle-based assays is amenable for in-situ applications as the test does not require expensive reagents and can be performed at room temperature. However, expensive and sophisticated detection systems are required for the detection of copper nanoparticles due to the low fluorescence emission signal from these nanoparticles. This restricts the use of the technology to centralized labs. Utilizing a recently developed chemical technique for fluorescence enhancement, this paper presents the first report of a handheld fluorometer capable of detecting DNA-templated copper nanoparticles. The fluorometer is portable and constructed with low-cost, off-the-shelf components like a UV-LED and a PIN photodiode. The performance of the developed system is demonstrated through the detection of melamine in milk samples via the interference synthesis of copper nanoparticles. Melamine is an adulterant used in dairy products that is harmful to human health if present in levels above 1 ppm. The developed system is capable of detecting up to 0.1 ppm of melamine in milk samples with a linear relationship observed between the detector output and concentration of melamine in the range from 0.1 ppm to 100 ppm (R² = 0.9979).

A graphene oxide-based fluorescence assay for the sensitive detection of DNA exonuclease enzymatic activity

The 3'-5' exonuclease enzyme plays a dominant role in multiple pivotal physiological activities, such as DNA replication and repair processes. In this study, we designed a sensitive graphene oxide (GO)-based probe for the detection of exonuclease enzymatic activity. In the absence of Exo III, the strong π-π interaction between the fluorophore-tagged DNA and GO causes the efficient fluorescence quenching via a fluorescence resonance energy transfer (FRET). In contrast, in the presence of Exo III, the fluorophore-tagged 3'-hydroxyl termini of the DNA probe was digested by Exo III to set the fluorophore free from adsorption when GO was introduced, causing an inefficient fluorescence quenching. As a result, the fluorescence intensity of the sensor was found to be proportional to the concentration of Exo III; towards the detection of Exo III, this simple GO-based probe demonstrated a highly sensitive and selective linear response in the low detection range from 0.01 U mL-1 to 0.5 U mL-1 and with the limit of detection (LOD) of 0.001 U mL-1. Compared with other fluorescent probes, this assay exhibited superior sensitivity and selectivity in both buffer and fetal bovine serum samples, in addition to being cost effective and having a simple setup.

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.

Fluorometric determination of microRNA-122 by using ExoIII-aided recycling amplification and polythymine induced formation of copper nanoparticles

The authors describe a method for the determination of microRNA-122 by using terminal deoxynucleotidyl transferase (TdT). It is based on the use of polythymine and exonuclease III-aided cycling amplification. A 3'-phosphorylated hairpin probe 1 (H₁) and a hairpin probe 2 (H₂) were designed. In the presence of the microRNA, hybridization and enzymatic cleavage will occur and produce lots of 3'-hydroxylated ssDNA which can be tailed by TdT and converted into long polythymine (polyT) sequences. These can be used to synthesize copper nanoparticles (CuNPs) with fluorescence excitation/emission maxima at 350 nm/630 nm. This method shows good selectivity and high sensitivity with a linear response in the 1.00 × 10² fM and 1.00 × 10⁶ fM microRNA concentration range and a 44 fM limit of detection. It was successfully applied to determination of microRNA in spiked serum samples. Graphical abstract A label-free and highly sensitive fluorometric method is described for the assay of microRNA on the basis of target-triggered two-cycle amplification and combining with terminal TdT. It produces a series superlong polyT that can be used for synthesis of copper nanoclusters (CuNCs) displaying red fluorecence.

Ultrasensitive Biosensor for Detection of Mercury(II) Ions Based on DNA-Cu Nanoclusters and Exonuclease III-assisted Signal Amplification

This paper describes a novel method for label-free mercury(II) ion detection based on exonuclease III-induced target signal recycling amplification using double-stranded DNA templated copper nanoclusters. The synthesized DNA-Cu nanoclusters were used with exonuclease III loop amplification technology for ultra-high sensitivity detection of mercury(II) ions, which were detected by significantly decreased fluorescence intensity. Under the optimal experimental conditions, there was a clear linear relationship between Hg²⁺ concentration in the range of 0.04 to 8 nM and fluorescence intensity. The detection limit for Hg²⁺ was 4 pM. In addition, the interference of other metal ions on the mercury(II) ion detection was also studied. To confirm the application of the fluorescent sensor, it was applied to determine the concentrations of mercury(II) ions in tap water, and the results showed that the method can be used to detect mercury(II) ions in water samples successfully.

DNA concatemer-silver nanoparticles as a signal probe for electrochemical prostate-specific antigen detection

A ultrasensitive electrochemical detection of prostate-specific antigen was reported based on hybridization chain reaction amplifying silver nanoparticles response signal.

Size-controlled atomically precise copper nanoclusters: Synthetic protocols, spectroscopic properties and applications

Noble metal nanoclusters (NCs) are a new class of nanomaterials which are considered being a missing link between isolated metal atoms and metal nanoparticles (NPs). The sizes of the NCs are comparable to the Fermi wavelength of the conduction electrons, and this renders them to be luminescent in nature. They exhibit size-dependent fluorescence properties spanning almost the entire breath of the visible spectrum. Among all the noble metal NCs being explored, copper NCs (CuNCs) are the most rarely investigated primarily because of their propensity of getting oxidised. In this chapter, we have given a comprehensive understanding as to why these NCs are luminescent in nature. We have also given a detailed overview regarding the various templates used for the synthesis of these CuNCs along with the respective protocols being followed. The various instrumental techniques used to characterize these CuNCs are discussed which provides an in-depth understanding as to how these CuNCs can be properly examined. Finally, we have highlighted some of the most recent applications of these CuNCs which make them unique to serve as the next-generation fluorophores.

Graphical Abstract:

DNA metallization: principles, methods, structures, and applications

This review summarizes the research activities on DNA metallization since the concept was first proposed in 1998, covering the principles, methods, structures, and applications.

A label-free ratiometric fluorescence strategy for 3′–5′ exonuclease detection

A label-free ratiometric fluorescent biosensor for detection of exonuclease was proposed through utilizing two individual DNA conformation-specific dyes (DAPI and NMM).

A novel label-free fluorescent molecular beacon for the detection of 3′–5′ exonuclease enzymatic activity using DNA-templated copper nanoclusters

A label-free biosensor was developed for highly sensitive and selective determination of Exo III based on poly(T) molecular beacon-templated CuNPs.

TTE DNA–Cu NPs: enhanced fluorescence and application in a target DNA triggered dual-cycle amplification biosensor

A crowded TTE DNA structure for the preparation of Cu NPs with enhanced fluorescence was prepared and applied for the ultrasensitive detection of target DNA.

Additive and enhanced fluorescence effects of hairpin DNA template-based copper nanoparticles and their application for the detection of NAD(.)

DNA is an excellent molecular scaffold for the preparation of copper nanoparticles (CuNPs). However, screening and designing an efficient template for the formation of fluorescent CuNPs remains a challenge. Herein, we synthesized CuNPs using a novel hairpin DNA template with a poly T loop and a random double strand stem which performs efficient in the formation of fluorescent CuNPs. Besides, the additive and enhanced effects between the loop and stem sequences on the fluorescence of induced CuNPs was first proposed and investigated. On comparing different sequences, we found that both the circular poly T sequence on the loop region and the stem sequence play important roles in this fluorescence enhancement effect. A label-free analytical system for the quantitative detection of NAD(+) was designed, demonstrating excellent sensitivity. Based on our design concept proposed herein, any random double-stranded DNA can be used for the design of efficient templates for the formation of fluorescent CuNPs in biochemical sensing.

Unique quenching of fluorescent copper nanoclusters based on target-induced oxidation effect: a simple, label-free, highly sensitive and specific bleomycin assay

A novel label-free fluorescence biosensor for bleomycin (BLM) detection was developed by combining the excellent fluorescence behavior of copper nanoclusters (CuNCs) and the unique oxidation capability of BLM–Fe²⁺ complex toward CuNCs.

A novel label-free fluorescence strategy for methyltransferase activity assay based on dsDNA-templated copper nanoparticles coupled with an endonuclease-assisted signal transduction system

A novel label-free fluorescence method by coupling dsDNA-templated CuNPs with endonuclease-assisted signal transduction has been developed for methyltransferase activity assay.

Transferrin-directed preparation of red-emitting copper nanoclusters for targeted imaging of transferrin receptor over-expressed cancer cells

Red-emitting fluorescent transferrin-functionalized copper nanoclusters were synthesized for the targeted bioimaging of HeLa cells.

H2O2-mediated fluorescence quenching of double-stranded DNA templated copper nanoparticles for label-free and sensitive detection of glucose

A label-free fluorescent sensor has been developed for glucose detection based on H₂O₂-mediated fluorescence quenching of ds-DNA templated Cu NPs.

Inhibition of double-stranded DNA templated copper nanoparticles as label-free fluorescent sensors for l-histidine detection

A label-free fluorescent sensing strategy was reported for l-histidine detection by the inhibition of double-stranded DNA templated copper nanoparticles.

Sequence-dependent dsDNA-templated formation of fluorescent copper nanoparticles

There are only a few systematic rules about how to selectively control the formation of DNA-templated metal nanoparticles (NPs) by varying sequence combinations of double-stranded DNA (dsDNA), although many attempts have been made. Herein, we develop a facile method for sequence-dependent formation of fluorescent CuNPs by using dsDNA as templates. Compared with random sequences, AT sequences are better templates for highly fluorescent CuNPs. Other specific sequences, for example, GC sequences, do not induce the formation of CuNPs. These results shed light on directed DNA metallization in a sequence-specific manner. Significantly, both the fluorescence intensity and the fluorescence lifetime of CuNPs can be tuned by the length or the sequence of dsDNA. In order to demonstrate the promising practicality of our findings, a sensitive and label-free fluorescence nuclease assay is proposed.