Signal-on electrochemical assay for label-free detection of TdT and BamHI activity based on grown DNA nanowire-templated copper nanoclusters

Copper nanocluster based cascade amplified DNA electrochemical detection combining with bio-barcode assay and surface-initiated enzyme polymerization

Early cancer diagnosis is paramount for enhancing treatment efficacy, extending patient survival, and improving the quality of life. We developed a highly sensitive electrochemical biosensor for the detection of target DNA (tDNA) associated with gastric cancer. This advancement integrates dual signal amplification strategies: bio-barcode amplification (BCA) and surface-initiated enzyme polymerization (SIEP), with copper nanoclusters (CuNCs) serving as signal labels. Silica nanoparticles (SiO2) were covalently linked with polythymine (poly T) and complementary DNA to create bio-barcode probes. These probes, through hybridization, were immobilized on the reduced graphene oxide and Au nanoparticle (rGO-AuNPs) modified interface and marking the first amplification of the electrical signal. Subsequently, the extended poly T prompted by SIEP bound additional CuNCs through the combination of T-Cu2+, leading to a second round of signal amplification. The biosensor demonstrated a minimum detection limit of 0.13 fmol/L over a linear response range from 1 fmol/L to 1 nmol/L. It also showcased excellent specificity, repeatability, and stability, making it a promising tool for the sensitive detection of gastric cancer biomarkers.

Template-independent enzymatic functionalization of DNA oligonucleotides with environment-sensitive nucleotide probes using terminal deoxynucleotidyl transferase

Given the emerging use of terminal deoxynucleotidyl transferase (TdT) in biotechnology and its clinical potential as a cancer marker and target, the development of a versatile probe system to study its processivity, substrate properties, and inhibition is highly desired. Here, we demonstrate a multilayered application of a series of environment-sensitive fluorescent 2'-deoxynucleotide probes that harness the activity of TdT in accessing site-specifically functionalized DNA oligonucleotides and devising a real-time fluorescence platform to monitor the enzyme activity and identify potential inhibitors. The nucleotides constructed by coupling heterocycles of progressively increasing chemical modifications (selenophene, benzothiophene, benzofuran, and fluorobenzofuran) at the C5 position of 2'-deoxyuridine serve as suitable substrates for TdT, albeit differences in incorporation efficiency. A battery of experiments provided valuable insights into the scope of this functionalization method. It revealed how a fine balance between steric hindrance and stacking interaction between the heterocycle moiety and primer 3'-end nucleobase in the active site modulates the recognition and processing of nucleotides based on their size. Remarkably, the excellent responsiveness of benzofuran-modified dUTP enabled the design of fluorescence assays to estimate TdT activity, and detect nucleotide and non-nucleotide inhibitors. The findings obtained using our probes should significantly advance TdT-based functionalization, diagnostic, and therapeutic strategies.

Periodically programmed building and collapse of DNA networks enables an ultrahigh signal amplification effect for ultrasensitive nucleic acids analysis

ANALYSIS

of molecular species is needed for applications in diagnosis of infections and genetic diseases. Herein, we demonstrate a target DNA-responsive ultrahigh fluorescence signal-on DNA amplification system via periodically programmed building and collapse of DNA networks. In this system, a pair of oligonucleotides of padlock probe (PP) and palindromic hairpin probe (PHP) are utilized. The presence of target DNA firstly hybridizes with PP, allowing the occurrence of rolling circle amplification (RCA) to produce RCA products with tandem repeats in abundance to bind and unfold numbers of PHPs. The conformational change of PHPs enables the building of DNA networks via the intermolecular palindrome pairing, but then makes the DNA networks collapsed via the palindrome-induced strand displacement polymerization. The displaced RCA products are dynamically reused to undergo periodically programmed multiple rounds of DNA network building and collapse. Depend on the bidirectional DNA assembly and disassembly, a strikingly amplified fluorescence can be collected to ultrasensitive and specific detection of target DNA. The practicability has been demonstrated by evaluating target-spiked human serum, saliva, and urine samples with acceptable recoveries and reproducibility. Therefore, this newly explored method opens a promising avenue for the detection of nucleic acids with low abundance in biochemical analysis and diseases diagnosis.

Alkaline phosphatase determination via regulation of enzymatically generated poly(thymine) as a template for fluorescent copper nanoparticle formation

We propose a new fluorometric method for alkaline phosphatase (ALP) determination. This method is based on the regulation of enzymatically generated poly(thymine) for the preparation of copper nanoparticles (CuNPs). 2'-Deoxythymidine 5'-triphosphate (dTTP) serves as the source for polymerization mediated by terminal deoxynucleotidyl transferase (TdT). This process generates poly(thymine), which acts as the template for synthesis of fluorescent CuNPs. However, if ALP catalyzes the hydrolysis of dTTP, the TdT-mediated polymerization will be disabled. This prevents the formation of CuNPs and causes a drop in fluorescence. The findings were used to design a sensitive and selective fluorometric method for ALP determination. A linear response in the activity range from 0.1 to 20 U L^-1 and a limit of quantification of 0.3 U L^-1 were obtained. The results indicate that the proposed method can be successfully applied to ALP assay in spiked diluted serum. This demonstrates the method's reliability and practicability. Graphical abstract A fluoromoetric method for alkaline phosphatase assay has been developed based on regulation of enzymatically generated poly(thymine) as template for the formation of fluorescent CuNPs.

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.

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.