A label-free and enzyme-free ultra-sensitive transcription factors biosensor using DNA-templated copper nanoparticles as fluorescent indicator and hairpin DNA cascade reaction as signal amplifier

Environmentally sensitive fluorescent nucleoside analogues as probes for nucleic acid - protein interactions: molecular design and biosensing applications

Fluorescent nucleoside analogues (FNAs) are indispensable in studying the interactions of nucleic acids with nucleic acid-binding proteins. By replacing one of the poorly emissive natural nucleosides, FNAs enable real-time optical monitoring of the binding interactions in solutions, under physiologically relevant conditions, with high sensitivity. Besides that, FNAs are widely used to probe conformational dynamics of biomolecular complexes using time-resolved fluorescence methods. Because of that, FNAs are tools of high utility for fundamental biological research, with potential applications in molecular diagnostics and drug discovery. Here I review the structural and physical factors that can be used for the conversion of the molecular binding events into a detectable fluorescence output. Typical environmentally sensitive FNAs, their properties and applications, and future challenges in the field are discussed.

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.

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.

Colorimetric nanoplatform for visual determination of cancer cells via target-catalyzed hairpin assembly actuated aggregation of gold nanoparticles

According to aptamer-mediated hairpin DNA cascade amplifier and gold nanoparticles aggregation, an optical platform for cancer cells determination has been proposed. High-affinity chimeric aptamers were used for cancer cell detection and also as an initiator for beginning hairpin assembly to construct three-way junction (3WJ) nanostructures. These three hairpins were modified at 3' ends with biotin. In the presence of target cell, chimeric aptamer binds to its ligand on cell surface and initiates 3WJ nanostructures formation. These 3WJ nanostructures interact with streptavidin-modified gold nanoparticles (AuNPs) via non-covalent biotin-streptavidin interactions and create a crossover lattice of nanoparticles. This event leads to AuNPs aggregation and red-shifting. The results were confirmed by gel electrophoresis and UV-visible spectrophotometry. The dynamic range of this assay is 25 to 10⁷ cells with a detection limit of 10 cells which is respectively 9 and 4 times more significant than the sensitivity of AuNP-based approaches without amplification and enzyme-mediated signal amplification. Graphical abstract.

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 and enzyme-free fluorescent aptasensor for sensitive detection of acetamiprid based on AT-rich dsDNA-templated copper nanoparticles

A label-free and enzyme-free aptasensor for sensitive assay of acetamiprid has been established using AT-rich double-stranded (ds) DNA-templated copper nanoparticles (CuNPs) as fluorescent probe. In this work, two hairpin DNA, HP1 and HP2, were elaborately designed with AT-rich DNA sequences in their loops. The aptamer of acetamiprid was located at the 3'-terminal of HP1, which was caged in the stem of HP1. Upon the addition of acetamiprid, the aptamer could combine with acetamiprid to form a target/aptamer complex, and thus its free 5'-terminal was released. Subsequently, the protruded 3'-terminal of HP2 could hybridize with the free 5'-terminal of HP1 to form a stable AT-rich dsDNA. When it interacted with Cu²⁺ and ascorbic acid (AA), the AT-rich dsDNA/CuNPs were generated with strong fluorescence, offering a "switch-on" detection of acetamiprid. The developed strategy could high selectively detect acetamiprid at the concentration as low as 2.37 nM. Moreover, the possibility of this strategy for the food sample analysis was also investigated. The obtained results demonstrate that the developed strategy has a promising application potential for acetamiprid assay in food safety fields.

Silver ion-stabilized DNA triplexes for completely enzyme-free and sensitive fluorescence detection of transcription factors via catalytic hairpin assembly amplification

A new silver ion-stabilized DNA triplex enables enzyme-free and amplified sensitive fluorescence detection of transcription factors.

Cu x O@DNA sphere-based electrochemical bioassay for sensitive detection of Pb2

The paper describes a one-step synthetic method to chemically reduce cupric sulfate by ascorbic acid in the presence of DNA strands to directly produce Cu _x O@DNA spheres. The DNA strands act as template to assist the preparation of Cu _x O, and also are capable of specifically binding  Pb(II) ions. The Cu _x O@DNA spheres possess high specific surface area and strong bioaffinity. They can be directly employed as platform for detecting Pb²⁺ sensitively. Electrochemical impedance spectroscopy data showed that the assay exhibits high sensitivity and a wide linear analytical range that extends from 0.1 to 100 nM, and the detection limit is 6.8 pM at a signal-to-noise ratio of 3. The assay is selective, acceptably reproducible, stable, and well feasible for the detection of Pb²⁺ in blood serum. Graphical abstract Schematic presentation of the preparation of DNA-templated Cu _x O spheres (Cu _x O@DNA) for use in electrochemical detection of Pb²⁺. The assay exhibits detection limit of 6.8 pM, high selectivity, acceptable reproducibility, stability, and good applicability for Pb²⁺ detection.

Hairpin loop-enhanced fluorescent copper nanoclusters and application in S1 nuclease detection

A novel hairpin DNA template with an AT24 double strand stem and a six-base loop was demonstrated for the first time to prepare CuNCs with dramatically enhanced fluorescence and applied for the sensitive detection of S1 nuclease.

Nanotechnology-Enhanced No-Wash Biosensors for in Vitro Diagnostics of Cancer

In vitro biosensors have been an integral component for early diagnosis of cancer in the clinic. Among them, no-wash biosensors, which only depend on the simple mixing of the signal generating probes and the sample solution without additional washing and separation steps, have been found to be particularly attractive. The outstanding advantages of facile, convenient, and rapid response of no-wash biosensors are especially suitable for point-of-care testing (POCT). One fast-growing field of no-wash biosensor design involves the usage of nanomaterials as signal amplification carriers or direct signal generating elements. The analytical capacity of no-wash biosensors with respect to sensitivity or limit of detection, specificity, stability, and multiplexing detection capacity is largely improved because of their large surface area, excellent optical, electrical, catalytic, and magnetic properties. This review provides a comprehensive overview of various nanomaterial-enhanced no-wash biosensing technologies and focuses on the analysis of the underlying mechanism of these technologies applied for the early detection of cancer biomarkers ranging from small molecules to proteins, and even whole cancerous cells. Representative examples are selected to demonstrate the proof-of-concept with promising applications for in vitro diagnostics of cancer. Finally, a brief discussion of common unresolved issues and a perspective outlook on the field are provided.

A nuclease-assisted label-free aptasensor for fluorescence turn-on detection of ATP based on the in situ formation of copper nanoparticles

Owing to their promising advantages in biochemical analysis, aptamer-based sensing systems for the fluorescence detection of important biomolecules are being extensively investigated. Herein, we propose a turn-on fluorescent aptasensor for label-free detection of adenosine triphosphate (ATP) by utilizing the in situ formation of copper nanoparticles (CuNPs) and the specific digestion capability of exonuclease I (Exo I). In this assay, the addition of ATP can effectively hinder the digestion of aptamer-derived oligonucleotides due to the G-quadruplex structure. Accordingly, the remaining poly thymine at 5'-terminus of substrate DNA can serve as an efficient template for red-emitting fluorescent CuNPs with a Mega-Stokes shifting in buffered solution, which can be used to evaluate the concentration of ATP. This method is cost-effective and facile, because it avoids the use of traditional dye-labeled DNA strands and complex operation steps. Under optimized conditions, this method achieves a selective response for ATP with a detection limit of 93nM, and exhibits a good detection performance in biological samples.