Target-induced in-situ formation of fluorescent DNA-templated copper nanoparticles by a catalytic hairpin assembly: application to the determination of DNA and thrombin

Electrochemical microfluidic biosensors for the detection of cancer biomarker miRNAs

Cancer is a formidable adversary in contemporary healthcare. Routine screening and early diagnosis are crucial for favourable therapeutic outcomes. Publications, clinical trials, and patent landscape analysis suggest miRNA as promising biomarkers for diagnosis and prognosis of various cancers. This review intends to shed a holistic view of the current and futuristic methods for electrochemical biosensing platforms, using miRNA as biomarkers, coupled with microfluidics, machine learning techniques, and portable electronic devices. Electrochemical biosensors are thoroughly reviewed as they are promising candidate in the design and development of such devices where there is an in-depth exploration of the existing molecular techniques and sophisticated electrochemical biosensing strategies developed for the detection of miRNAs. Additionally, the review will critically analyze diverse signal enhancement strategies and microfluidic platforms specifically tailored for the detection of miRNA. Practical examples of such integrated electrochemical microfluidic biosensors are thoroughly cited along with the prospect of integration of these techniques with portable electronics, highlighting the future potential of highly integrated and accessible diagnostic solutions. Furthermore, the review will also encompass an assessment of the ongoing clinical trials investigating the utility of miRNA as cancer biomarker in diagnostic settings. Moreover, by assessing existing patents, the review shall provide a nuanced understanding of the intellectual property landscape, identifying key players, emerging technologies, and potential future directions. Our review with a 360-degree updated view on molecular biology components, electrochemical biosensors, engineering device design, clinical trials and patent landscape would appeal to researchers, engineers and clinicians working in the area of cancer molecular diagnosis.

Simultaneous and Ultraspecific Optical Detection of Multiple miRNAs Using a Liquid Flow-Based Microfluidic Assay

Recent studies have reported that the cause and progression of many diseases are closely related to complex and diverse gene regulation involving multiple microRNAs (miRNAs). However, most existing methods for miRNA detection typically deal with one sample at a time, which limits the achievement of high diagnostic accuracy for diseases associated with multiple gene dysregulations. Herein, we develop a liquid flow-based microfluidic optical assay for the simple and reliable detection of two different target miRNAs simultaneously at room temperature without any enzymatic reactions. This assay utilizes the catalytic hairpin assembly cycling reaction in a mixture containing four types of hairpin DNAs to amplify two different dimeric DNA probes, each of which specifically recognizes one of the two different target miRNAs. The resultant two dimeric DNA probes effectively hybridize with anchor DNA grafted into two outlet channels of a microfluidic device, thus enabling i-motif-driven compact DNA hydrogels to form in the channels under acidic conditions. With this setup, the presence of two target miRNAs can be confirmed by the naked-eye observation of red-colored gold nanoparticles encountering a flow blockage in the two outlet channels. Notably, the developed assay demonstrates sensitive and sequence-specific detection that can precisely distinguish a single base mismatch mutant miRNA within 1.5 h. Our assay thus has the potential to serve as a powerful sensing platform for the simple and simultaneous detection of multiple miRNAs in clinical diagnostics at room temperature without analytic equipment or enzymatic reactions.

[Development of a Catalytic Hairpin Assembly-Based Fluorescent Assay for the Rapid Detection of SARS-CoV-2 Target RNA]

Objective

To develop a catalytic hairpin assembly (CHA)-based fluorescent assay for the detection of the target RNA of severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2), so as to realize the rapid nucleic acid testing of SARS-CoV-2.

Methods

A 24-nt segment of the SARS-CoV-2 nucleocapsid protein gene (N gene, NC_045512.2) was chosen as the target RNA and the hairpin motif 1 (H1) and hairpin motif 2 (H2) were designed based on the principle of CHA reaction. The H1 motif was labelled with a fluorophore group as well as a quencher group. When the target RNA was added to the hairpin motifs, CHA reaction was triggered at room temperature (25 ℃), which led to the amplification of fluorescence signal, thereby enabling the rapid detection of the target RNA. After the optimization of the hairpin motifs and the experimental conditions, the sensitivity and the specificity of the testing method were measured to evaluate its performance.

Results

We successfully constructed a CHA-based fluorescent assay specifically for the target RNA of SARS-CoV-2. With this method, testing could be completed at room temperature within 30 min. This testing method exhibited excellent specificity and could be used to accurately distinguish the perfectly-matched target RNA from the target RNA with single-base mutations. In addition, the testing method demonstrated good sensitivity, with a detection limit of 50 pmol/L.

Conclusion

The proposed assay enables the simple and rapid detection of the SARS-CoV-2 target RNA with excellent sensitivity and specificity, showing great promise for further optimization and subsequent clinical application for the rapid detection of SARS-CoV-2 nucleic acid.

The rate-limiting procedure of 3D DNA walkers and their applications in tandem technology

DNA walkers, artificial dynamic DNA nanomachines, can mimic actin to move rapidly along a predefined nucleic acid track. They can generally be classified as one- (1D), two- (2D), and three-dimensional (3D) DNA walkers. In particular, 3D DNA walkers demonstrate amazing sustainable walking ability, strong enrichment ability, and fantastic signal amplification ability. In light of these, 3D DNA walkers have been widely used in fields such as biosensors, bioanalysis and cell imaging. Most notably, the strong compatibility of 3D DNA walkers allows their integration with a range of amplification strategies, effectively enhancing signal transduction and amplifying biosensor sensing signals. Herein, we first systematically expound the walking principle of the 3D walkers in this review. Then, by presenting representative examples, the research direction of 3D walkers in recent years is discussed. Furthermore, we also categorize and evaluate diverse tandem signal amplification strategies in 3D walkers. Finally, the challenges and development trends of 3D DNA walkers in the emerging field of analysis are carefully discussed. It is believed that this work can provide new ideas for researchers to quickly understand 3D DNA walkers and their applications in diverse biosensors.

Carbon dots doped with nitrogen as an ultrasensitive fluorescent probe for thrombin activity monitoring and inhibitor screening

A simple and sensitive fluorometric assay based on nitrogen-doped carbon dots (N-CDs) was developed for the determination of thrombin (TB) activity in human serum samples and living cells. The novel N-CDs were prepared by a facile one-pot hydrothermal method using 1,2-ethylenediamine and levodopa as precursors. Such N-CDs exhibited green fluorescence with excitation/emission peaks at 390/520 nm and a high fluorescence quantum yield of approximately 39.2%. H-D-Phenylalanyl-L-pipecolyl-Larginine-p-nitroaniline-dihydrochloride (S-2238) was hydrolyzed by TB to produce p-nitroaniline which was capable of quenching the fluorescence of N-CDs due to an inner filter effect. This assay was used to detect TB activity with a low detection limit of 11.3 fM. The proposed sensing method was then expanded to the TB inhibitor screening and exhibited excellent applicability. As a typical TB inhibitor, argatroban was determined in a concentration as low as 1.43 nM. The method has also been successfully employed for the determination of TB activity in living HeLa cells. This work showed significant potential for TB activity assay in clinical and biomedicine applications.

A Pax-5a gene analysis approach enabled by selective digestion with lambda exonuclease

Owing to the rapid increase in acute leukemia patients, the detection of Pax-5a, which is a tumor marker, is very important for the early diagnosis of patients. Therefore, by combining the selective digestion function of lambda exonuclease and the hybridization chain reaction (HCR) enzyme-free amplification system, we design a biosensor to detect the Pax-5a gene with high sensitivity. Lambda exonuclease can cleave the blunt end formed by the hairpin probe and the Pax-5a gene, which exposes the nucleic acid sequence that can initiate the HCR. When the HCR is triggered, the fluorophore and quencher on H1 and H2 move away from each other, so that the fluorescence signal of the quenched fluorophore can be recovered. Under optimal experimental conditions, a good linear relationship was established between the fluorescence intensity and the logarithm of the target concentration, and the limit of detection (LOD) of Pax-5a was calculated to be 7.6 pM. In addition, the biosensor can not only discriminate the base mismatch sequences of the Pax-5a gene, but also be suitable for target detection in complex human serum samples. Therefore, this biosensor, with the advantages of simple operation, high sensitivity, and good selectivity, has a good application prospect and guiding role in the diagnosis of acute B lymphocytic leukemia and the design of biosensors.

Target DNA- and pH-responsive DNA hydrogel-based capillary assay for the optical detection of short SARS-CoV-2 cDNA

DNA is recognized as a powerful biomarker for clinical diagnostics because its specific sequences are closely related to the cause and development of diseases. However, achieving rapid, low-cost, and sensitive detection of short-length target DNA still remains a considerable challenge. Herein, we successfully combine the catalytic hairpin assembly (CHA) technique with capillary action to develop a new and cost-effective method, a target DNA- and pH-responsive DNA hydrogel–based capillary assay, for the naked eye detection of 24 nt short single-stranded target DNA. Upon contact of target DNA, three individual hairpin DNAs hybridize with each other to sufficiently amplify Y-shaped DNA nanostructures (Y-DNA) until they are completely consumed via CHA cycling reactions. Each arm of the resultant Y-DNA contains sticky ends with i-motif DNA structure-forming sequences that can be self-assembled in an acidic environment (pH 5.0) to form target DNA- and pH-responsive DNA hydrogels by means of i-motif DNA-driven crosslinking. When inserting a capillary tube in the resultant solution, the liquid level inside clearly reduces due to the decrease in capillary force induced by the gels. In this way, the developed assay demonstrates sensitive and quantitative detection, with a detection limit of approximately 10 pM of 24 nt short complementary DNA (cDNA) targeting SARS-CoV-2 RNA genes at room temperature within 1 h. The assay is further shown to successfully detect target cDNA in serum, and it is also applied to detect several types of target sequences. Requiring no analytic equipment, precise temperature control, or enzymatic reactions, the developed DNA hydrogel–based capillary assay has potential as a promising naked eye detection platform for target DNA in resource-limited clinical settings.

DNA dendrimer-templated copper nanoparticles: self-assembly, aggregation-induced emission enhancement and sensing of lead ions

Copper nanomaterials based on DNA scaffold (DNA-Cu NMs) are becoming a novel fluorescent material, but it is still challenging to obtain highly fluorescent DNA-Cu NMs with excellent stability. In this work, we report a kind of copper nano-assemblies (Cu NASs) with aggregation-induced emission enhancement (AIEE) property using DNA dendrimers with sticky end as template. The sticky end of the DNA dendrimers induced the formation of much bigger Cu NASs with average size ranging from 131 to 264 nm, depending on the length of the DNA dendrimer sticky end from 6 bases to 27 bases. Compared with complete complementary DNA dendrimer, nearly 6-fold fluorescence enhancement was achieved using DNA dendrimer with 27 bases sticky end. Moreover, the DNA dendrimer-Cu NASs demonstrated excellent stability in serum and could be rapidly quenched by Pb²⁺ ions. Based on the above property, highly sensitive and selective fluorescent detection of Pb²⁺ ions was possible with a linear range of 2.0-100 nM and a detection limit of 0.75 nM. Due to the sensitive and rapid response to Pb²⁺ as well as excellent stability in complex matrix, the proposed fluorescent Cu NASs demonstrated high potential as an excellent fluorescent probe for Pb²⁺ in complex matrix.

Hairpin DNA-Mediated isothermal amplification (HDMIA) techniques for nucleic acid testing

Nucleic acid detection is of great importance in a variety of areas, from life science and clinical diagnosis to environmental monitoring and food safety. Unfortunately, nucleic acid targets are always found in trace amounts and their response signals are difficult to be detected. Amplification mechanisms are then practically needed to either duplicate nucleic acid targets or enhance the detection signals. Polymerase chain reaction (PCR) is one of the most popular and powerful techniques for nucleic acid analysis. But the requirement of costly devices for precise thermo-cycling procedures in PCR has severely hampered the wide applications of PCR. Fortunately, isothermal molecular reactions have emerged as promising alternatives. The past decade has witnessed significant progress in the research of isothermal molecular reactions utilizing hairpin DNA probes (HDPs). Based on the nucleic acid strand interaction mechanisms, the hairpin DNA-mediated isothermal amplification (HDMIA) techniques can be mainly divided into three categories: strand assembly reactions, strand decomposition reactions, and strand creation reactions. In this review, we introduce the basics of HDMIA methods, including the sensing principles, the basic and advanced designs, and their wide applications, especially those benefiting from the utilization of G-quadruplexes and nanomaterials during the past decade. We also discuss the current challenges encountered, highlight the potential solutions, and point out the possible future directions in this prosperous research area.

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 sensitive biomolecules detection device with catalytic hairpin assembly and cationic conjugated polymer-assisted dual signal amplification strategy

A simple, sensitive, selective, and enzyme-free homogeneous fluorescent biosensing device for DNA and protein detection is fabricated based on catalytic hairpin assembly (CHA), cationic conjugated polymer (CCP), and graphene oxide (GO). In this biosensing device, CCP together with CHA, provides dual signal amplification, and GO suppresses the background when the target is absent. Thus, this CHA/CCP/GO-based biosensor shows improved sensitivity compared with conventional CHA-based biosensors. In the biosensor, two 6-carboxyfluorescein (FAM)-labeled hairpin DNA probes (H1 and H2) are designed, and in the initial state, they could absorb on the surface of GO, leading the system to produce a low background fluorescence signal. When the target DNA appears, it continually catalyzes the formation of H1-H2 double-stranded DNA (dsDNA) complex by CHA reaction, which could be regarded as the first-step amplification. At the same time, the H1-H2 dsDNA complex departures from the surface of GO and interacts with CCP through electrostatic interaction. Then, CCP provides the second-step amplification due to its high fluorescence resonance energy transfer (FRET) efficiency from CCP to FAM. The limit of detection (LOD) and the limit of quantification (LOQ) for the target DNA could reach 32 pM and 1 nM, respectively. The linear range was from 0.1 to 40 nM, and relative standard deviation (RSD) for the points on the calibration curve ranged from 2.8% to 13.9%. This strategy could also be applied to protein detection potentially by integrating the aptamer of the target protein into the hairpin DNA. As proof of concept, thrombin was detected, and the LOD and LOQ was 11 pM and 33 pM, respectively. The linear range was from 3 to 54 nM, and RSD ranged from 3.3% to 10.4%. It showed good selectivity for thrombin compared to equal concentrations of interferences. It was also applied to quantify the thrombin (5, 10, 20 nM) in 1% spiked human serum, which showed satisfying recovery in the range of 94.7 ± 5.3 to 103.7 ± 4.9%.

Bifunctional antibody and copper-based metal-organic framework nanocomposites for colorimetric α-fetoprotein sensing

Cu²⁺ are found to greatly reduce the photoinduced oxidase activity of fluorescein and then inhibit the chromogenic reaction catalyzed by fluorescein. A simple colorimetric assay for Cu²⁺ is established. Based on this, bifunctional nanocomposites of α-fetoprotein (AFP) antibody (Ab) and copper-based metal-organic framework (Ab2@Cu-MOF) are synthesized by the simple self-assembly of AFP Ab2, Cu²⁺, and 4,4'-dipyridyl: the binding site of AFP Ab2 exposed on the surface of the nanocomposites can specifically recognize AFP antigen; Cu²⁺ in nanocomposites can inhibit the visible light-induced activity of fluorescein. The structure of Ab2@Cu-MOF disintegrate and Cu²⁺ is released in an acetate buffer solution. The higher the amount of AFP antigens, the more significant the inhibitory effect. Thus, the Ab2@Cu-MOF immunoassay for AFP determination is established using 3,3',5,5'-tetramethylbenzidine as chromogenic substrate with a detection limit of 35 pg.mL^-1. This simple, cheap, and sensitive method sheds substantial light on practical clinical diagnosis. Meanwhile, the mechanism of inhibition is revealed to facilitate the targeted selection of enzyme regulators. Graphical abstract Diagrammatic illustration of Cu²⁺ detection (part a) and Ab2@Cu-MOF immunoassay for sensing α-fetoprotein based on the synthesized Ab2@Cu-MOF nanocomposites (parts a and b).