Molecular inversion probe-rolling circle amplification with single-strand poly-T luminescent copper nanoclusters for fluorescent detection of single-nucleotide variant of SMN gene in diagnosis of spinal muscular atrophy

Discrimination of Multiple Homologous Sequences Based on DNA Logic Gate and Elemental Labeling Technology

The simultaneous discrimination of multiple homologous sequences faces challenges due to the high similarity of sequences and the complexity of the discrimination system in most reported works. Herein, a simple and ingenious analysis method was developed to identify eight miRNAs of the let-7 family by combining logic gates and entropy-driven catalytic (EDC)-based lanthanide labeling inductively coupled plasma mass spectrometry (ICP-MS) technology. Specifically, eight miRNAs were first divided into four types according to the difference of bases in the domains 2 and 3 on sequences. To identify the type of targets, a DNA logic gate was constructed with two strand displacement reactions on magnetic beads that could be initiated by different types of targets. Based on the difference of the output signals after two strand displacement reactions, the type of targets was distinguished preliminarily. Then, the discrimination of a specific target was achieved with EDC-based lanthanide labeling ICP-MS detection. By labeling the different magnetic probes with different elemental tags, a specific element signal released from magnetic beads after EDC could be detected by ICP-MS, and therefore, simultaneous detection of homologous sequences was completed. This work provided a novel and simple method for highly specific identification of homologous sequences with the assistance of a logic gate and can promote further development of elemental labeling ICP-MS in the field of multiple analysis.

Recent Progress in Single-Nucleotide Polymorphism Biosensors

Single-nucleotide polymorphisms (SNPs), the most common form of genetic variation in the human genome, are the main cause of individual differences. Furthermore, such attractive genetic markers are emerging as important hallmarks in clinical diagnosis and treatment. A variety of destructive abnormalities, such as malignancy, cardiovascular disease, inherited metabolic disease, and autoimmune disease, are associated with single-nucleotide variants. Therefore, identification of SNPs is necessary for better understanding of the gene function and health of an individual. SNP detection with simple preparation and operational procedures, high affinity and specificity, and cost-effectiveness have been the key challenge for years. Although biosensing methods offer high specificity and sensitivity, as well, they suffer drawbacks, such as complicated designs, complicated optimization procedures, and the use of complicated chemistry designs and expensive reagents, as well as toxic chemical compounds, for signal detection and amplifications. This review aims to provide an overview on improvements for SNP biosensing based on fluorescent and electrochemical methods. Very recently, novel designs in each category have been presented in detail. Furthermore, detection limitations, advantages and disadvantages, and challenges have also been presented for each type.

The DNA-Cu nanocluster and exonuclease I integrated label-free reporting system for CRISPR/Cas12a-based SARS-CoV-2 detection with minimized background signal

CRISPR-driven biosensing is developing rapidly, but current works mostly adopt dye-labeled ssDNA as the signal reporter, which is costly and unstable. Herein, we developed a label-free and low-background reporter for...

Copper nanoclusters on specific-primer PCR fragments with magnetic capture for the label-free fluorescent sensing of the T315I single nucleotide variant in the BCR–ABL1 gene

A simple and facile strategy using the all or none formation of dsDNA-templated copper nanoclusters on specific-primer PCR fragments was designed to fluorescently identify the T315I single nucleotide variant on the BCR–ABL1 gene.

Rolling Circle Amplification as a Universal Method for the Analysis of a Wide Range of Biological Targets

Detection and quantification of biotargets are important analytical tasks, which are solved using a wide range of various methods. In recent years, methods based on the isothermal amplification of nucleic acids (NAs) have been extensively developed. Among them, a special place is occupied by rolling circle amplification (RCA), which is used not only for the detection of a specific NA but also for the analysis of other biomolecules, and is also a versatile platform for the development of highly sensitive methods and convenient diagnostic devices. The present review reveals a number of methodical aspects of RCA-mediated analysis; in particular, the data on its key molecular participants are presented, the methods for increasing the efficiency and productivity of RCA are described, and different variants of reporter systems are briefly characterized. Differences in the techniques of RCA-mediated analysis of biotargets of various types are shown. Some examples of using different RCA variants for the solution of specific diagnostic problems are given.

Stable Luminescent Poly(Allylaminehydrochloride)-Templated Copper Nanoclusters for Selectively Turn-Off Sensing of Deferasirox in β-Thalassemia Plasma

Highly stable and facile one-pot copper nanoclusters (Cu NCs) coated with poly(allylamine hydrochloride) (PAH) have been synthesized for selectively sensing deferasirox (DFX) in β-thalassemia plasma. DFX is an important drug used for treating iron overloading in β-thalassemia, but needs to be monitored due to certain toxicity. In this study, the PAH-Cu NCs showed highly stable fluorescence with emission wavelengths at 450 nm. The DFX specifically interacted with the copper nanocluster to turn off the fluorescence of the PAH-Cu NCs, and could be selectively quantified through the fluorescence quenching effect. The linear range of DFX in plasma analyzed by PAH-Cu NCs was 1.0-100.0 µg/mL (r = 0.985). The relative standard deviation (RSD) and relative error (RE) were lower than 6.51% and 7.57%, respectively, showing excellent reproducibility of PAH-Cu NCs for sensing DFX in plasma. This method was also successfully applied for an analysis of three clinical plasma samples from β-thalassemia patients taking DFX. The data presented high similarity with that obtained through a capillary electrophoresis method. According to the results, the PAH-Cu NCs could be used as a tool for clinically sensing DFX in human plasma for clinical surveys.

Smartphone-assisted fluorescent analysis of polyT-Cu-nanoprobes using nucleic acid amplification test for the diagnosis of tuberculosis

Tuberculosis is one of devastating infectious diseases in the world, and early diagnosis and treatment can help overcome this global burden. In this work, a new detection platform combining smartphone-assisted fluorescent analysis and highly sensitive fluorescent copper nanoprobes (CuNPs) in a specific nucleic acid amplification test (NAAT) for the diagnosis of tuberculosis (TB) was demonstrated and validated using clinical samples. To enhance the precision and accuracy of detection, polymerase chain reaction (PCR), padlock probe (PLP) ligation, and rolling circle amplification (RCA) were combined. Long poly(thymine) (polyT) single-stranded DNA was synthesized through RCA, and polyT-CuNPs were formed by adding copper(II) ions and sodium ascorbate as reducing agents; subsequently, the results were visualized through the excitation from a UV transilluminator and quantified with just a smartphone. After optimization, this proposed platform was validated by testing 18 residual DNA samples after TB PCR, including 8 TB-negative and 10 TB-positive samples, and exhibited a detection limit of 5 fg/μL. The findings indicate the potential of this platform for practical application, where it can be combined with a smartphone for image analysis to achieve accurate on-site detection of TB, especially in resource-limited settings.

A novel"turn-off"fluorescence assay based on acid-copper nanoclusters in deep eutectic solvent micelles for co-aggregation inducing fluorescence enhancement and its application

As mixtures, deep eutectic solvent (DES) is designability. By adjusting the long alkyl chain hydrogen bond acceptors (HBAs) or hydrogen bond donors (HBDs), the DES displays surfactant characteristics and can form micelles. Hence, a novel, simple, facile and green natural organic acids capped copper nanoclusters (Aci-CuNCs) was synthesized and the spectrum behavior of Aci-CuNCs in DES micelles was researched. It was found that the surfactant-like DES can form micellar co-aggregation with Aci-CuNCs, resulting in the fluorescence (FL) intensive of Aci-CuNCs increase. Corresponding performance of spectral properties of Aci-CuNCs in DES medium were systematically studied by fourier transform infrared spectrometer, 3D FL spectroscopy, FL emission/excitation spectra, ultraviolet absorption spectroscopy. In the mechanism exploration part, on the one hand, the existence of micellar co-aggregation was confirmed by the conductivity, the mass effect of DES, dynamic light scattering and transmission electron microscopy. On the other hand, the influence of different kinds of DESs (types of HBAs/HBDs, molar ratio) and some possible factors (ionic strength and temperature) were discussed in detail to investigate the main driving forces for the formation of micellar co-aggregates. The results of mechanism exploration prove that the long alkyl chain of DES is amphiphilic which can form micellar co-aggregation with Aci-CuNCs through hydrogen bonding. The DES micelle provides Aci-CuNCs with a relatively stable and closed micro-environment which can effectively prevent collisions with water molecules and weakening of fluorescence intensity. On the basic of the above research, a "turn-off" fluorimetric method based on Aci-CuNCs in DES medium was applied for the determination of Fe³⁺. Under the optimum conditions, the assay worked in the Fe³⁺ concentration ranges from 1 to -20 μM and had a detection limit of 0.0374 μM. Method validation study illustrates the proposed system can provide a good accuracy, repeatability and stability conditions. Furthermore, the real sample analysis result demonstrates that no obvious matrix effect is found. As a consequence, the FL assays (Aci-CuNCs-based DES) composed of natural organic acid capped CuNCs and green solvent DES provides a simple, gentle and environmentally friendly method for the detection of iron ions.

Highly Luminescent Copper Nanoclusters Stabilized by Ascorbic Acid for the Quantitative Detection of 4-Aminoazobenzene

As one of the widely studied metal nanoclusters, the preparation of copper nanoclusters (Cu NCs) by a facile method with high fluorescence performance has been the interest of researchers. In this paper, a simple, green, clean, and time-saving chemical etching method was used to synthesize water-soluble Cu NCs using ascorbic acid (AA) as the reducing agent. The as-prepared Cu NCs showed strong green fluorescence (with a quantum yield as high as 33.6%) and high ion stability, and good antioxidant activity as well. The resultant Cu NCs were used for the detection of 4-aminoazobenzene (one of 24 kinds of prohibited textile compounds) in water with a minimum detection limit of 1.44 μM, which has good potential for fabric safety monitoring.