Fluorescence based turn-on strategy for determination of microRNA-155 using DNA-templated copper nanoclusters

Application of CRISPR/Cas12a in miRNA-155 detection: A novel homogeneous electrochemiluminescence biosensor

BACKGROUND

MicroRNAs (miRNAs) are important non-coding RNA entities that affect gene expression and function by binding to target mRNAs, leading to degradation of the mRNAs or inhibiting their translation. MiRNAs are widely involved in a variety of biological processes, such as cell differentiation, development, metabolism, and apoptosis. In addition, miRNAs are associated with many diseases, including cancer. However, conventional detection techniques often suffer from shortcomings such as low sensitivity, so we need to develop a rapid and efficient detection strategy for accurate detection of miRNAs.

RESULTS

We have developed an innovative homogeneous electrochemiluminescence (ECL) biosensor. This biosensor employs CRISPR/Cas12a gene editing technology for accurate and efficient detection of microRNA (miRNA). Compared to conventional technologies, this biosensor employs a unique homogeneous detection format that eliminates laborious probe fixation steps and greatly simplifies the detection process. By using two amplification techniques - isothermal amplification and T7 RNA polymerase amplification - the biosensor improves the sensitivity and specificity of the assay, providing excellent detection performance in the assay. This makes it possible to evaluate miRNA directly from a variety of biological samples such as cell lysates and diluted human serum. Experimental results convincingly demonstrate the extraordinary performance of this biosensor, including its extremely low detection limit of 1.27 aM, high sensitivity, reproducibility and stability.

SIGNIFICANCE

The application of our constructed sensor in distinguishing between cancerous and non-cancerous cell lines highlights its potential for early cancer detection and monitoring. This innovative approach represents a major advancement in the field of miRNA detection, providing a user-friendly, cost-effective, and sensitive solution with broad implications for clinical diagnosis and patient care, especially in point-of-care settings.

Colorimetric and fluorescent dual-biosensor based on zirconium and preasodium metal-organic framework (zr/pr MOF) for miRNA-191 detection

MicroRNAs (miRNAs) are associated with certain types of cancer, tumor stages, and responses to treatment, thus efficient methods are required to identify them quickly and accurately. Abnormal expression of microRNA-191 (miR-191) has been linked to particular cancers and several other health conditions, such as diabetes and Alzheimer's disease. In this study, a new dual-biosensor based on the zirconium and preasodium-based metal-organic framework (Zr/Pr MOF) was developed for the rapid, ultrasensitive, and selective detection of miRNA-191. The synthesized Zr/Pr MOF exhibited peroxidase-like activity and fluorescence properties. Our dual method involves monitoring the fluorescence and peroxidase activity of metal-organic frameworks (MOFs) in the presence of miRNAs. The Zr/Pr MOF can catalyze hydrogen peroxide (H2O2) to oxidize the chromogenic substrate 3, 3', 5, 5'-tetramethylbenzidine (TMB) to produce blue oxidized TMB (oxTMB), which exhibits ultraviolet absorption at 660 nm. However, the addition of a label-free miRNA-191 probe caused a significant change in fluorescence intensity and absorbance, indicating the binding of single-stranded miRNAs to the MOF through van der Waals interactions and π-π stacking. The presence of the target miRNA-191 caused the probe to be released from the surface of the MOF owing to hybridization, which increased the peroxidase-like activity of Zr/Pr-MOF. Both response signals showed acceptable linear relationship and low detection limits. Fluorescence and colorimetry have an LOD of 0.69 and 8.62 pM, respectively. This study demonstrates the reliability and sensitivity of miRNA identification in human serum samples.

Advances in Ultra-small Fluorescence Nanoprobes for Detection of Metal Ions, Drugs, Pesticides and Biomarkers

Identification of trace level chemical species (drugs, pesticides, metal ions and biomarkers) plays key role in environmental monitoring. Recently, fluorescence assay has shown significant advances in detecting of trace level drugs, pesticides, metal ions and biomarkers in real samples. Ultra-small nanostructure materials (metal nanoclusters (NCs), quantum dots (QDs) and carbon dots (CDs)) have been integrated with fluorescence spectrometer for sensitive and selective analysis of trace level target analytes in various samples including environmental and biological samples. This review summarizes the properties of metal NCs and ligand chemistry for the fabrication of metal NCs. We also briefly summarized the synthetic routes for the preparation of QDs and CDs. Advances of ultra-small fluorescent nanosensors (NCs, QDs and CDs) for sensing of metal ions, drugs, pesticides and biomarkers in various sample matrices are briefly discussed. Additionally, we discuss the recent challenges and future perspectives of ultra-small materials as fluorescent sensors for assaying of wide variety of target analytes in real samples.

Turn -on FRET-based cysteine sensor by sulfur-doped carbon dots and Au nanoparticles decorated WS2 nanosheet

Cysteine is an essential biothiol that plays various functions in the human body. Decrease or exceeding of this excellent antioxidant from the expected range will lead to so many problems. Thus, appropriate sensing of it would be of great importance. Sulfur-doped carbon Dots(S-CDs) owe excellent fluorescence emission. Therefore, designing a Fluorescence resonance energy transfer (FRET) system between S-CDs as donor and Au nanoparticles (AuNPs) decorated tungsten disulfide nanosheet (WS2 NSs) would be a perfect strategy for cysteine detection. Excitation at 340 nm will give the maximum quantum yield of S-CDs (21%) and fluorescence emission peak at 460 nm. In the presence of cysteine, the FRET mechanism inhibited through the affinity of cysteine's functional groups (-SH and -NH2) toward AuNPs and S-CDs fluorescence emission was recovered. To find the best efficiency of the system, optimization of pH, temperature, and time was investigated. Here the linear range of 3-275 µM and limit of detection of 0.01 µM was obtained. Finally, the fluorescence method was applied to the analysis of cysteine in human blood serum, which poses the potential of rapid and sensitive sensing. It can detect both lower and higher amounts of serum cysteine.

Progress of metal nanoclusters in nucleic acid detection

The development and application of metal nanoclusters (MNCs) in nucleic acid testing in the past 10 years have been summarized. Fluorescence enhancement and red shift can occur when the G-rich sequence gets close to Ag NCs or the complementary DNA strand hybridizes with Ag NCs tail strand, which can be used to identify the nucleic acid. Ag NCs with the abasic site in DNA duplex can distinguish mutant genes such as cancer suppression gene p53. Ag NCs with auxiliary DNA can be used to detect miR-21, miR-16-5p, miR-19b-3p, and miR-141. Cu NCs/Cu NPs can recognize miRNA-155, miR-21, and miR-let-7d without auxiliary DNA. Au NCs can identify H1N1 gene fragments by fluorescence quenching caused by proximity to the G-rich sequence. Besides, Au NCs can recognize miRNA-21 and let-7a. SsDNA MNCs adsorbed on the surface of GO and CNPs oxide can be used to identify HBV and HIV gene fragments. The addition of enzymes or auxiliary amplification technologies is a popular way to improve probe sensitivity. Ag NCs combined with TAIEA has the best performance and can obtain LOD as low as aM for miRNA.

Gold nanoclusters: An ultrasmall platform for multifaceted applications

Gold nanoclusters (Au NCs) with a core size below 2 nm form an exciting class of functional nano-materials with characteristic physical and chemical properties. The properties of Au NCs are more prominent and extremely different from their bulk counterparts. The synthesis of Au NCs is generally assisted by template or ligand, which impart excellent cluster stability and high quantum yield. The tunable and sensitive physicochemical properties of Au NCs open horizons for their advanced applications in various interdisciplinary fields. In this review, we briefly summarize the solution phase synthesis and origin of the characteristic properties of Au NCs. A vast review of recent research work introducing biosensors based on Au NCs has been presented along with their specifications and detection limits. This review also highlights recent progress in the use of Au NCs as bio-imaging probe, enzyme mimic, temperature sensing probe and catalysts. A speculation on present challenges and certain future prospects have also been provided to enlighten the path for advancement of multifaceted applications of Au NCs.

Fluorometric Aptasensor for Determination of Escherichia coli O157:H7 by FRET Effect between Aminated Carbon Quantum Dots and Graphene Oxide

A fluorometric aptasensor based on Escherichia coli O157:H7 (E. coli O157:H7) aptamer labeled aminated carbon quantum dots (NH₂-CQDs) and graphene oxide (GO) for the determination of E. coli O157:H7 was developed. In this research, carboxyl group (-COOH) terminated E. coli O157:H7 aptamer was steadily labeled to NH₂-CQDs by amidation reaction, and played the role of energy donor and was responsible for chemical recognition. Correspondingly, GO served as an energy acceptor. The introduction of NH₂-CQDs not only made the aptamer bond stably through covalent bond, but also significantly enhanced the fluorescence intensity compared with general CQDs. The NH₂-CQDs-aptamer is adsorbed on the surface of GO through π-π stacking and hydrophobic interaction. The fluorescence of NH₂-CQDs-aptamer was quenched via fluorescence resonance energy transfer (FRET) between NH₂-CQDs and GO. After adding E. coli O157:H7, the specific binding affinity between NH₂-CQDs-aptamer and E. coli O157:H7 lead to desorption of NH₂-CQDs-aptamer from GO, and recovery of the fluorescence intensity of NH₂-CQDs-aptamer. Under the optimal conditions, the increased fluorescence intensity showed a good linear relationship to concentrations of E. coli O157:H7 in the range 10² - 10⁷ cells/mL, with a detection limit of 89 cells/mL. Furthermore, the developed method was successfully applied to the determination of E. coli O157:H7 in commercial milk samples.

Ratiometric fluorescent detection and imaging of microRNA in living cells with manganese dioxide nanosheet-active DNAzyme

MicroRNAs (miRNAs) play an important role in multiple biological processes and can be used as biomarkers for clinical disease diagnosis, so their detection is of great importance. Here, manganese dioxide (MnO₂) nanosheet acts as carrier to deliver DNAzyme probes into cells through endocytosis, where intracellular glutathione (GSH) reduces the MnO₂ nanosheet to manganese ions (Mn²⁺) and releases the probes. The generated Mn²⁺ can be further used as an effective cofactor to activate the DNAzyme probe, and cleave the DNA strand into two fragments. Then, the miRNA-155 in the cells can hybridize with the cleaved fragment to cause the fluorescence signal change of the probe. The proposed proportional fluorescent method has been applied to the imaging of miRNA-155 in HeLa cells and HepG2 cells with the estimated detection limit (LOD) as 1.6 × 10^-12 M. The new method can provide great help for cancer diagnosis and biological research related to miRNA.

Sensitive detection of S. Aureus using aptamer- and vancomycin -copper nanoclusters as dual recognition strategy

The proposed aptamer- and antibiotic-based dual detection sensor, combines copper nanoclusters (CuNCs) as an effective approach for the recognition and quantification of Staphylococcus aureus (S. aureus) as a pathogenic bacteria. A facile method for CuNCs based on vancomycin as the template using a fluorescence platform was proposed for the recognition of the S. aureus whole cells via antibiotic and aptamer. Using dual receptor functionalized CuNCs linked to vancomycin and a specific aptamer and during aggregation induce emission process enhanced fluorescence signal linearly with S. aureus concentrations between 10²-10⁸ CFU/mL, and the detection limit was 80 CFU/mL after 45 min as the optimum incubation time. Non-target bacteria generated negative results, proving the high specificity of the presented sensor. This strategy showed recoveries ranging 86%-98% in milk as real sample and can be used for the development of universal detection platforms for efficient and specific S. aureus detection with great potential applications for monitoring pathogenic bacteria.

A sensitive and label-free electrochemical microRNA biosensor based on Polyamidoamine Dendrimer functionalized Polypyrrole nanowires hybrid

The potential of functionalized polypyrrole nanowires (PPyNWs) are demonstrated as a platform for lable-free miRNA detection using electrochemical impedance spectroscopy (EIS). MicroRNAs (miRNAs) detection methods and sensors are mainly challenged by very low concentrations in physiological samples and high similarity among family members. Herein, a sensitive and selective miRNA biosensor was constructed based on electrochemically synthesized PPyNWs, which were functionalized with polyamidoamine dendrimer (PAMAM) by an electro-oxidation method. The prepared PPyNWs/PAMAM hybrid combines the excellent electrical conductivity of conducting polymer PPyNWs with high surface to volume ratio of PAMAM. DNA probes were immobilized onto the PPyNWs/PAMAM hybrid for the construction of the miRNA biosensor. Using the sensitive EIS technique to monitor DNA/miRNA hybridization, the developed biosensor demonstrated excellent sensing performances, such as wide linear range (10-14 M-10-8 M) and low detection limit (0.34 × 10-14 M). Even more encouraging, the response sensitivity of the biosensor was 3.12 times higher than that of the bulk PPy-modified sensor, which proved that the microstructure of the PPy nanowires array can greatly improve the performance of the biosensor. An ultrasensitive and selective miRNA biosensor was constructed based on electrochemically synthesized polypyrrole nanowires array (PPyNWs), which were functionalized with polyamidoamine dendrimer (PAMAM) by an electro-oxidation method.

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.

Biomarker sensing platforms based on fluorescent metal nanoclusters

Metal nanoclusters (NCs) and their unique properties are increasing in importance and their applications are covering a wide range of areas. Their remarkable fluorescence properties and easy synthesis procedure and the possibility of functionalizing them for the detection of specific targets, such as biomarkers, make them a very interesting biosensing tool. Nowadays the detection of biomarkers related to different diseases is critical. In this context, NCs scaffolded within an appropriate molecule can be used to detect and quantify biomarkers through specific interactions and fluorescence properties of the NCs. These methods include analytical detection and biolocalization using imaging techniques. This review covers a selection of recent strategies to detect biomarkers related to diverse diseases (from infectious, inflammatory, or tumour origin) using fluorescent nanoclusters.

Bright fluorescent nucleic acid detection with CRISPR-Cas12a and poly(thymine) templated copper nanoparticles

Fluorescence-based diagnostic tools are attractive and versatile tests with multiple advantages: ease of use, sensitivity and rapid results. The advent of CRISPR-Cas technology has created new avenues for the development of diagnostic testing tools. In this study, by effectively combining the specific functions of two enzymes, CRISPR-Cas12a and terminal deoxynucleotidyl transferase (TdT), we developed a DNA detection assay that generates copper nanoparticles (CuNPs) that are easily visible to the naked eye under UV-light; we named this detection assay Cas12a Activated Nuclease poly-T Reporter Illuminating Particles (CANTRIP). Upon specific target DNA recognition by Cas12a, single-stranded DNA (ssDNA) reporter oligos with blocked 3'-ends are cut into smaller ssDNA fragments, thereby generating neo 3'-hydroxyl moieties. TdT subsequently elongates these newly formed ssDNA fragments, incorporating only dTTP nucleotides, and these poly(thymine)-tails subsequently function as scaffolds for the formation of CuNPs. These CuNPs produce a bright fluorescent signal upon UV excitation, and thus, this bright orange signal indicates the presence of target DNA, which in this proof-of-concept study consisted of anthrax lethal factor plasmid DNA. CANTRIP, which combines two detection platforms consisting of CRISPR-Cas12a and fluorescent CuNPs into a single reaction, appears to be a robust, low-cost and simple diagnostic tool.

Photoluminescent hydrophilic cyclodextrin-stabilized cysteine-protected copper nanoclusters for detecting lysozyme

Lysozyme (LYZ) sensors have attracted increased attention because rapid and sensitive detection of LYZ is highly desirable for various diseases associated with humans. In this research, we designed L-cysteine-protected ultra small photoluminescent (PL) copper nanoclusters (CuNCs) conjugated with β-cyclodextrin (β-CD) for rapid detection of LYZ in human serum samples at room temperature. The proposed β-CD-CuNCs exhibited excellent water solubility, ultrafine size, good dispersion, bright photoluminescence, and good photostability. The β-CD-CuNCs exhibit an excitation and emission maximum at 370 nm and 492 nm, respectively, with an absolute quantum yield (QY) of 54.6%. β-CD-CuNCs showed a fluorescence lifetime of 12.7 ns. The addition of LYZ would result in PL quenching from β-CD-CuNCs. The lowest detectable LYZ concentration was 50 nM for the naked eye and the limit of detection (LOD) and limit of quantification (LOQ) were 0.36 nM and 1.21 nM, respectively, by emission measurement observed in the LYZ concentration range from 30 to 100 nM. It is important to note that the PL β-CD-CuNC strategy possessed great selectivity toward LYZ relative to other biomolecules. The proposed nanosensor was efficiently applied to determine the LYZ level in human serum sample average recoveries from 96.15 to 104.05% and relative standard deviation (RSD) values lower than 3.0%. Moreover, the proposed sensing system showed many advantages, including high speed, high sensitivity, high selectivity, low cost, and simple preparation.

Natural-based Hydrogels: A Journey from Simple to Smart Networks for Medical Examination

Natural hydrogels, due to their unique biological properties, have been used extensively for various medical and clinical examinations that are performed to investigate the signs of disease. Recently, complex-crosslinking strategies improved the mechanical properties and advanced approaches have resulted in the introduction of naturally derived hydrogels that exhibit high biocompatibility, with shape memory and self-healing characteristics. Moreover, the creation of self-assembled natural hydrogels under physiological conditions has provided the opportunity to engineer fine-tuning properties. To highlight recent studies of natural-based hydrogels and their applications for medical investigation, a critical review was undertaken using published papers from the Science Direct database. This review presents different natural-based hydrogels (natural, natural-synthetic hybrid and complex-crosslinked hydrogels), their historical evolution, and recent studies of medical examination applications. The application of natural-based hydrogels in the design and fabrication of biosensors, catheters and medical electrodes, detection of cancer, targeted delivery of imaging compounds (bioimaging) and fabrication of fluorescent bioprobes is summarised here. Without doubt, in future, more useful and practical concepts will be derived to identify natural-based hydrogels for a wide range of clinical examination applications.

Ultrasensitive Fluorescent miRNA Biosensor Based on a "Sandwich" Oligonucleotide Hybridization and Fluorescence Resonance Energy Transfer Process Using an Ln(III)-MOF and Ag Nanoparticles for Early Cancer Diagnosis: Application of Central Composite Design

Herein, a novel, rapid, highly sensitive, and selective fluorescent biosensor is presented, which is designed based on "sandwich-type" hybridization of oligonucleotides and the fluorescence resonance energy transfer (FRET) strategy. It senses and determines the MicroRNA-155 (miRNA-155) expression levels as a cancer biomarker. In this study, a modified La(III)-metal-organic framework(MOF) and silver nanoparticles (Ag NPs) were used as the energy donor-acceptor pairs in fluorescence quenching through the FRET process. La(III)-MOF was synthesized and then modified by glutaraldehyde as a cross-linking agent. The Ag NPs were also prepared, and then, the surface of both was conjugated with different 5'-amino-labeled ssDNA strands (aptamers). These prepared nanoprobes were characterized by various physicochemical techniques such as X-ray diffraction, energy-dispersive X-ray spectrometry, Fourier transform infrared, field emission scanning electron microscopy, UV-vis spectroscopy, elemental mapping, and gel electrophoresis. To optimize the detection conditions, several factors affecting biosensor performance were assessed by one variable-at-a-time and central composite design methods. Under optimum conditions, this "turn-off" fluorescent biosensor could detect and determine as low as 0.04 ppb (ng. mL^-1) or 5.5 fM of the miRNA-155 biomarker. Therefore, this biosensor provides highly promising potential for lung and breast cancer diagnosis.

A highly sensitive fluorescence sensor based on lucigenin/chitosan/SiO2 composite nanoparticles for microRNA detection using magnetic separation

In this paper, a convenient reverse-phase microemulsion method for the synthesis of SiO₂ nanoparticles (NPs) by simply introducing the chitosan and fluorescent dye of lucigenin during the formation reaction of SiO₂ NPs was proposed. Addition of chitosan can make the SiO₂ NPs porous, and increases lucigenin molecule incorporation into chitosan/SiO₂ NPs nanopores based on electrostatic interaction and supermolecular forces. Therefore, fluorescence quantum yield of the lucigenin/chitosan/SiO₂ composite nanoparticles was increased by introduction of chitosan and compared with lucigenin/SiO₂ NPs without chitosan. Because the number of negative charges carried when using single-stranded DNA (ssDNA) was different from that of double-stranded DNA (dsDNA), the numbers of lucigenin/chitosan/SiO₂ composite nanoparticles with positive charge adsorbed using ssDNA or dsDNA were different. Consequently, fluorescence intensity caused using ssDNA or dsDNA/miRNA was clearly discriminative. With increase in target DNA/miRNA concentration, the difference in fluorescence intensity also increased, resulting in a good linear relationship between fluorescence intensity sensitizing value and target miRNA concentrations. Therefore, a new fluorescence analysis method for direct detection of let-7a in human gastric cancer cell samples without enzyme, label free and no immobilization was established using lucigenin/chitosan/SiO₂ composite nanoparticles as a DNA hybrid indicator. The proposed method had high sensitivity and selectivity, low cost and the detection limit was 10 fM (S/N = 3).

Fluorescence Sensing of Caffeine in Tea Beverages with 3,5-diaminobenzoic Acid

A rapid, selective and sensitive method for the detection of caffeine in tea infusion and tea beverages are proposed by using 3,5-diaminobenzoic acid as a fluorescent probe. The 3,5-diaminobenzoic acid emits strong fluorescence around 410 nm under the excitation of light at 280 nm. Both the molecular electrostatic potential analysis and fluorescent lifetime measurement proved that the existence of caffeine can quench the fluorescence of 3,5-diaminobenzoic acid. Under the optimal experimental parameters, the 3,5-diaminobenzoic acid was used as a fluorescent probe to detect the caffeine aqueous solution. There exists a good linear relationship between the fluorescence quenching of the fluorescent probe and the concentration of caffeine in the range of 0.1–100 μM, with recovery within 96.0 to 106.2%, while the limit of detection of caffeine is 0.03 μM. This method shows a high selectivity for caffeine. The caffeine content in different tea infusions and tea beverages has been determined and compared with the results from HPLC measurement.

The synthesis of metal nanoclusters and their applications in bio-sensing and imaging

Noble metal nanomaterials have been studied by many researchers for their ultra-small size, excellent photophysical properties and good biocompatibility. Metal nanoclusters are a kind of nanoscale ultrafine particle, which have completely different properties from macroscopic metals. In the visible region, they do not usually show the characteristic surface plasmon resonance absorption but instead show fluorescence in the visible to near infrared region. In particular, the noble metallic (Au, Ag, Cu, etc) nanoclusters (NMNCs) have broad application prospects in the field of biomedicine as probes for fluorescence sensing. Their strong photoluminescence, living cell compatibility, and easy availability make up for the shortcomings of traditional fluorescent probes such as organic fluorescent dyes, fluorescent proteins, and fluorescent quantum dots. In this review, we summarize the synthetic method and application of metal nanoclusters as fluorescent probes in bio-sensing and imaging, especially in the early diagnosis of cancer cells.

Recent progress in copper nanocluster-based fluorescent probing: a review

Copper nanoclusters (CuNCs) are an attractive alternative to other metal nanoclusters. The synthesis of CuNCs is highly efficient and fast, with low-cost and without any complicated manipulation. Because of their tunable fluorescence and low toxicity, CuNCs have been highly exploited for biochemical sensing. This review (with 172 refs.) summarizes the progress that has been made in the field in the past years. Following an introduction into the fundamentals of CuNCs, the review first focuses on synthetic methods and the fluorescence properties of CuNCs (with subsections on the use of proteins, peptides, DNA and other molecules as templates). This is followed by a section on the use of CuNCs in fluorometric assays, with subsections on the detection of small molecules, proteins, nucleic acids, various other biomolecules including drugs, and of pH values. A further large chapter summarizes the work related to environmental analyses, specifically on determination of metal ions, anions and pollutants. Graphical abstract Schematic representation of the synthesis and potential applications of copper nanocluster (CuNCs) in biochemical analysis, emphatically reflected in some vital areas such as small molecule analysis, biomacromolecule monitoring, cell imaging, ions detection, toxic pollutant, etc.

Dual-signal-amplified electrochemiluminescence biosensor for microRNA detection by coupling cyclic enzyme with CdTe QDs aggregate as luminophor

In this work, a dual-signal-amplified electrochemiluminescence (ECL) biosensor was proposed for the first time to detect microRNAs (miRNAs) based on cyclic enzyme and seeded-watermelon-like mesoporous nanospheres (mSiO₂@CdTe@SiO₂, mSQS NSs). mSQS NSs were successfully fabricated by inlaying the CdTe quantum dots (QDs) into the mesoporous silica (mSiO₂) and future coating the surface with the silica layer. The obtained mSQS NSs contained tens of QDs and exhibited much stronger ECL signal than single QDs. The ECL biosensor achieved firstly signal amplification by using mSQS NSs to label the functional oligonucleotide probe (DNA-F) as enhanced ECL signal probes. Well-dispersed Fe₃O₄@Au nanoparticles were prepared as immobilization matrices to load hairpin-structured DNA probe (DNA-P). When the target miRNAs were present, hairpin DNA undertook conformation changes. Meanwhile, RNA/DNA duplexes was formed which cleaved by duplex-specific nuclease (DSN) to release miRNAs. Target miRNAs were cycled to hybridize with hairpin DNA, which achieved secondly signal amplification of the ECL biosensor. Thereafter, the complementarily parts between DNA-F and the rest DNA-P generated conjugates. The obtained conjugates would be collected on the surface of the electrode by effecting of magnet. Under the optimal conditions, the developed biosensor showed a wide linear range from 0.1 pM to 100 pM with a low detection limit of 33 fM (S/N = 3). The results of detection for the stability, specificity and reproducibility of ECL biosensor were outstanding. Simultaneously, the potential application of ECL biosensor was verified by using biosensor in serum sample.

A New Eye Dual-readout Method for MiRNA Detection based on Dissolution of Gold nanoparticles via LSPR by CdTe QDs Photoinduction

Breast cancer (BC) is the most frequent cancer that affects one in eight women worldwide. Recent advances in early cancer diagnosis anticipates more efficient treatment and prolong patient survival. MicroRNAs expression profiling plays a key role in diagnosis of cancer such as BC in early stages. For the first time we describe direct injection of hot electrons from plasmonic gold nanoparticles (AuNPs) to adsorbed water molecules with photoinduction of CdTe quantum dots (QDs) with emission wavelength at ~560 nm. As a result of hot electrons exiting from AuNPs with red color, gold cations (holes) are gradually discharged (AuNPs dissolution) leading to a colorless solution. Our group applied this phenomenon to propose a spectral method for miRNA recognition based on different responsive disaggregation and aggregation of CdTe QDs interacted with single strand DNA probes and DNA/RNA heteroduplex respectively resulting in a detection limit of 4.4 pM. This method has been applied also for the determination of miR-155 in the human breast carcinoma MCF-7 cells and normal human embryonic kidney cell line (HEK 293).

A colorimetric paper sensor for citrate as biomarker for early stage detection of prostate cancer based on peroxidase-like activity of cysteine-capped gold nanoclusters

Citrate is currently considered a preferred biomarker for the early stage detection of prostate cancer. In the present work, based on the highly efficient catalytic properties of gold nanoclusters, a novel system for optical determination of citrate was successfully established under optimized conditions. Cysteine-capped gold nanoclusters (Cys-AuNCs) are shown to have an intrinsic peroxidase-mimetic activity. In the presence of H₂O_2, Cys-AuNCs nanostructures are able to catalyse the oxidation of 3,3',5,5'-tetramethylbenzidine (TMB) with high efficiency to produce a blue dye (with an absorbance maximum at 650 nm). Citrate has carboxylic and hydroxyl groups that can bind with free amino and free carboxyl cysteine groups via hydrogen bonds, thus creating a coating on the surface of the gold nanocluster and inhibiting the cluster oxidation activity. Accordingly, a visual, sensitive and simple colorimetric method using Cys-AuNCs as peroxidase mimetic was developed for detecting citrate. A suitable linear relationship for citrate was obtained for the range of 0.5 to 1000 μM. The limit of detection (LOD) of the proposed method was calculated as 0.1 μM and the relative standard deviation (RSD) was obtained to be less than 4.0%. Moreover, the biosensor was used to perform a paper assay on a Y-shaped microfluidic device and make use of the distinctive features of microchannels such as short response time, very low reagent volume required, low fabrication cost etc. A detection limit of 0.4 μM was achieved through the paper test and a good linear range was observed between 1.0 μM-10 mM. The proposed method was further applied to citrate detection in the human urine sample.

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 unique FRET approach toward detection of single-base mismatch DNA in BRCA1 gene

Early detection of mutation carriers in predisposing genes such as BRCA1 plays an important role in disease prevention. This work developed a quantum dots-based (QDs-based) fluorescence resonance energy transfer (FRET) technique for the detection of single-base mismatch DNA in BRCA1 gene. The FRET between QDs as the donor and silver nanocluster (AgNCs) as the acceptor was designed by the strong interaction between CdTe QDs with appropriate size and dsDNA through binding to its major groove. The dsDNA was formed by the hybridization of ssDNA labeled to AgNCs with target DNA, which introduced CdTe QDs into the major grooves to place the AgNCs in close proximity to the QDs. The complementary and single-base mismatch DNA led to obviously different FRET signals. The FRET signal linearly correlated to the concentration of single-base mismatch DNA in the range of 1.5 × 10^-10-1.0 × 10^-6 mol L^-1. The proposed method showed a detection limit of 80 pmol L^-1 and the sensitivity comparable to the previously reported assays, indicating promising potential for single nucleotide polymorphisms diagnosis in clinical application.

Fluorometric determination of microRNA-155 in cancer cells based on carbon dots and MnO2 nanosheets as a donor-acceptor pair

A fluorometric method is presented for sensitive deternination of microRNA. It is making use of carbon dots (C-dots) loaded with a DNA probe as fluorophore and MnO₂ nanosheets as the quenching agent. The blue-green fluorescence of the DNA-loaded C-dots is quenched by the MnO₂ nanosheets, but restored on binding target microRNA-155. The maximum excitation wavelength and the maximum emission wavelength of C-dots are at 360 nm and 455 nm, respectively. Fluorescence correlates linearly with the log of the microRNA-155 concentration in two ranges, viz. from 0.15 to 1.65 aM and from 1.65 to 20 aM. The detection limit is as low as 0.1 aM. The assay can discriminate between fully complementary and single-base mismatch microRNA. The assay displayed high specificity when used to detect MCF-7 breast cancer cells which can be detected in concentrations from 1000 to 45,000 cells·mL^-1, with a 600 cells·mL^-1 detection limit. The method was applied to the analysis of serum samples spiked with microRNA, and satisfactory results were acquired. Graphical abstract Schematic of a fluorometric sensing platform for miRNA-155. The method relies on a FRET process between C-dots and MnO₂ nanosheets. This strategy has a practical application for detection of miRNA in cell lines and biological fluids.

Luminescence determination of microRNAs based on the use of terbium(III) sensitized with an enzyme-activated guanine-rich nucleotide

A method is reported for the fluorometric quantitation of microRNA. It is making use of a luminescent probe deribed from terbium(III) ion whose fluorescence is sensitized with a guanine-rich (G-rich) nucleotide. The probe has a large Stokes' shift and strong and sharp emission bands. The assay relies on the wide substrate specificity of terminal deoxynucleotidyl transferase (TdTase), which catalyzes the formation of long G-rich nucleotides when using microRNA primer as a trigger to start the polymerization. The addition of Tb(III) induces the formation of a G-quadruplex from the G-rich nucleotide, and this strongly enhances the green fluorescence of Tb(III) (peaking at 545 nm upon photoexcitation at 290 nm). Specifically, microRNA-21 was chosen as the analyte. The fluorescence intensity of Tb(III) increases linearly in the 1 pM to 1 nM microRNA concentration range, and the detection limit is as low as 0.11 pM. The method can distinguish between family members of microRNA and performs excellently even when applied to extracts of cancer cells. Graphical abstract A fluorometric technique is reported for the determination of microRNA. It is based on signal enhancement based on the sensitization of terbium(III) via a guanine-rich nucleotide sequence. Klenow Fragment exo^- (KFexo^-) generates DNA sequence at the 3'-OH of microRNA, and terminal deoxynucleotidyl transferase (TdTase) catalyzes the formation of long G-rich nucleotides.

Dual approach for the colorimetric determination of unamplified microRNAs by using citrate capped gold nanoparticles

The authors describe a method for the colorimetric determination of unamplified microRNA. It is based on the use of citrate-capped gold nanoparticles (AuNPs) and, alternatively, a microRNA-probe hybrid or a magnetically extracted microRNA that serve as stabilizers against the salt-induced aggregation of AuNPs. The absorbance ratios A₅₂₅/A₆₂₅ of the reacted AuNP solutions were used to quantify the amount of microRNA. The assay works in the range of 5-25 pmol microRNA. The lower limit of detection (LOD) is 10 pmol. The performance of the method was tested by detection of microRNA-210-3p in totally extracted urinary microRNA from normal, benign, and bladder cancer subjects. The sensitivity and specificity for qualitative detection of urinary microRNA-210-3p using the assay are 74% and 88% respectively, which is consistent with real time PCR based assays. The assay was applied to the determination of specific microRNA by using its specific oligo targeter or following magnetic isolation of the desired microRNA. The method is simple, cost-efficient, has a short turn-around time and requires minimal equipment and personnel. Graphical abstract Schematic of the two detection schemes: In the first approach, matched microRNA hybridizes with its specific probe to stabilize gold nanoparticles (AuNPs) against salt induced aggregation and to leave the red color of the AuNPs unchanged. In the second one, microRNA extracted via magnetic nanoparticles (MNP) stabilizes AuNPs against aggregation.

Detection of large deletion in human BRCA1 gene in human breast carcinoma MCF-7 cells by using DNA-Silver Nanoclusters

Here we describe a label-free detection strategy for large deletion mutation in breast cancer (BC) related gene BRCA1 based on a DNA-silver nanocluster (NC) fluorescence upon recognition-induced hybridization. The specific hybridization of DNA templated silver NCs fluorescent probe to target DNAs can act as effective templates for enhancement of AgNCs fluorescence, which can be used to distinguish the deletion of BRCA1 due to different fluorescence intensities. Under the optimal conditions, the fluorescence intensity of the DNA-AgNCs at emission peaks around 440 nm (upon excitation at 350 nm) increased with the increasing deletion type within a dynamic range from 1.0 × 10^-10 to 2.4 × 10^-6 M with a detection limit (LOD) of 6.4 × 10^-11 M. In this sensing system, the normal type shows no significant fluorescence; on the other hand, the deletion type emits higher fluorescence than normal type. Using this nanobiosensor, we successfully determined mutation using the non-amplified genomic DNAs that were isolated from the BC cell line.

Enzyme-free amplified detection of circulating microRNA by making use of DNA circuits, a DNAzyme, and a catalytic hairpin assembly

A homogeneous and enzyme-free fluorometric assay is described for the determination of microRNA-182. It is based on the use of DNA circuits and DNAzyme. The DNA circuits warrant strong signal amplification by virtue of catalytic hairpin assembly, a system that consists of two hairpin substrates. A part of the DNAzyme sequence is programmed to sequester into one of the two hairpin substrates. In the presence of target microRNA-182, the two hairpin substrates undergo catalytic assembling. This results in the formation of a DNA duplex and the release of the DNAzyme from the hairpin structure. Upon cyclic amplification, one target catalyzes the formation of Mg (II)-dependent DNAzymes. These bind to, and hydrolyze, the fluorescently labeled substrates for signal amplification and transduction. Based on nucleic acid programmability, this engineered assay has a limit of detection as low as 6.8 f. and a dynamic range that covers the 10 f. to10 nM microRNA-182 concentration range. Detection can be performed within 60 min. The assay is simple, rapid, homogenous, cost-effective, and enzyme-free. These features make the method an attractive tool in routine microRNA diagnosis and, conceivably, in point of care uses. Graphical abstract Schematic of a homogeneous and enzyme-free fluorometric assay for the determination of microRNA-182. It is based on the use of DNA circuits and DNAzymes. The DNA circuits warrant strong signal amplification by virtue of catalytic hairpin assembly that uses two hairpin substrates. The method represents an attractive tool for routine microRNA diagnosis and, conceivably, point of care uses.

Fluorescence enhancement for noble metal nanoclusters

Noble metal nanoclusters have attracted great attentions in the area of fluorescence related applications due to their special properties such as low toxicity, excellent photostability and bio-compatibility. However, they still describe disadvantages for low quantum yield compared to quantum dots and organic dyes though the brightness of the fluorescence play an important role for the efficiency of the applications. Attentions have been attracted for exploring strategies to enhance the fluorescence based on the optical fundamentals through various protocols. Some methods have already been successfully proposed for obtaining relative highly fluorescent nanoclusters, which will potentially describe advantages for the application. In this review, we summarize the approach for enhancement of the fluorescence of the nanoclusters based on the modification of the properties, improvement of the synthesis process and optimization of the environment. The limitation and directions for future development of the fabrication of highly fluorescent metal nanoclusters are demonstrated.