Single-step, homogeneous and sensitive detection for microRNAs with dual-recognition steps based on luminescence resonance energy transfer (LRET) using upconversion nanoparticles

miRNAs as Predictors of Barrier Integrity

The human body has several barriers that protect its integrity and shield it from mechanical, chemical, and microbial harm. The various barriers include the skin, intestinal and respiratory epithelia, blood-brain barrier (BBB), and immune system. In the present review, the focus is on the physical barriers that are formed by cell layers. The barrier function is influenced by the molecular microenvironment of the cells forming the barriers. The integrity of the barrier cell layers is maintained by the intricate balance of protein expression that is partly regulated by microRNAs (miRNAs) both in the intracellular space and the extracellular microenvironment. The detection of changes in miRNA patterns has become a major focus of diagnostic, prognostic, and disease progression, as well as therapy-response, markers using a great variety of detection systems in recent years. In the present review, we highlight the importance of liquid biopsies in assessing barrier integrity and challenges in differential miRNA detection.

A Comprehensive Review on Upconversion Nanomaterials-Based Fluorescent Sensor for Environment, Biology, Food and Medicine Applications

Near-infrared-excited upconversion nanoparticles (UCNPs) have multicolor emissions, a low auto-fluorescence background, a high chemical stability, and a long fluorescence lifetime. The fluorescent probes based on UCNPs have achieved great success in the analysis of different samples. Here, we presented the research results of UCNPs probes utilized in analytical applications including environment, biology, food and medicine in the last five years; we also introduced the design and construction of upconversion optical sensing platforms. Future trends and challenges of the UCNPs used in the analytical field have also been discussed with particular emphasis.

Small-Molecule Fluorescent Probes for Detecting Several Abnormally Expressed Substances in Tumors

Malignant tumors have always been the biggest problem facing human survival, and a huge number of people die from cancer every year. Therefore, the identification and detection of malignant tumors have far-reaching significance for human survival and development. Some substances are abnormally expressed in tumors, such as cyclooxygenase-2 (COX-2), nitroreductase (NTR), pH, biothiols (GSH, Cys, Hcy), hydrogen sulfide (H2S), hydrogen sulfide (H2O2), hypochlorous acid (HOCl) and NADH. Consequently, it is of great value to diagnose and treat malignant tumors due to the identification and detection of these substances. Compared with traditional tumor detection methods, fluorescence imaging technology has the advantages of an inexpensive cost, fast detection and high sensitivity. Herein, we mainly introduce the research progress of fluorescent probes for identifying and detecting abnormally expressed substances in several tumors.

Ratiometric Fluorescence Detection of Colorectal Cancer-Associated Exosomal miR-92a-3p with DSN-Assisted Signal Amplification by a MWCNTs@Au NCs Nanoplatform

The detection of miRNA shows great promise in disease diagnosis. In this work, a ratiometric fluorescent biosensor based on multi-walled carbon nanotubes@gold nanoclusters (MWCNTs@Au NCs) and duplex-specific nuclease (DSN)-assisted signal amplification was fabricated for miRNA detection. Colorectal cancer (CRC)-associated miR-92a-3p extracted from exosomes was selected as the target. MWCNTs@Au NCs performs the dual functions of fluorescence quencher and internal fluorescence reference. In the absence of miR-92a-3p, an Atto-425-modified single-stranded DNA probe is adsorbed on MWCNTs@Au NCs, resulting in the quenching of Atto-425. In the presence of miR-92a-3p, the duplex is formed by hybridization of the probe and miR-92a-3p and leaves the MWCNTs@Au NCs, resulting in the fluorescence recovery of Atto-425. DSN can cleave the probe and result in the release of miR-92a-3p. The released miR-92a-3p can hybridize with other probes to form a signal amplification cycle. The fluorescence of MWCNTs@Au NCs remains stable and constitutes a ratiometric fluorescence system with that of Atto-425. A detection concentration interval of 0.1–10 pM and a limit of detection of 31 fM was obtained under optimized measurement conditions. In addition, the accuracy of the biosensor was validated by detecting the concentration of miR-92a-3p extracted from clinical exosome samples.

Microfluidics for detection of exosomes and microRNAs in cancer: State of the art

Exosomes are small extracellular vesicles with sizes ranging from 30-150 nanometers that contain proteins, lipids, mRNAs, microRNAs, and double-stranded DNA derived from the cells of origin. Exosomes can be taken up by target cells, acting as a means of cell-to-cell communication. The discovery of these vesicles in body fluids and their participation in cell communication has led to major breakthroughs in diagnosis, prognosis, and treatment of several conditions (e.g., cancer). However, conventional isolation and evaluation of exosomes and their microRNA content suffers from high cost, lengthy processes, difficult standardization, low purity, and poor yield. The emergence of microfluidics devices with increased efficiency in sieving, trapping, and immunological separation of small volumes could provide improved detection and monitoring of exosomes involved in cancer. Microfluidics techniques hold promise for advances in development of diagnostic and prognostic devices. This review covers ongoing research on microfluidics devices for detection of microRNAs and exosomes as biomarkers and their translation to point-of-care and clinical applications.

Flow-homogeneous electrochemical sensing system based on 2D metal-organic framework nanozyme for successive microRNA assay

Considering DNA-based homogeneous electrochemical assay allows identification of targets to be carried out in a homogeneous solution, it would be of significance to develop the successive homogeneous assay system in dynamic solution for rapid disease diagnosis and high-throughput bioanalysis. In homogeneous assay, the work electrodes generally have capability of DNA capture but lack signal amplification, restricting its sensitivity. Here, a flow-homogeneous sensing system was proposed to realize the successive assay of microRNA, a model biomarker. Ultrathin 2D metal-organic framework (MOF) nanozymes with thickness of about 1 nm were facilely prepared by ultrasonic approach. Due to the excellent enzyme-like activity and adsorption capacity towards single-strand DNA (ssDNA), MOF nanozymes adsorbed on electrode simultaneously played two roles of ssDNA collector and signal-amplifier. To adapt the recoverable electrode to on-line monitoring, duplex-specific nuclease-assisted circle reaction was conducted to produce the turn-on amplified signal. Flow injection device was employed to realize the recycling of electrodes and the successive microRNA assay. The assay strategy showed low limit of detection (0.12 pM, S/N = 3) for microRNA, excellent renewability and acceptable reliability for real sample assay. The established system exerts the advantages of DNA-based homogeneous electrochemical sensing strategy. This work would not only expand homogeneous electrochemical assay to successive bioassay, but also provide the possibility for practical application of homogeneous sensing strategy.

Advances in fluorescence sensing enabled by lanthanide-doped upconversion nanophosphors

Lanthanide-doped upconversion nanoparticles (UCNPs), characterized by converting low-energy excitation to high-energy emission, have attracted considerable interest due to their inherent advantages of large anti-Stokes shifts, sharp and narrow multicolor emissions, negligible autofluorescence background interference, and excellent chemical- and photo-stability. These features make them promising luminophores for sensing applications. In this review, we give a comprehensive overview of lanthanide-doped upconversion nanophosphors including the fundamental principle for the construction of UCNPs with efficient upconversion luminescence (UCL), followed by state-of-the-art strategies for the synthesis and surface modification of UCNPs, and finally describing current advances in the sensing application of upconversion-based probes for the quantitative analysis of various analytes including pH, ions, molecules, bacteria, reactive species, temperature, and pressure. In addition, emerging sensing applications like photodetection, velocimetry, electromagnetic field, and voltage sensing are highlighted.

Multifunctional nanoparticles as optical biosensing probe for breast cancer detection: A review

Optical biosensors show attractive performance in medical sensing in the event of using different nanoparticles in their design. Owing to their unique optical characteristics and biological compatibility, gold nanoparticles (GNPs), silver nanoparticles (AgNPs), bimetallic nanoparticles and magnetic nanoparticles have been broadly implemented in making sensing tools. The functionalization of these nanoparticles with different components provides an excellent opportunity to assemble selective and sensitive sensing materials to detect various biological molecules related to breast cancer. This review summarizes the recent application of optical biosensing devices based on nanomaterials and discusses their pros and cons to improve breast cancer detection in real samples. In particular, the main constituent elements of these optical biosensors including recognition and transducer elements, types of applied nanostructures, analytical sensing procedures, sensor detection ranges and limit of detection (LOD), are expressed in detail.

Sensors/nanosensors based on upconversion materials for the determination of pharmaceuticals and biomolecules: An overview

Upconversion materials have been the focus of a large body of research in analytical and clinical fields in the last two decades owing to their ability to convert light between various spectral regions and their particular photophysical features. They emit efficient and sharp ultraviolet (UV) or visible luminescence after excitation with near-infrared (NIR) light. These features overcome some of the disadvantages reported for conventional fluorescent materials and provide opportunities for high sensitivity chemo-and bio-sensing. Here, we review studies that used upconversion materials as sensors for the determination of pharmaceuticals and biomolecules in the last two decades. The articles included in this review were retrieved from the SCOPUS database using the search phrases: "upconversion nanoparticles for determination of pharmaceutical compounds", and "upconversion nanoparticles for determination of biomolecules". Details of each developed upconversion nanoparticles based sensor along with their relevant analytical parameters are reported and carefully explained.

A sensitive upconverting nanoprobe based on signal amplification technology for real-time in situ monitoring of drug-induced liver injury

Drug-induced liver injury (DILI) is increasingly recognized as one of the most challenging global health problems. Conventional in vitro detection methods not only lack specificity and sensitivity but also cannot achieve real-time, straightforward visualization of hepatotoxicity in vivo. Liver-specific miR122 has been observed to be a superior and sensitive biomarker for DILI diagnosis. Herein, a sensitive upconverting nanoprobe synthesized with upconversion nanoparticles (UCNPs) and gold nanorods (GNR) was designed to diagnose hepatotoxicity in vivo. After injection, the nanoprobes accumulated in the liver and were activated by miR122, and the signal amplification technology fully yielded luminescent amplification; hence, the detection sensitivity was improved. Because of the high tissue penetration capability of near-infrared light, this nanoprobe can achieve real-time in situ detection, thereby providing a novel technology for precise biological and medical analysis.

A dual signal amplification strategy for the highly sensitive fluorescence detection of nucleic acids

A dual signal amplification strategy comprising target-triggered recycling and DSN-mediated amplifications was designed and proposed for a highly sensitive fluorescence assay of nucleic acids.

Turn-on detection of MicroRNA155 based on simple UCNPs-DNA-AuNPs luminescence energy transfer probe and duplex-specific nuclease signal amplification

A novel luminescence energy transfer (LET) probe for detection of tumor related microRNAs using NaGdF₄:Yb,Er@NaYF₄ upconversion nanoparticles (UCNPs) as energy donors and gold nanoparticles (AuNPs) as energy acceptors was developed. Using the double modified complementary DNA sequences of microRNA155 (miRNA155) as a bridge, NaGdF₄:Yb,Er@NaYF₄ UCNPs and AuNPs were conjugated to form NaGdF₄:Yb,Er@NaYF₄ UCNPs-DNA-AuNPs nanocomplexes (UCNPs-DNA-AuNPs) probe. The energy transfer would occur when the distance between donor and acceptor gets closer. In the presence of target miRNA155, DNA-RNA heteroduplexes appeared as product, but the luminescence intensity was not changed obviously. In the existence of duplex-specific nuclease (DSN), DSN could hydrolyze the DNA strand of DNA-RNA heteroduplexes, the bridge linked NaGdF₄:Yb,Er@NaYF₄ UCNPs and AuNPs was destroyed, which induced that the quenched luminescence intensity was recovered and RNA was released. The released miRNA155 could react with another UCNPs-DNA-AuNPs probe to form DNA-RNA heteroduplexes again. This cyclic reaction generates an amplification of luminescence signal for quantitative detection of miRNA155. Under the illumination of 980 nm laser, the concentration ranges from 0.1 nM to 15 nM and the detection of limits was 0.045 nM for detection of miRNA155. Moreover, the UCNPs-DNA-AuNPs probe was used in quantify miRNA155 in cell lysates with satisfactory results.

Dual-Acceptor-Based Upconversion Luminescence Nanosensor with Enhanced Quenching Efficiency for in Situ Imaging and Quantification of MicroRNA in Living Cells

Upconversion nanoparticles (UCNPs) have become competitive materials for bioanalysis, bioimaging, and early diagnosis of diseases, especially cancers. However, traditional upconversion luminescence (UCL) nanosensors are often challenged with complicated covalent modification and relatively poor stability. As efficient energy acceptors in the luminescence resonance energy-transfer (LRET) process, organic dyes exhibit unique advantages such as easy modification and stable property. Herein, a simple and universal bioplatform is constructed for in situ imaging and quantitation of intracellular microRNA-21 (miR-21) using dual-acceptor-based upconversion nanoprobes with enhanced quenching efficiency. In this assay, UCNPs with core-shell structures are synthesized, in which the emitting ions are confined in the shell to take the energy donors and acceptors in close proximity. The complementary DNA (cDNA) that can specifically recognize target miR-21 is labeled with organic dyes TAMRA and black hole quencher as dual acceptors and easily assembled on UCNPs via electrostatic adsorption. Compared with only one acceptor for LRET, two dyes quench more luminescence of UCNPs (>60%), which thus reduce the background and improve the sensitivity. With the enhanced quenching efficiency and simple assembly process, the proposed system is readily applied to in situ imaging of miR-21 in different cancer cells, which further achieves quantification of miR-21 in MCF-7 cells. Therefore, our proposed dual-acceptor-based upconversion nanoplatform opens up new opportunities for sensitive analysis of miRNA and provides potential applications in biomedical and clinical research.

Upconversion Luminescence Sandwich Assay For Detection of Influenza H7 Subtype

With large anti-Stokes shifts and background-free signals, upconversion luminescent (UCL) screening assays have been a promising method to reduce the transmission of influenza epidemic, which can critically alleviate the disease burden and extra annual deaths. In this work, a luminescent resonance energy transfer sandwich assay is developed, which utilizes core-shell upconversion nanoparticles and gold nanoparticles as the donor and acceptor, respectively. The influenza H7 gene of H7N9 virus is used as the target for optimization of the assay. Importantly, the hybridization time of the assay is ≈40 min and the specificity test indicates the probes are specific toward the H7 target. The limit of detection of the system is ≈134 × 10^-12 m (≈3.22 × 10¹⁰ molecules). Moreover, the assay is tested with the use of polymerase chain reaction validated samples from human isolates. The results are promising for implanting future on-site rapid influenza screening application.

Advances in DNA/RNA detection using nanotechnology

Specific nucleic acid detection in vitro or in vivo has become increasingly important in the discovery of genetic diseases, diagnosing pathogen infection and monitoring disease treatment. One challenge, however, is that the amount of target nucleic acid in specimens is limited. Furthermore, direct sensing methods are also unable to provide sufficient sensitivity and specificity. Fortunately, due to advances in nanotechnology and nanomaterials, nanotechnology-based bioassays have emerged as powerful and promising approaches providing ultra-high sensitivity and specificity in nucleic acid detection. This chapter presents an overview of strategies used in the development and integration of nanotechnology for nucleic acid detection, including optical and electrical detection methods, and nucleic acid assistant recycling amplification strategies. Recent 5 years representative examples are reviewed to demonstrate the proof-of-concept with promising applications for DNA/RNA detection and the underlying mechanism for detection of DNA/RNA with the higher sensitivity and selectivity. Furthermore, a brief discussion of common unresolved issues and future trends in this field is provided both from fundamental and practical point of view.

Lighting Up MicroRNA in Living Cells by the Disassembly of Lock-Like DNA-Programmed UCNPs-AuNPs through the Target Cycling Amplification Strategy

Intracellular microRNAs imaging based on upconversion nanoprobes has great potential in cancer diagnostics and treatments. However, the relatively low detection sensitivity limits their application. Herein, a lock-like DNA (LLD) generated by a hairpin DNA (H1) hybridizing with a bolt DNA (bDNA) sequence is designed, which is used to program upconversion nanoparticles (UCNPs, NaYF₄ @NaYF₄ :Yb, Er@NaYF₄ ) and gold nanoparticles (AuNPs). The upconversion emission is quenched through luminescence resonance energy transfer (LRET). The multiple LLD can be repeatedly opened by one copy of target microRNA under the aid of fuel hairpin DNA strands (H2) to trigger disassembly of AuNPs from the UCNP, resulting in the lighting up of UCNPs with a high detection signal gain. This strategy is verified using microRNA-21 as model. The expression level of microRNA-21 in various cells lines can be sensitively measured in vitro, meanwhile cancer cells and normal cells can be easily and accurately distinguished by intracellular microRNA-21 imaging via the nanoprobes. The detection limit is about 1000 times lower than that of the previously reported upconversion nanoprobes without signal amplification. This is the first time a nonenzymatic signal amplification method has been combined with UCNPs for imaging intracellular microRNAs, which has great potential for cancer diagnosis.

Aptasensors as the future of antibiotics test kits-a case study of the aptamer application in the chloramphenicol detection

Antibiotics are a type of antimicrobial drug with the ubiquitous presence in foodstuff that effectively applied to treat the diseases and promote the animal growth worldwide. Chloramphenicol as one of the antibiotics with the broad action spectrum against Gram-positive and Gram-negative bacteria is widely applied for the effective treatment of infectious diseases in humans and animals. Unfortunately, the serious side effects of chloramphenicol, such as aplastic anemia, kidney damage, nausea, and diarrhea restrict its application in foodstuff and biomedical fields. Development of the sufficiently sensitive methods to detect chloramphenicol residues in food and clinical diagnosis seems to be an essential demand. Biosensors have been introduced as the promising tools to overcome the requirement. As one of the newest types of the biosensors, aptamer-based biosensors (aptasensors) are the efficient sensing platforms for the chloramphenicol monitoring. In the present review, we summarize the recent achievements of the accessible aptasensors for qualitative detection and quantitative determination of chloramphenicol as a candidate of the antibiotics. The present chloramphenicol aptasensors can be classified in two main optical and electrochemical categories. Also, the other formats of the aptasensing assays like the high performance liquid chromatography (HPLC) and microchip electrophoresis (MCE) have been reviewed. The enormous interest in utilizing the diverse nanomaterials is also highlighted in the fabrication of the chloramphenicol aptasensors. Finally, some results are presented based on the advantages and disadvantages of the studied aptasensors to achieve a promising perspective for designing the novel antibiotics test kits.

Simultaneous detection and determination of mercury (II) and lead (II) ions through the achievement of novel functional nucleic acid-based biosensors

The serious threats of mercury (Hg²⁺) and lead (Pb²⁺) ions for the public health makes it important to achieve the detection methods of the ions with high affinity and specificity. Metal ions usually coexist in some environment and foodstuff or clinical samples. Therefore, it is very necessary to develop a fast and simple method for simultaneous monitoring the amount of metal ions, especially when Hg²⁺ and Pb²⁺ coexist. DNAzyme-based biosensors and aptasensors have been highly regarded for this purpose as two main groups of the functional nucleic acid (FNA)-based biosensors. In this review, we summarize the recent achievements of functional nucleic acid-based biosensors for the simultaneous detection of Hg²⁺ and Pb²⁺ ions in two main optical and electrochemical groups. The tremendous interest in utilizing the various nanomaterials is also highlighted in the fabrication of the FNA-based biosensors. Finally, some results are presented based on the advantages and disadvantages of the studied FNA-based biosensors to compare their validation.

Fluorescence turn-on detection of target sequence DNA based on silicon nanodot-mediated quenching

We have developed a new enzyme-free method for target sequence DNA detection based on the dynamic quenching of fluorescent silicon nanodots (SiNDs) toward Cy5-tagged DNA probe. Fascinatingly, the water-soluble SiNDs can quench the fluorescence of cyanine (Cy5) in Cy5-tagged DNA probe in homogeneous solution, and the fluorescence of Cy5-tagged DNA probe can be restored in the presence of target sequence DNA (the synthetic target miRNA-27a). Based on this phenomenon, a SiND-featured fluorescent sensor has been constructed for "turn-on" detection of the synthetic target miRNA-27a for the first time. This newly developed approach possesses the merits of low cost, simple design, and convenient operation since no enzymatic reaction, toxic reagents, or separation procedures are involved. The established method achieves a detection limit of 0.16 nM, and the relative standard deviation of this method is 9% (1 nM, n = 5). The linear range is 0.5-20 nM, and the recoveries in spiked human fluids are in the range of 90-122%. This protocol provides a new tactic in the development of the nonenzymic miRNA biosensors and opens a promising avenue for early diagnosis of miRNA-associated disease. Graphical abstract The SiND-based fluorescent sensor for detection of S-miR-27a.

A Universal Upconversion Sensing Platform for the Sensitive Detection of Tumour-Related ncRNA through an Exo III-Assisted Cycling Amplification Strategy

Here, a sensitive and universal noncoding RNA (ncRNA) upconversion sensing nanoplatform is developed. Gold nanoparticles bearing one hairpin DNA (Hp) molecule are conjugated to the linker DNA modified NaYF₄ :Yb, Er@NaYF₄ upconversion nanoparticles by DNA hybridization, leading to quenching of the upconversion emission through fluorescence resonance energy transfer. A signal DNA (SDNA) sequence is designed to open Hp, recovering the upconversion emission. To achieve universality and high sensitivity of the nanoprobe, an exonuclease III (Exo III)-assisted cycling amplification strategy is introduced. A multifunctional hairpin DNA (mHp) containing ncRNA recognition sequence and SDNA sequence is designed to recognize ncRNA and trigger Exo III as a biocatalyst to stepwise disintegrate itself, releasing both ncRNA and SDNA. The released ncRNA can be reused to release more SDNA, which greatly improves the sensing sensitivity. By changing the recognition portion of mHp, various ncRNA can be detected. The sensitive detection of both homeobox (HOX) transcript antisense RNA segment and miR-21 is achieved with this novel strategy, even in human serum, indicating the universality and sensitivity of the proposed strategy. Additionally, the expression level of miR-21 in human breast cancer cell (MCF-7) lysate is successfully measured, suggesting its potential in clinical diagnosis.