An innovative paradigm of methods in microRNAs detection: highlighting DNAzymes, the illuminators

MicroRNA biosensors for the detection of liver cancer

Liver cancer is one of the deadliest types worldwide and early diagnosis is highly important for successful treatment. Therefore, it is necessary to develop rapid, sensitive, simple, and inexpensive analytical tools for its detection. MicroRNAs (miRNA) represent unique biomarkers whose expression in biofluids is strongly associated with cancer in general and miR-21, -31, -122, -145, -146a, -200c, -221, -222, and -223 in liver cancer, specifically. Various biosensors for miRNA detection have been developed. These include electrochemical biosensors based on amperometric, potentiometric, conductometric and impedimetric technology. Furthermore, the use of advanced nanomaterials with enhanced chemical stability, conductivity and electrocatalytic activity have greatly increased the sensitivity and specificity of these devices. The present review focuses on recent advances in electrochemical biosensors for miRNA detection in liver cancer.

Duplex-specific nuclease powered 3D DNA walker and quantum dots barcodes for homogeneous electrochemical detection of microRNAs

Multiplex microRNAs (miRNAs) detection is beneficial for early diagnosis and prognosis of cancer. Herein, duplex-specific nuclease (DSN) powered 3D DNA walker and quantum dots (QDs) barcodes were designed for the simultaneous detection of miRNAs in a homogeneous electrochemical sensor. In the proof-of-concept experiment, the effective active area of the as-prepared graphene aerogel-modified carbon paper (CP-GAs) electrode was ∼14.30 times larger than that of the traditional glassy carbon electrode (GCE), endowing the enhanced capability of loading more metal ions for ultrasensitive detection of miRNAs. In addition, DSN-powered target recycling and DNA walking strategy assured the sensitive detection of miRNAs. After the introduction of magnetic beads (MNs) and electrochemical double enrichment strategies, the integration of triple signal amplification methods yielded good detection results. Under optimal conditions, towards simultaneous detection of microRNA-21 (miR-21) and miRNA-155 (miR-155), a linear range of 10^-16-10^-7 M and a sensitivity of 10 aM (miR-21) and 2.18 aM (miR-155) were achieved, respectively. It was worth mentioning that the prepared sensor can detect miR-155 down to 0.17 aM, which was also extremely advantageous among the sensors reported so far. What's more, through verification, the prepared sensor had good selectivity and reproducibility, and exhibited good detection ability in complex serum environments, showing great potential in early clinical diagnosis and screening.

Web hybrid chain reaction enhanced fluorescent magnetic bead array for digital nucleic acid detection

The detection of biomarkers at low concentrations is important in clinical diagnostic analyses and has attracted continuous research. In this work, absolute quantification of hepatitis B virus (HBV) DNA was achieved using magnetic beads with isothermal, enzyme-free DNA nanostructure for fluorescence amplification. Firstly, the DNA-functionalized bead captured the target nucleic acid in the form of sandwich hybridization, and the individual target lighted up the entire bead by isothermal web hybridization chain reaction (wHCR). After the microarray scanning, the target nucleic acids can be digitally quantified based on the Poisson statistics. Therefore, the fluorescent bead assay enabled precise detection of HBV DNA down to 5 fM level without external calibration curves. Moreover, this method not only specifically distinguished single-base mismatched sequences, but also obtained the quantitative detection of HBV DNA in serum samples. Unlike routine digital detection usually combined with complex compartment partitioning operations, the amplification structure immobilized on beads can be conducted in microcentrifuge tubes with a volume of microliter scale. This work expands the application of magnetic beads in the digital quantitative detection via enzyme-free and isothermal method.

DNAzyme-Based Biosensors: Immobilization Strategies, Applications, and Future Prospective

Since their discovery almost three decades ago, DNAzymes have been used extensively in biosensing. Depending on the type of DNAzyme being used, these functional oligonucleotides can act as molecular recognition elements within biosensors, offering high specificity to their target analyte, or as reporters capable of transducing a detectable signal. Several parameters need to be considered when designing a DNAzyme-based biosensor. In particular, given that many of these biosensors immobilize DNAzymes onto a sensing surface, selecting an appropriate immobilization strategy is vital. Suboptimal immobilization can result in both DNAzyme detachment and poor accessibility toward the target, leading to low sensing accuracy and sensitivity. Various approaches have been employed for DNAzyme immobilization within biosensors, ranging from amine and thiol-based covalent attachment to non-covalent strategies involving biotin-streptavidin interactions, DNA hybridization, electrostatic interactions, and physical entrapment. While the properties of each strategy inform its applicability within a proposed sensor, the selection of an appropriate strategy is largely dependent on the desired application. This is especially true given the diverse use of DNAzyme-based biosensors for the detection of pathogens, metal ions, and clinical biomarkers. In an effort to make the development of such sensors easier to navigate, this paper provides a comprehensive review of existing immobilization strategies, with a focus on their respective advantages, drawbacks, and optimal conditions for use. Next, common applications of existing DNAzyme-based biosensors are discussed. Last, emerging and future trends in the development of DNAzyme-based biosensors are discussed, and gaps in existing research worthy of exploration are identified.

A fluorescent microarray platform based on catalytic hairpin assembly for MicroRNAs detection

The DNA microarray has distinctive advantages of high-throughput and less complicated operations, but tends to have a relatively low sensitivity. Catalytic hairpin assembly (CHA) is one of the most promising enzyme-free, isothermal DNA circuit for high efficient signal amplification. Here, a microarray-based catalytic hairpin assembly (mi-CHA) biosensing method has been developed to detect various miRNAs in a single test simultaneously. The target miRNA can trigger conformational transformations of hairpin-structured DNA probes on the chip surface and lead to the specific signal amplification. A significant advantage of this approach is that each duplex produced by the solid-phase CHA will be immobilized on the certain location of the chip and release fluorescent signal via the universal domain, eliminating the requirement of different fluorophores. This method has manifested a high detection sensitivity of human cancer-associated miRNAs (miR-21 and miR-155) down to 1.33 fM and promised a high specificity to distinguish single-base mismatches. Furthermore, the practicability of this method was demonstrated by analyzing target miRNAs in human serum and cancer cells. The experimental results suggest that the proposed method has high-throughput analytical potential and could be applied to many other clinical diagnosis.

MiR-1539 and Its Potential Role as a Novel Biomarker for Colorectal Cancer

Purpose

We investigated microRNA (miR) 1539 as a potential biomarker for predicting the risk and pathobiological behavior of colorectal cancer (CRC).

Methods

Our strategy consisted of analyzing 100 serum samples from 51 CRC patients, 49 healthy controls (HCs), and another 56 CRC tissue and matched normal adjacent to tumor (NAT) samples. The relative expression levels of miR-1539 in exosomes, serum and tissues were detected and compared in the different groups, using reverse transcription-polymerase chain reaction (RT-qPCR). The diagnostic value and potential function of miR-1539 were investigated using clinicopathological data combined with bioinformatics analysis.

Results

MiR-1539 expression was significantly up-regulated in exosomes (p = 0.003) and cancer tissue (p < 0.001) from CRC patients. MiR-1539 expression levels in serum varied according to different tumor sites (right-sided vs. left-sided, p = 0.047; left-side CRC vs. HCs, p = 0.031). In terms of diagnostic efficacy, miR-1539 expression in exosomes may help distinguish CRC cases from HCs with a sensitivity of 92.2%, and miR-1539 expression in serum may improve the specificity to 96.6% for left-sided CRC diagnosis. When combined with clinicopathological data, serum miR-1539 levels were positively associated with vascular endothelial growth factor (VEGF) expression (p = 0.028), whilst levels in CRC tissue were positively associated with increased Ki-67 levels (p = 0.035). Poorer pathologic differentiation was potentially related to an increased tendency of miR-1539 expression in CRC tissue (p = 0.071). Based on our bioinformatics analysis, miR-1539 may have a significant mechanistic influence on CRC genesis and progression.

Conclusions

Circulating or tissue based miR-1539 may be used as a novel potential biomarker for CRC screening, and a predictor of poor clinicopathological behavior in tumors.

A platform for multiplexed colorimetric microRNA detection using shape-encoded hydrogel particles

We report a platform utilizing a reporter enzyme, which produces a chromogenic indigo precipitate that preferentially localizes within a hydrogel microparticle. The 3D network of the hydrogel maintains the rapid target binding kinetics found in solution, while multiplexed target detection is achieved through shape-encoding of the particles. Moreover, the precipitate-laden hydrogels can be imaged with a simple phone camera setup. We used this system to detect microRNA (miRNA) down to 0.22 fmol. We then showed the compatibility of this system with real samples by performing multiplexed miRNA measurements from total RNA from matched colon cancer and normal adjacent tissue.

Porphyrins as Colorimetric and Photometric Biosensors in Modern Bioanalytical Systems

Advances in porphyrin chemistry have provided novel materials and exciting technologies for bioanalysis such as colorimetric sensor array (CSA), photo-electrochemical (PEC) biosensing, and nanocomposites as peroxidase mimetics for glucose detection. This review highlights selected recent advances in the construction of supramolecular assemblies based on the porphyrin macrocycle that provide recognition of various biologically important entities through the unique porphyrin properties associated with colorimetry, spectrophotometry, and photo-electrochemistry.

Rational design and development of a universal baby spinach-based sensing platform for the detection of biomolecules

Here, we designed and developed a Universal Baby Spinach-based Probe (UBSP) for biomolecule detection by introducing a DNA repressor containing a target recognition element. By employing different interaction modes between targets and repressors, we applied the UBSP to detect diverse classes of analytes, including microRNA, proteins, and heavy metal ions.

The interaction of an amorphous metal–organic cage-based solid (aMOC) with miRNA/DNA and its application on a quartz crystal microbalance (QCM) sensor

The interaction between an aMOC and miRNA/DNA is studied and the use of the aMOC as an effective amplifier in a QCM sensor to detect miRNA is developed for the first time.

Multiplexed detection of micro-RNAs based on microfluidic multi-color fluorescence droplets

In this work, simple, rapid, and low-cost multiplexed detection of tumor-related micro-RNAs (miRNAs) was achieved based on multi-color fluorescence on a microfluidic droplet chip, which simplified the complexity of light path to a half. A four-T-junction structure was fabricated to form uniform nano-volume droplet arrays with customized contents. Multi-color quantum dots (QDs) used as the fluorescence labels were encapsulated into droplets to develop the multi-path fluorescence detection module. We designed an integrated multiplex fluorescence resonance energy transfer system assisted by multiple QDs (four colors) and one quencher to detect four tumor-related miRNAs (miRNA-20a, miRNA-21, miRNA-155, and miRNA-221). The qualitative analysis of miRNAs was realized by the color identification of QDs, while the quantitative detection of miRNAs was achieved based on the linear relationship between the quenching efficiency of QDs and the concentration of miRNAs. The practicability of the multiplex detection device was further confirmed by detecting four tumor-related miRNAs in real human serum samples. The detection limits of four miRNAs ranged from 35 to 39 pmol/L was achieved without any target amplification. And the linear range was from 0.1 nmol/L to 1 μmol/L using 10 nL detection volume (one droplet) under the detection speed of 320 droplets per minute. The multiple detection system for miRNAs is simple, fast, and low-cost and will be a powerful platform for clinical diagnostic analysis. Graphical abstract.

Improved performances of catalytic G-quadruplexes (G4-DNAzymes) via the chemical modifications of the DNA backbone to provide G-quadruplexes with double 3'-external G-quartets

Here we report on the design of a new catalytic G-quadruplex-DNA system (G4-DNAzyme) based on the modification of the DNA scaffold to provide the DNA pre-catalyst with two identical 3'-ends, known to be more catalytically proficient than the 5'-ends. To this end, we introduced a 5'-5' inversion of polarity site in the middle of the G4-forming sequences AG₄A and AG₆A to obtain d(^3'AGG^5'-^5'GGA^3') (or AG₂-G₂A) and d(^3'AGGG^5'-^5'GGGA^3') (or AG₃-G₃A) that fold into stable G4 whose tetramolecular nature was confirmed via nuclear magnetic resonance (NMR) and circular dichroism (CD) investigations. Both AG₂-G₂A and AG₃-G₃A display two identical external G-quartets (3'-ends) known to interact with the cofactor hemin with a high efficiency, making the resulting complex competent to perform hemoprotein-like catalysis (G4-DNAzyme). A systematic comparison of the performances of modified and unmodified G4s lends credence to the relevance of the modification exploited here (5'-5' inversion of polarity site), which represents a new chemical opportunity to improve the overall activity of catalytic G4s.

Nondestructive Characterization of Stem Cell Neurogenesis by a Magneto-Plasmonic Nanomaterial-Based Exosomal miRNA Detection

The full realization of stem cell-based treatments for neurodegenerative diseases requires precise control and characterization of stem cell fate. Herein, we report a multifunctional magneto-plasmonic nanorod (NR)-based detection platform to address the limitations associated with the current destructive characterization methods of stem cell neurogenesis. Exosomes and their inner contents have been discovered to play critical roles in cell-cell interactions and intrinsic cellular regulations and have received wide attention as next-generation biomarkers. Moreover, exosomal microRNAs (miRNA) also offer an essential avenue for nondestructive molecular analyses of cell cytoplasm components. To this end, our developed nondestructive, selective, and sensitive detection platform has (i) an immunomagnetic active component for exosome isolation and (ii) a plasmonic/metal-enhanced fluorescence component for sensitive exosomal miRNA detection to characterize stem cell differentiation. In a proof-of-concept demonstration, our multifunctional magneto-plasmonic NR successfully detected the expression level of miRNA-124 and characterized neurogenesis of human-induced pluripotent stem cell-derived neural stem cells in a nondestructive and efficient manner. Furthermore, we demonstrated the versatility and feasibility of our multifunctional magneto-plasmonic NRs by characterizing a heterogeneous population of neural cells in an ex vivo rodent model. Collectively, we believe our multifunctional magneto-plasmonic NR-based exosomal miRNA detection platform has a great potential to investigate the function of cell-cell interactions and intrinsic cellular regulators for controlling stem cell differentiation.

A conformational switch-based aptasensor for the chemiluminescence detection of microRNA

A simple microRNA (miRNA) aptasensor has been developed combining the conformational switch of a streptavidin aptamer and isothermal strand displacement amplification. In the presence of its target miRNA, the allosteric molecular beacon (aMB) probe immobilized on the plate can be 'switched on' and release the streptavidin aptamer. At the same time, Klenow fragment (3'→5' exo-) is utilized to initiate DNA-strand displacement, which starts the target recycling process. Based on the aptamer' high binding affinity and subsequent catalytic chemiluminescence (CL) detection, this CL strategy is highly specific in distinguishing mature miRNAs in same family. It exhibits a dynamic range of four orders of magnitude with a detection limit of 50 fM, and shows great potential for miRNA-related clinical practices and biochemical research.

Avenues Toward microRNA Detection In Vitro: A Review of Technical Advances and Challenges

Over the decades, the biological role of microRNAs (miRNAs) in the post-transcriptional regulation of gene expression has been discovered in many cancer types, thus initiating the tremendous expectation of their application as biomarkers in the diagnosis, prognosis, and treatment of cancer. Hence, the development of efficient miRNA detection methods in vitro is in high demand. Extensive efforts have been made based on the intrinsic properties of miRNAs, such as low expression levels, high sequence homology, and short length, to develop novel in vitro miRNA detection methods with high accuracy, low cost, practicality, and multiplexity at point-of-care settings. In this review, we mainly summarized the newly developed in vitro miRNA detection methods classified by three key elements, including biological recognition elements, additional micro-/nano-materials and signal transduction/readout elements, their current challenges and further applications are also discussed.

Advances in biosensors for the detection of ochratoxin A: Bio-receptors, nanomaterials, and their applications

Ochratoxin A (OTA) is a class of mycotoxin mainly produced by the genera Aspergillus and Penicillium. OTA can cause various forms of kidney, liver and brain diseases in both humans and animals although trace amount of OTA is normally present in food. Therefore, development of fast and sensitive detection technique is essential for accurate diagnosis of OTA. Currently, the most commonly used detection methods are enzyme-linked immune sorbent assays (ELISA) and chromatographic techniques. These techniques are sensitive but time consuming, and require expensive equipment, highly trained operators, as well as extensive preparation steps. These drawbacks limit their wide application in OTA detection. On the contrary, biosensors hold a great potential for OTA detection at for both research and industry because they are less expensive, rapid, sensitive, specific, simple and portable. This paper aims to provide an extensive overview on biosensors for OTA detection by highlighting the main biosensing recognition elements for OTA, the most commonly used nanomaterials for fabricating the sensing interface, and their applications in different read-out types of biosensors. Current challenges and future perspectives are discussed as well.

Molecular methods in electrochemical microRNA detection

High-throughput profiling/sensing of nucleic acids has recently emerged as a highly promising strategy for the early diagnosis and improved prognosis of a broad range of pathologies, most notably cancer. Among the potential biomarker candidates, microRNAs (miRNAs), a class of non-coding RNAs of 19-25 nucleotides in length, are of particular interest due to their role in the post-transcriptional regulation of gene expression. Developing miRNA sensing technologies that are quantitative, ultrasensitive and highly specific has proven very challenging because of their small size, low natural abundance and the high degree of sequence similarity among family members. When compared to optical based methods, electrochemical sensors offer many advantages in terms of sensitivity and scalability. This non-comprehensive review aims to break-down and highlight some of the most promising strategies for electrochemical sensing of microRNA biomarkers.

Advanced Selection Methodologies for DNAzymes in Sensing and Healthcare Applications

DNAzymes have been widely explored owing to their excellent catalytic activity in a broad range of applications, notably in sensing and biomedical devices. These newly discovered applications have built high hopes for designing novel catalytic DNAzymes. However, the selection of efficient DNAzymes is a challenging process but one that is of crucial importance. Initially, systemic evolution of ligands by exponential enrichment (SELEX) was a labor-intensive and time-consuming process, but recent advances have accelerated the automated generation of DNAzyme molecules. This review summarizes recent advances in SELEX that improve the affinity and specificity of DNAzymes. The thriving generation of new DNAzymes is expected to open the door to several healthcare applications. Therefore, a significant portion of this review is dedicated to various biological applications of DNAzymes, such as sensing, therapeutics, and nanodevices. In addition, discussion is further extended to the barriers encountered for the real-life application of these DNAzymes to provide a foundation for future research.

RNA-Cleaving DNAzymes: Old Catalysts with New Tricks for Intracellular and In Vivo Applications

DNAzymes are catalytically active DNA molecules that are normally isolated through in vitro selection methods, among which RNA-cleaving DNAzymes that catalyze the cleavage of a single RNA linkage embedded within a DNA strand are the most studied group of this DNA enzyme family. Recent advances in DNA nanotechnology and engineering have generated many RNA-cleaving DNAzymes with unique recognition and catalytic properties. Over the past decade, numerous RNA-cleaving, DNAzymes-based functional probes have been introduced into many research areas, such as in vitro diagnostics, intracellular imaging, and in vivo therapeutics. This review focus on the fundamental insight into RNA-Cleaving DNAzymes and technical tricks for their intracellular and in vivo applications, highlighting the recent progress in the clinical trial of RNA-Cleaving DNAzymes with selected examples. The challenges and opportunities for the future translation of RNA-cleaving DNAzymes for biomedicine are also discussed.

Multiplex microRNA imaging in living cells using DNA-capped-Au assembled hydrogels

Non-invasively imaging multiplex microRNAs (miRNAs) in living cells is pivotal to understanding their physiological functions and pathological development due to the key regulatory roles of miRNAs in gene expression. However, developing smart delivery systems with large gene loading capacity, biocompatibility and responsiveness remains a significant challenge. Herein, we successfully incorporated DNA-capped Au nanoparticles (NPs) and their complementary fluorescent DNA sequences into a porous 3D hydrogel network (AuDH), in which hairpin-locked DNAzyme strands and active metal ions were loaded (AuDH/M n+/H) for simultaneously imaging multiplex miRNAs in living cells. After transfection into cells, the specific miRNAs trigger the strand-displacement reaction and sequentially activate the DNAzyme-assisted target recycling, leading to a strong increase in the corresponding fluorescence intensity for imaging. This enables simultaneous assessment of the abundance of multiplex cancer-related miRNAs, even if at a very low expression level, in different cells through the different fluorescence intensities due to the dual signal amplification, and the change in abundance of miRNAs induced by siRNA or miRNA mimics in living cells can also be efficiently monitored. The versatile and responsive DNA hydrogel system holds great potential for miRNA biomedical applications.

An enzyme-free electrochemical biosensor combining target recycling with Fe3O4/CeO2@Au nanocatalysts for microRNA-21 detection

In this study, an electrochemical biosensor was proposed for microRNA-21 detection based on Fe₃O₄/CeO₂ @Au magnetite nanoparticles (Fe₃O₄/CeO₂ @Au MNPs) as nanocatalyst and catalytic hairpin assembly (CHA) for signal application. Firstly, target microRNA-21 hybridized with hairpin H₂ to form H₂-T duplex stranded DNA (dsDNA), which could further open the hairpin H₁ for the formation of H₁-H₂ dsDNA. Simultaneously, the Fe₃O₄/CeO₂ @Au-S₁ not only hybridized with single stranded fragment of H₁-H₂ dsDNA with producing long dsDNA to absorb a large amount of electroactive substances of methylene blue (MB), but also acted as nanocatalyst to directly catalyze the reduction of MB for amplifying the electrochemical signal. Herein, compared with pure Fe₃O₄ nanoparticles, Fe₃O₄/CeO₂ @Au MNPs exhibited excellent catalytic performance since the cerium oxide (CeO₂) nanoparticles and Au nanoparticles can greatly improve the catalytic activity of Fe₃O₄ nanoparticles and effectively prevent the agglomeration of Fe₃O₄ nanoparticles. Owing to the signal amplification strategy, the proposed biosensor provided a wide linear range of 1 fM to 1 nM with a low detection limit of 0.33 fM (defined as S/N = 3) for microRNA-21 detection, and exhibited excellent specificity and sensitivity. This strategy provided a novel avenue for the detection of other biomarkers in electrochemical biosensors.

Therapeutic Potential of DNAzyme Loaded on Chitosan/Cyclodextrin Nanoparticle to Recovery of Chemosensitivity in the MCF-7 Cell Line

Commonly, acquired resistances to anticancer drug are mediated by overexpression of a membrane-associated protein that encode via multi-drug resistance gene-1 (MDR1). Herein, the mRNA-cleaving DNAzyme that targets the mRNA of MDR1 gene in doxorubicin-resistant breast cancer cell line (MCF-7/DR) loaded on the chitosan β-cyclodextrin complexes was used as a tropical agent. Chitosan/β-cyclodextrin complexes were used to deliver DNAzymes into cancer cells. Determination of the physicochemical characteristics of the particles was done by photon correlation spectroscopy and scanning electron microscopy. The encapsulation efficiency of the complexes was tested by using gel retardation assay. Positively charged nanoparticles interacted with DNAzyme that could perform as an efficient DNAzyme transfection system. The rationale usage of this platform is to sensitize MCF-7/DR to doxorubicin by downregulating the drug-resistance gene MDR1. Results demonstrated a downregulation of MDR1 mRNAs in MCF-7/DR/DNZ by real-time PCR, compared to the MCF-7/DR as control. WST1 assay showed the 22-fold decrease in drug resistance on treated cells 24 h after transfection. Results showed the intracellular accumulation of Rh123 increased in the treated cells with DNAzyme. Results suggested a potential platform in association with chemotherapy drug for cancer therapy and indicated extremely efficient at delivery of DNAzyme in restoring chemosensitivity.