Carbon nanotube enhanced label-free detection of microRNAs based on hairpin probe triggered solid-phase rolling-circle amplification

Entropy-Driven Molecular Beacon Assisted Special RCA Assay with Enhanced Sensitivity for Room Temperature DNA Biosensing

The Phi29 DNA polymerase is renowned for its processivity in synthesizing single-stranded DNA amplicons by rolling around a circularized DNA template. However, DNA synthesis rolling circle amplification (RCA) is significantly hindered by the secondary structure in the circular template. To overcome this limitation, an engineered circular template without secondary structure could be utilized to improve the sensitivity of RCA-based assays without increasing its complexity. We herein proposed an entropy-driven special RCA technology for the detection of HPV16 E7 gene at room temperature. The strategy is composed of a molecular beacon containing a loop region for nucleic acid target recognition and a stem region to initiate RCA. With the target analyte, the stem region of the molecular beacon will be exposed and then hybridized with a special circular template to initiate the DNA amplification. We tested different designs of the molecular beacon sequence and optimized the assay's working conditions. The assay achieved a sensitivity of 1 pM in 40 min at room temperature. The sensitivity of this assay, at 1 pm, is about a hundred-fold greater than that of conventional linear RCA performed in solution. Our proposed sensor can be easily reprogrammed for detecting various nucleic acid markers by altering the molecular beacon's loop. Its simplicity, rapid assay time, and low cost make it superior to RCA sensors that utilize similar strategies.

Nano revolution of DNA nanostructures redefining cancer therapeutics-A comprehensive review

DNA nanostructures are a promising tool in cancer treatment, offering an innovative way to improve the effectiveness of therapies. These nanostructures can be made solely from DNA or combined with other materials to overcome the limitations of traditional single-drug treatments. There is growing interest in developing nanosystems capable of delivering multiple drugs simultaneously, addressing challenges such as drug resistance. Engineered DNA nanostructures are designed to precisely deliver different drugs to specific locations, enhancing therapeutic effects. By attaching targeting molecules, these nanostructures can recognize and bind to cancer cells, increasing treatment precision. This approach offers tailored solutions for targeted drug delivery, enabling the delivery of multiple drugs in a coordinated manner. This review explores the advancements and applications of DNA nanostructures in cancer treatment, with a focus on targeted drug delivery and multi-drug therapy. It discusses the benefits and current limitations of nanoscale formulations in cancer therapy, categorizing DNA nanostructures into pure forms and hybrid versions optimized for drug delivery. Furthermore, the review examines ongoing research efforts and translational possibilities, along with challenges in clinical integration. By highlighting the advancements in DNA nanostructures, this review aims to underscore their potential in improving cancer treatment outcomes.

Label-Free Field Effect Transistors (FETs) for Fabrication of Point-of-Care (POC) Biomedical Detection Probes

Field effect transistors (FETs)-based detection probes are powerful platforms for quantification in biological media due to their sensitivity, ease of miniaturization, and ability to function in biological media. Especially, FET-based platforms have been utilized as promising probes for label-free detections with the potential for use in real-time monitoring. The integration of new materials in the FET-based probe enhances the analytical performance of the developed probes by increasing the active surface area, rejecting interfering agents, and providing the possibility for surface modification. Furthermore, the use of new materials eliminates the need for traditional labeling techniques, providing rapid and cost-effective detection of biological analytes. This review discusses the application of materials in the development of FET-based label-free systems for point-of-care (POC) analysis of different biomedical analytes from 2018 to 2024. The mechanism of action of the reported probes is discussed, as well as their pros and cons were also investigated. Also, the possible challenges and potential for the fabrication of commercial devices or methods for use in clinics were discussed.

A ratiometric electrochemical DNA-biosensor for detection of miR-141

A sensitive biosensor for the detection of miR-141 has been constructed. The DNA-biosensor is prepared by first immobilizing the thiolated methylene blue-labeled hairpin capture probe (MB-HCP) on two-layer nanocomposite film graphene oxide-chitosan@ polyvinylpyrrolidone-gold nanourchin modified glassy carbon electrode. We used the hematoxylin as an electrochemical auxiliary indicator in the second stage to recognize DNA hybridization via the square wave voltammetry (SWV) responses that record the accumulated hematoxylin on electrode surfaces. The morphology and chemical composition of nanocomposite was characterized using TEM, FE-SEM, and FT-IR techniques. The preparation stages of the DNA-biosensor were screened by electrochemical impedance spectroscopy and cyclic voltammetry. The proposed DNA-biosensor can distinguish miR-141 from a non-complementary and mismatch sequence. A detection limit of 0.94 fM and a linear range of 2.0 -5.0 × 10⁵ fM were obtained using SWV for miR-141 detection. The working potential for methylene blue and hematoxylin was -0.28 and + 0.15 V vs. Ag/AgCl, respectively. The developed biosensor can be successfully used in the early detection of non-small cell lung cancer (NSCLC) by directly measuring miR-141 in human plasma samples. This novel DNA-biosensor is of promise in early sensitive clinical diagnosis of cancers with miR-141 as its biomarker.

Application of Nanomaterials in Isothermal Nucleic Acid Amplification

Because of high sensitivity and specificity, isothermal nucleic acid amplification are widely applied in many fields. To facilitate and improve their performance, various nanomaterials, like nanoparticles, nanowires, nanosheets, nanotubes, and nanoporous films are introduced in isothermal nucleic acid amplification. However, the specific application, roles, and prospect of nanomaterials in isothermal nucleic acid amplification have not been comprehensively reviewed. Here, the application of different nanomaterials (0D, 1D, 2D, and 3D) in isothermal nucleic acid amplification is comprehensively discussed and recent progress in the field is summarized. The nanomaterials are mainly used for reaction enhancer, signal generation/amplification, or surface loading carriers. In addition, 3D nanomaterials can be also functioned as isolated chambers for digital nucleic acid amplification and the tools for DNA sequencing of amplified products. Challenges and future recommendations are also proposed to be better used for recent covid-19 detection, point-of-care diagnostic, food safety, and other fields.

DNAzyme recognition triggered cascade signal amplification for rapid and highly sensitive visual detection of uranyl ions

A 40 min rapid and highly sensitive assay for visualized detection of UO22+ in water samples is reported. A dynamic range 1~50 nM and a LOD of 0.48 nM were obtained. Concentrations as low as 5 nM UO22+ could be distinguished by the naked eye.

DNA Based and Stimuli-Responsive Smart Nanocarrier for Diagnosis and Treatment of Cancer: Applications and Challenges

The rapid development of multidrug co-delivery and nano-medicines has made spontaneous progress in tumor treatment and diagnosis. DNA is a unique biological molecule that can be tailored and molded into various nanostructures. The addition of ligands or stimuli-responsive elements enables DNA nanostructures to mediate highly targeted drug delivery to the cancer cells. Smart DNA nanostructures, owing to their various shapes, sizes, geometry, sequences, and characteristics, have various modes of cellular internalization and final disposition. On the other hand, functionalized DNA nanocarriers have specific receptor-mediated uptake, and most of these ligand anchored nanostructures able to escape lysosomal degradation. DNA-based and stimuli responsive nano-carrier systems are the latest advancement in cancer targeting. The data exploration from various studies demonstrated that the DNA nanostructure and stimuli responsive drug delivery systems are perfect tools to overcome the problems existing in the cancer treatment including toxicity and compromised drug efficacy. In this light, the review summarized the insights about various types of DNA nanostructures and stimuli responsive nanocarrier systems applications for diagnosis and treatment of cancer.

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.

Accurate Detection of Target MicroRNA in Mixed Species of High Sequence Homology Using Target-Protection Rolling Circle Amplification

The close relationships of miRNAs with human diseases highlight the urgent needs for miRNA detection. However, the accurate detection of a target miRNA in mixed miRNAs of high sequence homology presents a great challenge. Herein, a novel method called target-protection rolling circle amplification (TP-RCA) is proposed for this purpose. The protective probe is designed so that it can form a fully complementary duplex with the target miRNA and can also mismatch duplexes with other nontarget miRNAs. These duplexes are treated with a single strand-specific nuclease. Consequently, only the target miRNA in a perfect-match duplex can resist the cleavage of nuclease, whereas the nontarget miRNAs in mismatched duplexes will be digested completely. The protected target miRNA can be detected using RCA reactions. MicroRNA let-7 family members (let-7a-let-7f) and nuclease CEL I were used as proof-of-concept models to evaluate the feasibility of the TP-RCA method under different experimental conditions. The experimental results show that the TP-RCA method can unambiguously detect the target let-7 species in mixtures of let-7 family members even though they may differ by only a single nucleotide. This TP-RCA method significantly improves the detection specificity of miRNAs.

Dual-Signal Amplification Strategy for Sensitive MicroRNA Detection Based on Rolling Circle Amplification and Enzymatic Repairing Amplification

MicroRNAs (miRNAs) play crucial regulatory roles as post-transcriptional regulators for gene expression and serve as promising biomarkers for diagnosis and prognosis of diseases. Herein, a dual-signal amplification method has been developed for sensitive and selective detection of miRNA based on rolling circle amplification (RCA) and enzymatic repairing amplification (ERA) with low nonspecific background. This strategy designs a padlock probe that can be cyclized in the presence of target miRNA to initiate the RCA reaction, after which the TaqMan probes that are complementary to the RCA products can be cyclically cleaved to produce obvious fluorescence signals with the help of endonuclease IV (Endo IV). Attributed to the dual-signal amplification procedure and the high fidelity of Endo IV, the RCA-ERA method allows quantitative detection of miR-21 in a dynamic range from 2 pM to 5 nM with a low background signal. Moreover, it has the ability to discriminate single-base difference between miRNAs and shows good performance for miRNA detection in complex biological samples. The results demonstrate that the RCA-ERA assay holds a great promise for miRNA-based diagnostics.

Electrochemical Biosensors for Detection of MicroRNA as a Cancer Biomarker: Pros and Cons

Cancer is the second most fatal disease in the world and an early diagnosis is important for a successful treatment. Thus, it is necessary to develop fast, sensitive, simple, and inexpensive analytical tools for cancer biomarker detection. MicroRNA (miRNA) is an RNA cancer biomarker where the expression level in body fluid is strongly correlated to cancer. Various biosensors involving the detection of miRNA for cancer diagnosis were developed. The present review offers a comprehensive overview of the recent developments in electrochemical biosensor for miRNA cancer marker detection from 2015 to 2020. The review focuses on the approaches to direct miRNA detection based on the electrochemical signal. It includes a RedOx-labeled probe with different designs, RedOx DNA-intercalating agents, various kinds of RedOx catalysts used to produce a signal response, and finally a free RedOx indicator. Furthermore, the advantages and drawbacks of these approaches are highlighted.

An enzyme-free electrochemical biosensor based on target-catalytic hairpin assembly and Pd@UiO-66 for the ultrasensitive detection of microRNA-21

MicroRNA-21 (miR-21) has been widely investigated as important biomarkers for cancer diagnosis and treatment. Herein, a highly sensitive nonenzymatic electrochemical biosensor based on Pd@metal-organic frameworks (Pd@UiO-66) and target-catalytic hairpin assembly (CHA) with target recycling approach has been proposed for the detection of miR-21. The proposed biosensor integrates the efficient CHA strategy and excellent electrocatalytic performance of Pd@UiO-66 nanocomposites. The concentration of miRNA-21 is related to the amount of the adsorbed electrocatalyst, leading to the different electrochemical signals for readout towards paracetamol (AP). This biosensor shows a low limit of detection of 0.713 fM with the dynamic range of 20 fM -600 pM under the optimal experimental conditions, providing a powerful platform for detecting miR-21. Furthermore, the designed biochemical self-assembly strategy of this electrochemical biosensor is promising candidate for potential applications in the analysis of other important genetic biomarkers for early diagnosis of cancers.

Low-Dimension Nanomaterial-Based Sensing Matrices for Antibiotics Detection: A Mini Review

Antibiotics, a kind of secondary metabolite with antipathogen effects as well as other properties, are produced by microorganisms (including bacterium, fungi, and actinomyces) or higher animals and plants during their lives. Furthermore, as a chemical, an antibiotic can disturb the developmental functions of other living cells. Moreover, it is impossible to avoid its pervasion into all kinds of environmental media via all kinds of methods, and it thus correspondingly becomes a trigger for environmental risks. As described above, antibiotics are presently deemed as a new type of pollution, with their content in media (for example, water, or food) as the focus. Due to their special qualities, nanomaterials, the most promising sensing material, can be adopted to produce sensors with extraordinary detection performance and good stability that can be applied to detection in complicated materials. For low-dimensional (LD) nanomaterials, the quantum size effect, and dielectric confinement effect are particularly strong. Therefore, they are most commonly applied in the detection of antibiotics. This article focuses on the influence of LD nanomaterials on antibiotics detection, summarizes the application of LD nanomaterials in antibiotics detection and the theorem of sensors in all kinds of antibiotics detection, illustrates the approaches to optimizing the sensitivity of sensors, such as mixture and modification, and also discusses the trend of the application of LD nanomaterials in antibiotics detection.

Precision medicine, bioanalytics and nanomaterials: toward a new generation of personalized portable diagnostics

The customization of disease treatment focused on genetic, environmental and lifestyle factors of individual patients, including tailored medical decisions and treatments, is identified as precision medicine. This approach involves the combination of various aspects such as the collection and processing of a large amount of data, the selection of optimized and personalized drug dosage for each patient and the development of selective and reliable analytical tools for the monitoring of clinical, genetic and environmental parameters. In this context, miniaturized, compact and ultrasensitive bioanalytical devices play a crucial role for achieving the goals of personalized medicine. In this review, the latest analytical technologies suitable for providing portable and easy-to-use diagnostic tools in clinical settings will be discussed, highlighting new opportunities arising from nanotechnologies, offering peculiar perspectives and opportunities for precision medicine.

A carbon nanocoil-based flexible tip for a live cell study of mechanotransduction and electro-physiological characteristics

The responses of living cells to external mechanical and electrical stimulation play important roles in regulating their biological functions and behaviors, and the response mechanisms have attracted great attention. Global stimulation on cells is generally used in traditional methods, but it is insufficient to investigate the mechanism of a dynamic physiological response at the subcellular level. At present, there is still lack of a low-cost and easy-operated method to apply local mechanical force and electrical stimulation on living cells. In this study, an individual carbon nanocoil (CNC) is used as a microscale noninvasive tool for local stimulation on a single cell, and a living cell imaging technology, fluorescence resonance energy transfer (FRET), is adopted to determine the responses of cells. After demonstrating that CNCs have low cytotoxicity to be applied in the biological field, an individual CNC is used as a needle tip to apply local mechanical force on a single osteosarcoma cell, which is transfected with a Src FRET biosensor to explore the mechano-physiological response. A spatially increasing and polarized Src protein activation is observed on the stimulated cell. Moreover, a single CNC is also used as an electrode to exert periodic local electrical stimulation. Osteosarcoma cells transfected with calcium-FRET biosensors show notable spatial-polarized FRET emission ratio distribution, and the FRET ratio shows a recoverable tendency towards the initial state after withdrawing the electrical stimulation. The cell biofunctions and structures are not damaged during the experiment process, which indicates that CNC is a kind of non-invasive and bio-safe tip. The CNC tip is a powerful tool for exploring the mechanotransduction and electro-physiological characteristics of living cells.

Detection of microRNA using enzyme-assisted amplifying and DNA-templated silver nanoclusters signal-off fluorescence bioassay

A Simple and fast analysis strategy of fluorescence quenching based on DNA-templated silver nanoclusters was developed for detection of miR-122 related to diseases such as human liver. We used Exo III to cleave the silver cluster template and assist in the DNA-RNA complex cycle. When the target is absent, the silver cluster template remains intact, and DNA-AgNCs are generated under the action of AgNO₃/NaBH₄, producing a strong background fluorescence signal. Once the target is added, the site of the Exo III occurs after a series of hybridization cycles, the Exo III acts, the template DNA is continuously hydrolyzed, and the fluorescence intensity of the system is significantly reduced. By comparing the changes in the fluorescence signal, we found that this strategy has good sensitivity and the detection limit is as low as 84.0 pM. The strategy also has excellent discriminating ability and good selectivity, it can provide a persuasive reference for the early diagnosis of liver cancer and hepatitis.

Colorimetric and fluorescent dual-mode detection of microRNA based on duplex-specific nuclease assisted gold nanoparticle amplification

MicroRNAs (miRNAs) are attractive candidates for biomarkers for early cancer diagnosis, and play vital roles in physiological and pathological processes. In this work, we developed a colorimetric and fluorescent dual-mode sensor for miRNA detection based on the optical properties of gold nanoparticles (AuNPs) and the duplex-specific nuclease (DSN)-assisted signal amplification technique. In brief, FAM labelled hairpin probes (HPs) were immobilized on AuNPs, and fluorescence was efficiently quenched by the vicinity of the fluorophores to the AuNPs surface. In the presence of target miRNAs, the HPs could specifically hybridize with miRNAs and the DNA strand in the DNA/RNA heteroduplexes could be subsequently hydrolyzed by DSN. As a result, numbers of fluorophores were released into the solution, resulting in obvious fluorescence signal recovery. Meanwhile, the target miRNAs were able to participate in other hybridization reactions. With the DSN-assisted signal amplification technique, lots of gold nanoparticles were produced with short-chain DNA on their surface, which could aggregate in salt solution and result in a colorimetric detection. The proposed dual-mode strategy offers a sensitive, accurate and selective detection method for miRNAs. One reason is that the stem of the HPs was elaborately designed to avoid hydrolyzation by DSN under optimal conditions, which ensures a relatively low background and high sensitivity. The other is that the dual-mode strategy is more beneficial for enhancing the accuracy and reproducibility of the measurements. Moreover, the unique selective-cutting ability and single-base mismatch differentiation capability of the DSN also give rise to a satisfactory selectivity. This demonstrated that the developed method could quantitatively detect miR-21 down to 50 pM with a linear calibration range from 50 pM to 1 nM, and the analytical assay of target miRNAs in cell lysate samples revealed its great potential for application in biomedical research and clinical diagnostics.

Facile and Label-Free Electrochemical Biosensors for MicroRNA Detection Based on DNA Origami Nanostructures

MicroRNAs (miRNAs) have emerged as the promising molecular biomarkers for early diagnosis and enhanced understanding of the molecular pathogenesis of cancers as well as certain diseases. Here, a facile, label-free, and amplification-free electrochemical biosensor was developed to detect miRNA by using DNA origami nanostructure-supported DNA probes, with methylene blue (MB) serving as the hybridization redox indicator, for the first time. Specifically, the use of cross-shaped DNA origami nanostructures containing multiple single-stranded DNA probes at preselected locations on each DNA nanostructure could increase the accessibility and the recognition efficiency of the probes (due to the rational controlled density of DNA probes). The successful immobilization of DNA origami probes and their hybridization with targeted miRNA-21 molecules was confirmed by electrochemical impedance spectroscopy and cyclic voltammetry methods. A differential pulse voltammetry technique was employed to record the oxidation peak current of MB before and after target hybridization. The linear detection range of this biosensor was from 0.1 pM to 10.0 nM, with a lower detection limit of 79.8 fM. The selectivity of the miRNA biosensor was also studied by observing the discrimination ability of single-base mismatched sequences. Because of the larger surface area and unprecedented customizability of DNA origami nanostructures, this strategy demonstrated great potential for sensitive, selective, and label-free determination of miRNA for translational biomedical research and clinical applications.

Exonuclease-assisted target recycling for ultrasensitive electrochemical detection of microRNA at vertically aligned carbon nanotubes

As an important biomarker for early disease diagnosis, microRNA-21 (miRNA-21) has attracted considerable attention owing to its accurate detection. Herein we combine the one-step biorecognition reaction at a vertically aligned nanostructure-based biosensor with the T7 exonuclease (Exo)-assisted target recycling to develop a novel electrochemical bioassay method for miRNA-21 detection. The vertically aligned nanointerface is constructed through the covalent attachment of terminally carboxylated single-walled carbon nanotubes (SWCNTs) at an aryldiazonium salt-modified electrode, which enables the noncovalent adsorption of a ferrocene-labeled single-stranded signal DNA to obtain the biosensor. Upon its incubation with a target miRNA-21 solution, DNA/RNA hybridized duplexes will form and release from the electrode surface, leading to the corresponding electrochemical signal decrease of the biosensor. Moreover, this biorecognition reaction can also trigger the T7 Exo-assisted target recycling to achieve great signal amplification. Together with the highly efficient biorecognition and excellent electron transfer promotion at the vertically aligned SWCNTs, this biosensor exhibits a wide linear range varying from 0.01 to 100 pM and a low detection limit down to 3.5 fM. Considering its obvious performance superiority and convenient manipulations, this vertically aligned SWCNT-based electrochemical biosensing method has extensive potential for practical applications.

Nanoarchitecture Frameworks for Electrochemical miRNA Detection

With revolutionary advances in next-generation sequencing, the human transcriptome has been comprehensively interrogated. These discoveries have highlighted the emerging functional and regulatory roles of a large fraction of RNAs suggesting the potential they might hold as stable and minimally invasive disease biomarkers. Although a plethora of molecular-biology- and biosensor-based RNA-detection strategies have been developed, clinical application of most of these is yet to be realized. Multifunctional nanomaterials coupled with sensitive and robust electrochemical readouts may prove useful in these applications. Here, we summarize the major contributions of engineered nanomaterials-based electrochemical biosensing strategies for the analysis of miRNAs. With special emphasis on nanostructure-based detection, this review also chronicles the needs and challenges of miRNA detection and provides a future perspective on the presented strategies.

High-Fidelity and Rapid Quantification of miRNA Combining crRNA Programmability and CRISPR/Cas13a trans-Cleavage Activity

MicroRNAs (miRNAs) are short noncoding RNAs that post-transcriptionally regulate gene expression. It has been proved that the aberrant expression of miRNAs is related to disease and miRNAs can serve as potential biomarkers for early tumor diagnosis. The clustered regularly interspaced short palindromic repeats (CRISPR)/Cas13a is a recently discovered CRISPR-RNA (crRNA) guided RNA manipulation tool. The recognition of target RNA can morphologically activate the robust nonspecific trans ribonuclease activity of Cas13a. This unique property makes Cas13a ideal for nucleic acid detection. Herein, we first exploited CRISPR/LbuCas13a to directly detect miRNAs with high specificity and simplicity. A limit of detection (LOD) as low as 4.5 amol was achieved by this one-step assay within 30 min, and the dynamic range spanned 4 orders of magnitude from 10 amol to 100 fmol. More importantly, single nucleotide variation, even at the end of target miRNA, can be discriminated by rationally programmed crRNA. In addition, the practical application ability of this Cas13a/crRNA-based signal amplification strategy was demonstrated by miRNA quantification in complex biological samples (total small RNA). With excellent reliability, sensitivity, and simple to implement features, this method promises a great potential for early diagnosis of miRNA-related disease. Moreover, the systematic analysis of the crRNA design could provide guidance to further develop Cas13a-based molecular diagnoses.

Highly sensitive and specific electrochemical biosensor for microRNA-21 detection by coupling catalytic hairpin assembly with rolling circle amplification

BACKGROUND

MicroRNA plays a significant role in gene regulation and is usually regarded as an important biological marker. Electrochemical biosensors are excellent tools for microRNA detection.

METHODS

In this experiment, we take miRNA-21 as a target, combining catalytic hairpin assembly (CHA) and rolling circle amplification (RCA) as a dual signal amplification strategy for the detection of microRNA in an electrochemical biosensor.

RESULTS

This strategy has a good linear range of 0.5-12 500 pmol of microRNA. The limit of detection (LOD) for miRNA is as low as 290 fmol, showing excellent performance. Finally, this method has been successfully applied to the detection of miRNA-21 from HeLa cells.

CONCLUSION

This method can be applied not only for microRNA detection with high sensitivity and speed, but can also detect small molecules and proteins combined with aptamers.

Substrate-free and label-free electrocatalysis-assisted biosensor for sensitive detection of microRNA in lung cancer cells

We develop a substrate-free and label-free electrocatalysis-assisted biosensor for sensitive detection of microRNA using the iron-embedded nitrogen-rich carbon nanotubes (FeCN) as the catalytic elements. This biosensor exhibits excellent selectivity and high sensitivity with a detection limit of 8.53 × 10^-16 M and a large dynamic range of 6 orders of magnitude. It can be further applied for accurate quantification of microRNA in lung cancer cells.

Recent advances in nanomaterial-based electrochemical and optical sensing platforms for microRNA assays

This review describes recent efforts in the application of nanomaterials as sensing elements in electrochemical and optical miRNAs assays.

Triple-helix molecular-switch-actuated exponential rolling circular amplification for ultrasensitive fluorescence detection of miRNAs

We have developed a rapid and high-efficiency fluorescent biosensing platform based on triple-helix molecular-switch (THMS)-actuated exponential rolling circular amplification (RCA) strategy for the ultrasensitive detection of miR-21.

A universal photoelectrochemical biosensor for dual microRNA detection based on two CdTe nanocomposites

A universal photoelectrochemical biosensor for dual microRNA detection has been successfully developed.

Liquid biopsy in combination with solid-state electrochemical sensors and nucleic acid amplification

Solid-state electrochemical sensors are developing as a new platform for liquid biopsy, combining detection and analysis of nucleic acids with isothermal nucleic acid amplification reactions.

Versatile fluorescence detection of microRNA based on novel DNA hydrogel-amplified signal probes coupled with DNA walker amplification

A novel DNA hydrogel-amplified versatile fluorescence platform combined with hybridization chain reaction (HCR) and DNA walking multiple amplification was developed for ultrasensitive detection of miRNA.

Classical Triplex Molecular Beacons for MicroRNA-21 and Vascular Endothelial Growth Factor Detection

Triplex molecular beacons (tMBs) possess great potential in biological sensing because of the pH responsiveness and controllability of binding strength. Here, we systematically investigate and rationally design a classical tMB for convenient detection of microRNA-21, a well-known biomarker of cardio-cerebrovascular diseases. In the tMB, we employ the complementary sequence of miR-21 as the loop and the sequences of protonated cytosine-guanine-cytosine (C-G•C+) and thymine-adenine-thymine (T-A•T) as the triplex stem, in which both the Watson-Crick and Hoogsteen base-pairing control the binding strength in cooperation. It is demonstrated for the first time that the presence of miR-21 would only break the Hoogsteen base-pairing in the stem and hybridize with the tMB to form the rigid heterozygous hybrid duplex structure. These would hinder the fluorescence resonance energy transfer (FRET) between the fluorophore (FAM) and quencher (BHQ1) labeled at the ends of the oligonucleotide, and the fluorescence recovery degree of FAM can be used as the standard to quantitate the miR-21. More significantly, the excellent adjustability and sensitivity of our tMBs have been confirmed by constructing the corresponding duplex molecular beacon (dMB) for comparison. The fluorophore FAM in the tMB could be replaced by the fluorescent DNA/silver nanoclusters, which exhibits the universal applicability of energy donor and receptor selection for tMB. Furthermore, our proposed tMB could also be developed as an aptasensor for the detection of vascular endothelial growth factor (VEGF) by only introducing the complementary sequence of its aptamer into the tMB. This work is of great significance for the systematic study of tMBs for the detection of biomarkers such as nucleic acids and proteins.

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.

Sandwich DNA Hybridization Fluorescence Resonance Energy-Transfer Strategy for miR-122 Detection by Core-Shell Upconversion Nanoparticles

An upconversion nanoparticle (UCNP)-based fluorescence resonance energy-transfer (FRET) strategy is normally restricted by the complicated preparations, low energy-transfer efficiency, and the challenge on improving specificity. Herein, simple DNA-functionalized UCNPs were designed as energy donors for constructing a FRET-based probe to detect the liver-specific microRNA 122 (miR-122). To improve FRET efficiency, UCNPs were constructed with confined core-shell structures, in which emitting ions were precisely located in the thin shell to make them close enough to external energy acceptors. Subsequently, capture DNA was simply functionalized on the outer surface of UCNPs based on ligand exchange that contributed to shortening the energy-transfer distance without extra modification. To gain high specificity, the donor-to-acceptor distance of FRET was controlled by a sandwich DNA hybridization structure using two shorter DNAs with designed complementary sequences (capture DNA and dye-labeled report DNA) to capture the longer target of miR-122. Therefore, the sensitive detection of miR-122 was achieved based on the decreased signals of UCNPs and the increased signals of the dye labeled on reported DNA. With good biocompatibility, this method has been further applied to cancer cell imaging and in vivo imaging, which opened up a new avenue to the sensitive detection and imaging of microRNA in biological systems.

A common anchor facilitated GO-DNA nano-system for multiplex microRNA analysis in live cells

The design of a nano-system for the detection of intracellular microRNAs is challenging as it must fulfill complex requirements, i.e., it must have a high sensitivity to determine the dynamic expression level, a good reliability for multiplex and simultaneous detection, and a satisfactory biostability to work in biological environments. Instead of employing a commonly used physisorption or a full-conjugation strategy, here, a GO-DNA nano-system was developed under graft/base-pairing construction. The common anchor sequence was chemically grafted to GO to base-pair with various microRNA probes; and the hybridization with miRNAs drives the dyes on the probes to leave away from GO, resulting in "turned-on" fluorescence. This strategy not only simplifies the synthesis but also efficiently balances the loading yields of different probes. Moreover, the conjugation yield of GO with a base-paired hybrid has been improved by more than two-fold compared to that of the conjugation with a single strand. We demonstrated that base-paired DNA probes could be efficiently delivered into cells along with GO and are properly stabilized by the conjugated anchor sequence. The resultant GO-DNA nano-system exhibited high stability in a complex biological environment and good resistance to nucleases, and was able to accurately discriminate various miRNAs without cross-reaction. With all of these positive features, the GO-DNA nano-system can simultaneously detect three miRNAs and monitor their dynamic expression levels.

Fluorescent analysis of bioactive molecules in single cells based on microfluidic chips

Single-cell analysis of bioactive molecules is an essential strategy for a better understanding of cell biology, exploring cell heterogeneity, and improvement of the ability to detect early diseases. In single-cell analysis, highly efficient single-cell manipulation techniques and high-sensitive detection schemes are in urgent need. The rapid development of fluorescent analysis techniques combined with microfluidic chips have offered a widely applicable solution. Thus, in this review, we mainly focus on the application of fluorescence methods in components analysis on microchips at a single-cell level. By targeting different types of biological molecules in cells such as nucleic acids, proteins, and active small molecules, we specially introduce and comment on their corresponding fluorescent probes, fluorescence labelling and sensing strategies, and different fluorescence detection instruments used in single-cell analysis on a microfluidic chip. We hope that through this review, readers will have a better understanding of single-cell fluorescence analysis, especially for single-cell component fluorescence analysis based on microfluidic chips.

Recent advances in microRNA detection

Recent advances in miRNA detection methods and new applications.

Methods and novel technology for microRNA quantification in colorectal cancer screening

The screening and diagnosis of colorectal cancer (CRC) currently relies heavily on invasive endoscopic techniques as well as imaging and antigen detection tools. More accessible and reliable biomarkers are necessary for early detection in order to expedite treatment and improve patient outcomes. Recent studies have indicated that levels of specific microRNA (miRNA) are altered in CRC; however, measuring miRNA in biological samples has proven difficult, given the complicated and lengthy PCR-based procedures used by most laboratories. In this manuscript, we examine the potential of miRNA as CRC biomarkers, summarize the methods that have commonly been employed to quantify miRNA, and focus on novel strategies that can improve or replace existing technology for feasible implementation in a clinical setting. These include isothermal amplification techniques that can potentially eliminate the need for specialized thermocycling equipment. Additionally, we propose the use of near-infrared (NIR) probes which can minimize autofluorescence and photobleaching and streamline quantification without tedious sample processing. We suggest that novel miRNA quantification tools will be necessary to encourage new discoveries and facilitate their translation to clinical practice.

Carbon Nanomaterial Based Biosensors for Non-Invasive Detection of Cancer and Disease Biomarkers for Clinical Diagnosis

The early diagnosis of diseases, e.g., Parkinson's and Alzheimer's disease, diabetes, and various types of cancer, and monitoring the response of patients to the therapy plays a critical role in clinical treatment; therefore, there is an intensive research for the determination of many clinical analytes. In order to achieve point-of-care sensing in clinical practice, sensitive, selective, cost-effective, simple, reliable, and rapid analytical methods are required. Biosensors have become essential tools in biomarker sensing, in which electrode material and architecture play critical roles in achieving sensitive and stable detection. Carbon nanomaterials in the form of particle/dots, tube/wires, and sheets have recently become indispensable elements of biosensor platforms due to their excellent mechanical, electronic, and optical properties. This review summarizes developments in this lucrative field by presenting major biosensor types and variability of sensor platforms in biomedical applications.

A universal colorimetry for nucleic acids and aptamer-specific ligands detection based on DNA hybridization amplification

We present a universal amplified-colorimetric for detecting nucleic acid targets or aptamer-specific ligand targets based on gold nanoparticle-DNA (GNP-DNA) hybridization chain reaction (HCR). The universal arrays consisted of capture probe and hairpin DNA-GNP. First, capture probe recognized target specificity and released the initiator sequence. Then dispersed hairpin DNA modified GNPs were cross-linked to form aggregates through HCR events triggered by initiator sequence. As the aggregates accumulate, a significant red-to purple color change can be easily visualized by the naked eye. We used miRNA target sequence (miRNA-203) and aptamer-specific ligand (ATP) as target molecules for this proof-of-concept experiment. Initiator sequence (DNA2) was released from the capture probe (MNP/DNA1/2 conjugates) under the strong competitiveness of miRNA-203. Hairpin DNA (H1 and H2) can be complementary with the help of initiator DNA2 to form GNP-H1/GNP-H2 aggregates. The absorption ratio (A₆₂₀/A₅₂₀) values of solutions were a sensitive function of miRNA-203 concentration covering from 1.0 × 10^-11 M to 9.0 × 10^-10 M, and as low as 1.0 × 10^-11 M could be detected. At the same time, the color changed from light wine red to purple and then to light blue have occurred in the solution. For ATP, initiator sequence (5'-end of DNA3) was released from the capture probe (DNA3) under the strong combination of aptamer-ATP. The present colorimetric for specific detection of ATP exhibited good sensitivity and 1.0 × 10^-8 M ATP could be detected. The proposed strategy also showed good performances for qualitative analysis and quantitative analysis of intracellular nucleic acids and aptamer-specific ligands.