Ultrasensitive electrochemical detection of microRNA with star trigon structure and endonuclease mediated signal amplification

A versatile upconversion-based multimode lateral flow platform for rapid and ultrasensitive detection of microRNA towards health monitoring

MicroRNAs are small single-stranded RNA molecules associated with gene expression and immune response, suggesting their potential as biomarkers for health monitoring. Herein, we designed a novel upconversion-based multimode lateral flow assay (LFA) system to detect microRNAs in body fluids by simultaneously producing three unique signals within a detection strip. The core-shell Au-DTNB@Ag nanoparticles act as both the Raman reporters and acceptors, quenching fluorescence from upconversion nanoparticles (UCNPs, NaYF4: Yb3+, Er3+) via the Förster resonance energy transfer mechanism. Using microRNA-21 as a representative analyte, the LFA system offers remarkable detection range from 2 nM to 1 fM, comparable to outcomes from signal amplification methods, due to the successful single-layer self-assembly of UCNPs on the NC membrane, which greatly enhances both the convenience and sensitivity of the LFA technique. Additionally, our proprietary fluorescence-Raman detection platform simplifies result acquisition by reducing procedural intricacies. The biosensor, when evaluated with diverse bodily fluids, showed remarkable selectivity and sustained stability. Importantly, our LFA biosensor effectively identified periodontitis and lung cancer patients from healthy subjects in genuine samples, indicating significant potential for disease prediction, early diagnosis, and progression tracking. This system holds promise as a multifunctional tool for various biomarker assays.

A label-free electrochemical biosensor based on PBA-Au-MXene QD for miR-122 detection in serum samples

A poly(n-butyl acrylate)-gold-MXene quantum dots (PBA-Au-MXene QD) nanocomposite-based biosensor is presented that is modified by unique antisense single-stranded DNA (ssDNA) and uses the electrochemical detection methods of DPV, CV, and EIS to early detect miR-122 as a breast cancer biomarker in real clinical samples. This fabrication method is based on advanced nanotechnology, at which a poly(n-butyl acrylate) (PBA) as a non-conductive polymer transforms into a conductive composite by incorporating Au-MXene QD. This biosensor had a limit of detection (LOD) of 0.8 zM and a linear range from 0.001 aM to 1000 nM, making it capable of detecting the low concentrations of miR-122 in patient samples. Moreover, it allows approximately 100% sensitivity and 100% specificity for miR-122 without extraction. The synthesis and detection characteristics were evaluated by different complementary tests such as AFM, FTIR, TEM, and FESEM. This new biosensor can have a high potential in clinical applications to detect breast cancer early and hence improve patient outcomes.

Modern Methods for Assessment of microRNAs

The review discusses modern methods for the quantitative and semi-quantitative analysis of miRNAs, which are small non-coding RNAs affecting numerous biological processes such as development, differentiation, metabolism, and immune response. miRNAs are considered as promising biomarkers in the diagnosis of various diseases.

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.

New trends in the development of electrochemical biosensors for the quantification of microRNAs

MicroRNAs (miRNAs) are non-coding regulatory RNAs that play an important role in RNA silencing and post-transcriptional gene expression regulation. Since their dysregulation has been associated with Alzheimer disease, cardiovascular diseases and different types of cancer, among others, miRNAs can be used as biomarkers for early diagnosis and prognosis of these diseases. The methods commonly used to quantify miRNAs are, in general, complex, costly, with limited application for point-of-care devices or resource-limited facilities. Electrochemical biosensors, mainly those based on nanomaterials, have emerged as a promising alternative to the conventional miRNA detection methods and have paved the way to the development of sensitive, fast, and low-cost detection systems. This review is focused on the most relevant contributions performed in the field of electrochemical miRNAs biosensors between 2017 and the beginning of 2020. The main contribution of this article is the critical discussion of the different amplification strategies and the comparative analysis between amplified and non-amplified miRNA electrochemical biosensing and between the different amplification schemes. Particular emphasis was given to the importance of the nanostructures, enzymes, labelling molecules, and special sequences of nucleic acids or analogues on the organization of the different bioanalytical platforms, the transduction of the hybridization event and the generation the analytical signal.

A T7 exonuclease assisted dual-cycle signal amplification assay of miRNA using nanospheres-enhanced fluorescence polarization

Based on streptavidin coated nanospheres and T7 exonuclease assisted dual-cycle signal amplification, we developed a novel sensitive fluorescence polarization detection method for miRNA. When target miRNA was present in the system, hairpin probe hybridized with miRNA, forming a double-stranded structure. The 5' end of hairpin probe was then recognized and digested by T7 exonuclease, releasing the non-degraded single strand DNA fragments and miRNA. The released target miRNA could trigger the next cycle of hybridization and digestion, releasing more non-degraded fragments from hairpin probe. The fragments could hybridize with a signal probe (with carboxyfluorescein modification at 5'-end and biotin modification at 3'-end). The formed blunt 5'-end of signal probe was then recognized and degraded by T7 exonuclease, releasing the fragments and the fluorophore carboxyfluorescein. The next cycle of hybridization and digestion of signal probe was triggered by the released fragment at the same time. The free carboxyfluorescein cannot connect with streptavidin coated nanospheres which were used as the fluorescence polarization signal amplifier. So, there was a big change of fluorescence polarization signal after adding miRNA into the detection system, due to the different fluorescence polarization signal between nanospheres-captured intact signal probe and free carboxyfluorescein. The detection limit of this method is about 0.001 nM, and it has a good selectivity. In addition, it was also applicable to determine target miRNA in total miRNA extracts and compare the expression level of target miRNA in different cells. Consequently, the proposed method is expected to be used for the potential cancer diagnosis and the related biomedical research.

Unusual fluorescence of o-phenylazonaphthol derivatives with aggregation-induced emission and their use in two-photon cell imaging

Unusual fluorescence of o-phenylazonaphthol derivatives with aggregated-induced emission (AIE) is reported for the first time, which can be used in two-photon cell imaging applications.

A bright red-emitting flavonoid for Al3+ detection in live cells without quenching ICT fluorescence

A bright red-emitting flavonoid derivative was synthesized, which exhibited a large Stokes shift (Δλ > 150 nm) and high fluorescence quantum yields (ϕ_fl = 0.10–0.35).

An enzyme-free sensitive electrochemical microRNA-16 biosensor by applying a multiple signal amplification strategy based on Au/PPy-rGO nanocomposite as a substrate

In present study, a sensitive and effective electrochemical microRNA (miRNA) sensing platform is successfully developed by integrating gold nanoparticles/polypyrrole-reduced graphene oxide (Au/PPy-rGO), catalyzed hairpin assembly (CHA) and hybridization chain reaction (HCR) multiple signal amplification strategy. Firstly, Au/PPy-rGO was employed onto a bare GCE by electrodeposition that can greatly enhanced conductivity and effectively immobilize probes. Then, the thiolated capture probes (SH-CP) were self-assembled on the Au/PPy-rGO modified GCE via Au-S bond. The target miRNA triggered the dynamic assembly of the two hairpin substrates (H1 and H2), leading to the cyclicality of the target miRNA and the formation of H1-H2 complexes without the assistance of enzyme. Subsequently, the newly emerging DNA fragment of H2 triggered the HCR when a mixture solution (hairpins H3 and H4) and produced dsDNA polymers. Finally, a substantial amount of methylene blue (MB) as signal indicator was intercalated into the minor groove of the long dsDNA polymers to achieve detected electrochemical signal. The fabricated sensor is able to detect miRNA-16 (model target) with concentration range from 10 fM to 5 nM with a low detection limit (LOD) of 1.57 fM (S/N = 3). Current research suggests that the developed multiple signal amplification platform has a great potential for the applications in the field of biomedical research and clinical analysis.

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.

Label-free ultrasensitive detection of breast cancer miRNA-21 biomarker employing electrochemical nano-genosensor based on sandwiched AgNPs in PANI and N-doped graphene

MicroRNAs (miRNAs) are small, endogenous, noncoding RNAs, shown to be expressed abnormally in many tumors and identified as predictive biomarkers for early diagnosis of several cancers including the breast. Therefore, the label-free and highly sensitive detection of miRNAs is of critical significance. In this work, a highly sensitive and label-free nano-genosensor is developed for the detection of miRNA-21, a known breast cancer biomarker, based on a specific architecture of nitrogen-doped functionalized graphene (NFG), silver nanoparticles (AgNPs), and polyaniline (PANI) that resulted in a remarkable effect on signal amplification. Following the successful functionalization of the nanocomposite and immobilization of the specific sequence of the aminated complementary oligonucleotide of miRNA-21, the detection was performed using differential pulse voltammetry (DPV). The oxidation peak current of the redox probe under optimal conditions was determined to monitor the event hybridization of miRNA-21 biomarker. Applying this highly sensitive and optimized nano-biosensor enabled detection of a wide dynamic range of 10 fM-10 µM with a sensitivity of 2.5 µA cm^-2 and a low detection limit of 0.2 fM. This nano-biosensor also demonstrated highly reproducible results in the analysis of blood samples, with recoveries between 94% and 107%, and could be used for early detection of breast cancer by direct detection of the miRNA-21 in real clinical samples without any need to sample preparation, RNA extraction and/or amplification.

An isothermal electrochemical biosensor for the sensitive detection of microRNA based on a catalytic hairpin assembly and supersandwich amplification

A novel isothermal electrochemical biosensor was proposed for the sensitive detection of microRNA (miRNA) based on the ingenious combination of the target-catalyzed hairpin assembly (CHA) and supersandwich amplification strategies. Since miRNA-221 has been reported to be overexpressed in cancers and has been a potentially useful biomarker for the diagnosis of the related diseases, miRNA-221 was chosen as a model target miRNA. The target miRNA-221 triggered a toehold strand displacement assembly of the two hairpin substrates, which led to the cyclicality of the target miRNA and the CHA products. Subsequently, the CHA products hybridized with a capture probe on the electrode and the exposed stem of the CHA products was further used to propagate the supersandwich. After this, the signal probe was modified with horseradish peroxidase (HRP) to form a supersandwich multiplex HRP-DNA label, which could achieve an amplified electrochemical signal. Using the isothermal dual signal amplification strategies, miRNA-221 as low as 0.6 pM (3σ) could be detected. In addition, this biosensor showed high selectivity and could discriminate miRNA-221 from the homologous miRNAs. Note that human miRNA from cancer cells could also be detected and the results were in excellent agreement with those obtained using qRT-PCR. Given that the biosensor avoided the introduction of nanoparticles, the limitation of using the nanoparticles was overcome. The proposed biosensor has great potential for broad applications in the field of clinical analysis.

Research progresses on the functional polypeptides in the detection and imaging of breast cancer

Polypeptides as functional groups continue to garner significant interest in the detection and imaging of breast cancer, working as recognition elements, signal sources, building blocks and therapeutic reagents, etc.

Anion directing self-assembly of 2D and 3D water-stable silver(i) cation metal organic frameworks and their applications in real-time discriminating cysteine and DNA detection

Two water-stable silver(i) cation metal organic frameworks (MOFs), namely 2D MOF {[Ag(L)₂]BF₄}_n (1) and 3D MOF {[Ag₃(L)₃]·(H₂O)·(CF₃SO₃)₃}_n (2) (L = 1-(4-aminobenzyl)-1,2,4-triazole), have been prepared.

Electrochemical sensing of attomolar miRNA combining cascade strand displacement polymerization and reductant-mediated amplification

An electrochemical biosensor for miRNA assay with attomolar sensitivity was developed based on cascade strand displacement polymerization and reductant-mediated amplification.

Surface-Modified Mesh Filter for Direct Nucleic Acid Extraction and its Application to Gene Expression Analysis

Rapid and convenient isolation of nucleic acids (NAs) from cell lysate plays a key role for onsite gene expression analysis. Here, this study achieves one-step and efficient capture of NA directly from cell lysate by developing a cationic surface-modified mesh filter (SMF). By depositing cationic polymer via vapor-phase deposition process, strong charge interaction is introduced on the surface of the SMF to capture the negatively charged NAs. The NA capturing capability of SMF is confirmed by X-ray photoelectron spectroscopy, fluorescent microscopy, and zeta potential measurement. In addition, the genomic DNAs of Escherichia Coli O157:H7 can be extracted by the SMF from artificially infected food, and fluorescent signal is observed on the surface of SMF after amplification of target gene. The proposed SMF is able to provide a more simplified, convenient, and fast extraction method and can be applied to the fields of food safety testing, clinical diagnosis, or environmental pollutant monitoring.

Non-Invasive Breast Cancer Diagnosis through Electrochemical Biosensing at Different Molecular Levels

The rapid and accurate determination of specific circulating biomarkers at different molecular levels with non- or minimally invasive methods constitutes a major challenge to improve the breast cancer outcomes and life quality of patients. In this field, electrochemical biosensors have demonstrated to be promising alternatives against more complex conventional strategies to perform fast, accurate and on-site determination of circulating biomarkers at low concentrations in minimally treated body fluids. In this article, after discussing briefly the relevance and current challenges associated with the determination of breast cancer circulating biomarkers, an updated overview of the electrochemical affinity biosensing strategies emerged in the last 5 years for this purpose is provided highlighting the great potentiality of these methodologies. After critically discussing the most interesting features of the electrochemical strategies reported so far for the single or multiplexed determination of such biomarkers with demonstrated applicability in liquid biopsy analysis, existing challenges still to be addressed and future directions in this field will be pointed out.

Ultrasensitive electrochemical detection of Dicer1 3'UTR for the fast analysis of alternative cleavage and polyadenylation

Alternative cleavage and polyadenylation (APA) is involved in several important biological processes in animals, e.g. cell growth and development, and cancer progression. The increasing data show that cancer cells are inclined to produce mRNA isoforms with a shortened 3'UTR undergoing APA. For example, the Dicer1 isoform with a shorter 3'untranslated region (3'UTR) was found to be overexpressed in some cancer cells, which may be used as a potential novel prognostic biomarker for cancer. In the present work, a novel electrochemical biosensor for ultrasensitive determination of Dicer1 was designed by using gold nanoparticles and p-sulfonated calix[6]arene functionalized reduced graphene oxide (Au@SCX6-rGO) as nanocarriers. The results showed that the expressions of the shorter 3'UTR (Dicer1-S) both in BT474 and SKBR3 were obviously higher than those of the longer Dicer1 (Dicer1-L) by the constructed biosensor, which agreed well with the result analyzed by the RT-qPCR method. The detection ranges of Dicer1-S and Dicer1-L were 10^-14-10^-9 M and 10^-15-10^-10 M. The LODs were 3.5 and 0.53 fM. The specificity of the proposed biosensor was also very high. For the first time, the expressional analysis of different 3'UTRs caused by APA was studied by an electrochemical method. Moreover, the use of a macrocyclic host for constructing an electrochemical/biosensing platform has rarely been reported. The proposed electrochemical sensing strategy is thus expected to provide a new method for determination of novel biomarkers and a novel method for fast and cheap analysis of APA.

DNA Modified Fe3O4@Au Magnetic Nanoparticles as Selective Probes for Simultaneous Detection of Heavy Metal Ions

Driven by the urgent need to detect trace heavy metal ions in various real water samples, this article demonstrates for the first time an electrochemical biosensor based on DNA modified Fe₃O₄@Au magnetic nanoparticles (NPs). Three DNA probes are designed to contain certain mismatched base pairs. One is thiolated and modified on the surface of Fe₃O₄@Au NPs (DNA 1). The other two probes (DNA 2 and 3) are labeled with two independent electrochemical species. Stable structures of cytosine-Ag⁺-cytosine and thymine-Hg²⁺-thymine formed in the presence of Ag⁺ and Hg²⁺ can assist the hybridization of DNA 1/DNA 2 and DNA 1/DNA 3, which locate corresponding electrochemical species onto the surface of the magnetic NPs. The achieved nanocomposites are then used as selective electrochemical probes for the detection of heavy metal ions by recording the square wave voltammetry signals. Simultaneous detection of Ag⁺ and Hg²⁺ is demonstrated without significant interference, and their individual high sensitivities are fundamentally preserved, which meet the requirements of U.S. Environmental Protection Agency (USEPA). Furthermore, the proposed method has been challenged by various real water samples. The results confirm the DNA modified magnetic NPs based sensing method may have potential applications for the monitoring of heavy metal ions in real sample analysis.

Au nanoparticles/hollow molybdenum disulfide microcubes based biosensor for microRNA-21 detection coupled with duplex-specific nuclease and enzyme signal amplification

An ultrasensitive electrochemical biosensor for detecting microRNAs is fabricated based on hollow molybdenum disulfide (MoS₂) microcubes. Duplex-specific nuclease, enzyme and electrochemical-chemical-chemical redox cycling are used for signal amplification. Hollow MoS₂ microcubes constructed by ultrathin nanosheets are synthesized by a facile template-assisted strategy and used as supporting substrate. For biosensor assembling, biotinylated ssDNA capture probes are first immobilized on Au nanoparticles (AuNPs)/MoS₂ modified electrode in order to combine with streptavidin-conjugated alkaline phosphatase (SA-ALP). When capture probes hybridize with miRNAs, duplex-specific nuclease cleaves the formative duplexes. At the moment, the biotin group strips from the electrode surface and SA-ALP is incapacitated to attach onto electrode. Then, ascorbic acids induce the electrochemical-chemical-chemical redox cycling to produce electrochemical response in the presence of ferrocene methanol and tris (2-carboxyethyl) phosphine. Under optimum conditions, the proposed biosensor shows a good linear relationship between the current variation and logarithm of the microRNAs concentration ranging from 0.1fM to 0.1pM with a detection limit of 0.086fM (S/N=3). Furthermore, the biosensor is successfully applied to detect target miRNA-21 in human serum samples.

A plasmonic colorimetric strategy for visual miRNA detection based on hybridization chain reaction

In this work, a novel colorimetric strategy for miRNA analysis is proposed based on hybridization chain reaction (HCR)-mediated localized surface plasmon resonance (LSPR) variation of silver nanoparticles (AgNPs). miRNA in the sample to be tested is able to release HCR initiator from a solid interface to AgNPs colloid system by toehold exchange-mediated strand displacement, which then triggers the consumption of fuel strands with single-stranded tails for HCR. The final produced long nicked double-stranded DNA loses the ability to protect AgNPs from salt-induced aggregation. The stability variation of the colloid system can then be monitored by recording corresponding UV-vis spectrum and initial miRNA level is thus determined. This sensing system involves only four DNA strands which is quite simple. The practical utility is confirmed to be excellent by employing different biological samples.

Biosensors for breast cancer diagnosis: A review of bioreceptors, biotransducers and signal amplification strategies

Breast cancer is highly prevalent in females and accounts for second highest number of deaths, worldwide. Cumbersome, expensive and time consuming detection techniques presently available for detection of breast cancer potentiates the need for development of novel, specific and ultrasensitive devices. Biosensors are the promising and selective detection devices which hold immense potential as point of care (POC) tools. Present review comprehensively scrutinizes various breast cancer biosensors developed so far and their technical evaluation with respect to efficiency and potency of selected bioreceptors and biotransducers. Use of glycoproteins, DNA biomarkers, micro-RNA, circulatory tumor cells (CTC) and some potential biomarkers are introduced briefly. The review also discusses various strategies used in signal amplification such as nanomaterials, redox mediators, p19 protein, duplex specific nucleases (DSN) and redox cycling.

Ultrasensitive electrochemical sensing platform for microRNA based on tungsten oxide-graphene composites coupling with catalyzed hairpin assembly target recycling and enzyme signal amplification

An ultrasensitive electrochemical biosensor for microRNA (miRNA) is developed based on tungsten oxide-graphene composites coupling with catalyzed hairpin assembly target recycling and enzyme signal amplification. WO3-Gr is prepared by a simple hydrothermal method and then coupled with gold nanoparticles to act as a sensing platform. The thiol-terminated capture probe H1 is immobilized on electrode through Au-S interaction. In the presence of target miRNA, H1 opens its hairpin structure by hybridization with target miRNA. This hybridization can be displaced from the structure by another stable biotinylated hairpin DNA (H2), and target miRNA is released back to the sample solution for next cycle. Thus, a large amount of H1-H2 duplex is produced after the cyclic process. At this point, a lot of signal indicators streptavidin-conjugated alkaline phosphatase (SA-ALP) are immobilized on the electrode by the specific binding of avidin-biotin. Then, thousands of ascorbic acid, which is the enzymatic product of ALP, induces the electrochemical-chemical-chemical redox cycling to produce a strongly electrochemical response in the presence of ferrocene methanol and tris (2-carboxyethyl) phosphine. Under the optimal experimental conditions, the established biosensor can detect target miRNA down to 0.05fM (S/N=3) with a linear range from 0.1fM to 100pM, and discriminate target miRNA from mismatched miRNA with a high selectivity.

Design of a molecular imprinting biosensor with multi-scale roughness for detection across a broad spectrum of biomolecules

The molecular imprinting technique has tremendous applications in artificial enzymes, bioseparation, and sensor devices.

Isothermal Amplification of Nucleic Acids

Isothermal amplification of nucleic acids is a simple process that rapidly and efficiently accumulates nucleic acid sequences at constant temperature. Since the early 1990s, various isothermal amplification techniques have been developed as alternatives to polymerase chain reaction (PCR). These isothermal amplification methods have been used for biosensing targets such as DNA, RNA, cells, proteins, small molecules, and ions. The applications of these techniques for in situ or intracellular bioimaging and sequencing have been amply demonstrated. Amplicons produced by isothermal amplification methods have also been utilized to construct versatile nucleic acid nanomaterials for promising applications in biomedicine, bioimaging, and biosensing. The integration of isothermal amplification into microsystems or portable devices improves nucleic acid-based on-site assays and confers high sensitivity. Single-cell and single-molecule analyses have also been implemented based on integrated microfluidic systems. In this review, we provide a comprehensive overview of the isothermal amplification of nucleic acids encompassing work published in the past two decades. First, different isothermal amplification techniques are classified into three types based on reaction kinetics. Then, we summarize the applications of isothermal amplification in bioanalysis, diagnostics, nanotechnology, materials science, and device integration. Finally, several challenges and perspectives in the field are discussed.