Detection of microRNA by Electrocatalytic Amplification: A General Approach for Single-Particle Biosensing

Nanomaterials promote the fast development of electrochemical MiRNA biosensors

Cancer has become the leading cause of death worldwide. In recent years, molecular diagnosis has demonstrated great potential in the prediction and diagnosis of cancer. MicroRNAs (miRNAs) are short oligonucleotides that regulate gene expression and cell function and are considered ideal biomarkers for cancer detection, diagnosis, and patient prognosis. Therefore, the specific and sensitive detection of ultra-low quantities of miRNA is of great significance. MiRNA biosensors based on electrochemical technology have advantages of high sensitivity, low cost and fast response. Nanomaterials show great potential in miRNA electrochemical detection and promote the rapid development of electrochemical miRNA biosensors. Some methods and signal amplification strategies for miRNA detection in recent years are reviewed herein, followed by a discussion of the latest progress in electrochemical miRNA detection based on different types of nanomaterial. Future perspectives and challenges are also proposed for further exploration of nanomaterials to bring breakthroughs in electrochemical miRNA detection.

Impact electrochemistry for biosensing: advances and future directions

Impact electrochemistry allows for the investigation of the properties of single entities, ranging from nanoparticles (NPs) to soft bio-particles. It has introduced a novel dimension in the field of biological analysis, enhancing researchers' ability to comprehend biological heterogeneity and offering a new avenue for developing novel diagnostic devices for quantifying biological analytes. This review aims to summarize the recent advancements in impact electrochemistry-based biosensing over the past two to three years and provide insights into the future directions of this field.

Artificial Intelligence-Assisted Multiparameter Size Discrimination of Silver Nanoparticles through Electrochemical Collision

Single particle collision is an important tool for size analysis at the individual particle level; however, due to complex dynamic behaviors of nanoparticles on the surface of an electrode, the accuracy of size discrimination is limited. A silver (Ag) nanoparticle (NP) was chosen as the research target, and the dynamic behavior of Ag NPs was simplified by enhancing adsorption between Ag NP and Au ultramicroelectrode (UME) in alkaline media. Immediately after, accurate dynamic and thermodynamic information on single Ag NP was accurately extracted from collision events, including current intensity, transferred charge, and duration time. On the basis that there were differences between parameters of different-sized Ag NPs, multiparameter size discrimination was proposed, which improved the accuracy compared to single-parameter discrimination. More intriguingly, multiparameter analysis was combined with artificial intelligence, a tool adept at processing multidimensional data, for the first time. Finally, artificial intelligence-assisted multiparameter size discrimination was successfully used to intelligently distinguish mixed Ag NPs, with an optimal accuracy of more than 95%. To sum up, the artificial intelligence-assisted multiparameter method showed an excellent ability to quickly achieve the most accurate size discrimination of nanoparticles at the level of individual particle and provide an effective guidance for the application of nanoparticles.

A Simple and Robust Exponential Amplification Reaction (EXPAR)-Based Hairpin Template (exp-Hairpin) for Highly Specific, Sensitive, and Universal MicroRNA Detection

Specific and sensitive detection of microRNAs continues to encounter significant challenges, especially in the development of rapid and efficient isothermal amplification strategies for point-of-care settings. The exponential amplification reaction (EXPAR) has garnered significant attention owing to its simplicity and rapid amplification of signals within a short period. However, a substantial loss of amplification efficiency, difficulty in distinguishing closely related homologous sequences, and adapting the designed templates to other targets seriously hamper the practical application of the EXPAR. In this work, a hairpin template tailored for the EXPAR system (exp-Hairpin) was constructed by adding identical trigger sequences and enzyme cleavage sites on two arms of the hairpin, achieving theoretically more than 2n amplification efficiency and minimal background amplification of EXPAR. Modulating the stability of the exp-Hairpin template by increasing the stem length, the specificity of detecting target miRNA in highly homologous sequences could be significantly improved. Using miRNA let-7a as a target model, the exp-Hairpin with 8 bp stem length for EXPAR amplification curves could effectively distinguish target let-7a and nontarget let-7b/7c/7f/7g/7i homologous sequences. This strategy enabled the sensitive and accurate analysis of let-7a in diluted human serum with satisfactory recoveries. By simply replacing the loop recognition sequence of exp-Hairpin, the specific detection of miR-200b was also achieved, demonstrating the universality of this strategy. The exp-Hairpin EXPAR accelerates simple and rapid molecular diagnostic applications for short nucleic acids.

MicroRNA biosensors in lung cancer

Lung cancer has been one of the leading causes of death over the past century. Unfortunately, the reliance on conventional methods to diagnose the phenotypic properties of tumors hinders early-stage cancer diagnosis. However, recent advancements in identifying disease-specific nucleotide biomarkers, particularly microRNAs, have brought us closer to early-stage detection. The roles of miR-155, miR-197, and miR-182 have been established in stage I lung cancer. Recent progress in synthesizing nanomaterials with higher conductivity has enhanced the diagnostic sensitivity of electrochemical biosensors, which can detect low concentrations of targeted biomarkers. Therefore, this review article focuses on exploring electrochemical biosensors based on microRNA in lung cancer.

Nano-Impact Electrochemical Biosensing Based on a CRISPR-Responsive DNA Hydrogel

Nano-impact electrochemistry (NIE) enables simple, rapid, and high-throughput biocoupling and biomolecular recognition. However, the low effective collision frequency limits the sensitivity. In this study, we propose a novel NIE sensing strategy amplified by the CRISPR-responsive DNA hydrogel and cascade DNA assembly. By controlling the phase transition of DNA hydrogel and the self-electrolysis of silver nanoparticles, we can obtain significant electrochemical responses. The whole process includes target miRNA-induced strand displacement amplification, catalytic hairpin assembly, and CRISPR/Cas trans-cutting. Thus, ultrahigh sensitivity is promised. This NIE biosensing strategy achieves a limit of detection as low as 4.21 aM for miR-141 and demonstrates a high specificity for practical applications. It may have wide applicability in nucleic acid sensing and shows great potential in disease diagnosis.

Sensitive detection of microRNA by dynamic light scattering based on DNAzyme walker-mediated AuNPs self-assembly

As an important biomarker, microRNAs (miRNAs) play an important role in gene expression, and their detection has attracted increasing attention. In this study, a DNAzyme walker that could provide power to perform autonomous movement was designed. Based on the continuous mechanical motion characteristics of DNAzyme walker, a miRNA detection strategy for the self-assembly of AuNPs induced by the hairpin probe-guided DNAzyme walker "enzyme cleavage and walk" was established. In this strategy, DNAzyme walker continuously cleaved and walked on the hairpin probe on the surface of AuNPs to induce the continuous shedding of some segments of the hairpin probe. The remaining hairpin sequences on the surface of the AuNP pair with each other, causing the nanoparticles to self-assemble. This strategy uses the autonomous movement mechanism of DNAzyme walker to improve reaction efficiency and avoid the problem of using expensive and easily degradable proteases. Secondly, using dynamic light scattering technology as the signal output system, ultra-sensitive detection with a detection limit of 3.6 fM is achieved. In addition, this strategy has been successfully used to analyze target miRNAs in cancer cell samples.

Multiplex Assays of MicroRNAs by Using Single Particle Electrochemical Collision in a Single Run

It is important to quantify multiple biomarkers in a single run due to the advantages of precious samples and diagnostic accuracy. Based on the distinguishability of two types of current signals from single particle electrochemical collision (SPEC), step-type current transients produced by Pt nanoparticles (PtNPs) catalyzed hydrazine oxidation and peak-type current transients produced by Ag nanoparticles (AgNPs) oxidation, a kind of multiplex immunoassay of target microRNAs (miRNA-21 and Let-7a) have been established during SPEC in a single run. When the single-stranded DNA (ssDNA1) that was perfectly complementary to miRNA-21 was coupled to the surface of PtNPs, the SPEC of PtNPs electrocatalysis was inhibited and the step-type current transients disappeared, while the single-stranded DNA (ssDNA2) that was perfectly complementary to Let-7a was coupled to the surface of AgNPs, the SPEC of AgNPs oxidation was inhibited, and the peak-type current transients disappeared, thus the signals were in the "off" state at this time. After that, miRNA-21 and Let-7a were added into solution, complementary base pairing disrupted the weak DNA-NP interaction and restored the electrocatalysis of PtNPs and the electrooxidation of AgNPs, and the step-type current signals and peak-type current signals were in the "on" state. Moreover, the frequencies from two different recovered signals (PtNPs catalysis and AgNPs oxidation) corresponded to the amount of added miRNA-21 and Let-7a, thus a multiplex immunoassay method for dual quantification of miRNA-21 and Let-7a in a single run was established.

Magnetically Assisted Immobilization-Free Detection of microRNAs Based on the Signal Amplification of Duplex-Specific Nuclease

The double specific nuclease (DSN)-based methods for microRNAs (miRNAs) detection usually require the immobilization of DNA probes on a solid surface. However, such strategies have the drawbacks of low hybridization and cleavage efficiency caused by steric hindrance effect and high salt concentration on the solid surface. Herein, we proposed an immobilization-free method for miRNA detection on the basic of DSN-assisted signal amplification. The biotin- and fluorophore-labeled probes were captured by streptavidin-modified magnetic beads through streptavidin-biotin interactions, thus producing a poor fluorescence signal. Once the DNA probes were hybridized with target miRNA in solution to form DNA-miRNA duplexes, DNA stands in the duplexes would be selectively digested by DSN. The released target miRNA could initiate the next hybridization/cleavage recycling in the homogeneous solution, finally resulting in the release of numerous fluorophore-labeled fragments. The released fluorophores remained in solution and emitted strong fluorescence after treatment by the streptavidin-modified magnetic beads. The immobilization-free method achieved the assays of miRNA-21 with a detection limit down to 0.01 pM. It was employed to evaluate the expression levels of miRNA-21 in different cancer cells with satisfactory results.

Enhanced Single-Particle Collision Electrochemistry at Polysulfide-Functionalized Microelectrodes for SARS-CoV-2 Detection

Single-particle collision electrochemistry (SPCE) has shown great promise in biosensing applications due to its high sensitivity, high flux, and fast response. However, a low effective collision frequency and a large number of interfering substances in complex matrices limit its broad application in clinical samples. Herein, a novel and universal SPCE biosensor was proposed to realize sensitive detection of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) based on the collision and oxidation of single silver nanoparticles (Ag NPs) on polysulfide-functionalized gold ultramicroelectrodes (Ps-Au UMEs). Taking advantage of the strong interaction of the Ag-S bond, collision and oxidation of Ag NPs on the Ps-Au UME surface could be greatly promoted to generate enhanced Faraday currents. Compared with bare Au UMEs, the collision frequency of Ps-Au UMEs was increased by 15-fold, which vastly improved the detection sensitivity and practicability of SPCE in biosensing. By combining magnetic separation, liposome encapsulation release, and DNAzyme-assisted signal amplification, the SPCE biosensor provided a dynamic range of 5 orders of magnitude for spike proteins with a detection limit of 6.78 fg/mL and a detection limit of 21 TCID50/mL for SARS-CoV-2. Furthermore, SARS-CoV-2 detection in nasopharyngeal swab samples of infected patients was successfully conducted, indicating the potential of the SPCE biosensor for use in clinically relevant diagnosis.

Bidirectional motivated bimodal isothermal strand displacement amplifier with a table tennis-like movement for the ultrasensitive fluorescent and colorimetric detection of depression-related microRNA

An increasing number of studies have highlighted the potential of microRNAs (miRNAs) as physiological indicators of major depressive disorder (MDD). Herein, we developed a bidirectional-motivated bimodal isothermal strand displacement amplifier (BB-ISDA) for the ultrasensitive fluorescent and colorimetric detection of MDD-related miRNA-132. In the BB-ISDA system, a pair of functionalized hairpin probes (HP1 and HP2) with nicking recognition sites are designed to recognize target miRNA. The recognition of target miRNA by HP1 (or HP2) generates copious numbers of nicked triggers by HP1 (or HP2)-based ISDA to recognize HP2 (or HP1) by autonomous strand polymerization, cleavage, and displacement, which in turn induces the subsequent generation of copious numbers of nicked G-quadruplex triggers by HP2 (or HP1)-based ISDA to recognize HP1 (or HP2) along a same line. After many cycles, this bidirectional motivated table-tennis-like movement amplifies the fluorescent signal from HP1 and the colorimetric signal from HP2, simultaneously. The dual-signal output pattern was cross-validated for sensing miRNA-132. Each of the detection modal shows the capability for qualitative and quantitative detection of miRNA-132 with high sensitivity and specificity. The adaptability of the bimodal mechanism was verified via the detection of target miRNA-132 from clinical human blood samples. We envision that this BB-ISDA with dual-signal output for accurate and reliable analysis of miRNA is promising for the molecular diagnosis of human mental diseases.

Mass Nanotags Mediate Parallel Amplifications on Nanointerfaces for Multiplexed Profiling of RNAs

Multiplexed profiling of RNAs aids in a comprehensive understanding of multiparameter-defined cellular processes and pathological states. We herein present a mass nanotags-enabled interfacial assembly system (MNTs-AS) with parallel amplification motors for simultaneous assaying of multiple RNAs in biosystems by matrix-assisted laser desorption/ionization mass spectrometry (MALDI MS). Four kinds of MNTs encoding corresponding RNA can be cyclically assembled on magnetic beads by target-triggered catalytic hairpin assembly (CHA) machineries on nanointerfaces, generating multiplexed and amplified characteristic ion signals assigned to target RNAs upon MALDI MS interrogation. By virtue of high sensitivity and multiplexing capability, the MNTs-AS-based MS assay allows precision subtyping of diverse breast cancer cells and their exosomes by multiplexed profiling of miRNA-21, miRNA-373, miRNA-155, and manganese superoxide dismutase mRNA via a single MS inquiry. This method provides a promising tool for unraveling multiple RNA-involved biological events in fundamental research and distinguishing different cancer subtypes in clinical practice.

An isolated single-particle-based SECM tip interface for single-cell NO sensing

As a key factor in cellular metabolic processes, nitric oxide (NO) is a challenging target for in situ real-time monitoring due to its transient property and short diffusion distance. Scanning electrochemical microscopy (SECM) has unique advantages in single-cell analysis, which can obtain the electrochemical current by scanning the cell surface with a tip microelectrode. In particular, it can further improved the electrochemical response by enhancing the interface properties of its tip. Here, an interface design strategy based on platinum single nanoparticle (Pt NP) was developed, and fluorinated self-assembled monolayers (SAMs) were used to further improve its performance. This modified tip was used as an SECM probe for NO concentration monitoring and morphological imaging of single MCF-7 cells. It has the high sensitivity (164.7 μA/μM·cm²) and good selectivity for NO detection, which benefits from the efficient catalytic properties of Pt NPs and high mass transport and hydrophobic antifouling properties of the interface. Notably, it shows a superior performance in detecting the fluctuation of NO released by a single MCF-7-cell under the stimulation of cadmium (Cd), which demonstrates a promising method for using a single-particle-based tip in SECM applications.

Homogeneous Electrochemical Immunoassay Using an Aggregation-Collision Strategy for Alpha-Fetoprotein Detection

Homogeneous immunoassays represent an attractive alternative to traditional heterogeneous assays due to their simplicity and high efficiency. Homogeneous electrochemical assays, however, are not commonly accessed due to the requirement of electrode immobilization of the recognition elements. Herein, we demonstrate a new homogeneous electrochemical immunoassay based on the aggregation-collision strategy for the quantification of tumor protein biomarker alpha-fetoprotein (AFP). The detection principle relies on the aggregation of AgNPs induced by the molecular biorecognition between AFP and AgNPs-anti-AFP probes, which leads to an increased AgNP size and decreased AgNP concentration, allowing an accurate self-validated dual-mode immunoassay by performing nanoimpact electrochemistry (NIE) of the oxidation of AgNPs. The intrinsic one-by-one analytical capability of NIE as well as the participation of all of the atoms of the AgNPs in signal transduction greatly elevates the detection sensitivity. Accordingly, the current sensor enables a limit of detection (LOD) of 5 pg/mL for AFP analysis with high specificity and efficiency. More importantly, reliable detection of AFP in diluted human sera of hepatocellular carcinoma (HCC) patients is successfully achieved, indicating that the NIE-based homogeneous immunoassay shows great potential in HCC liquid biopsy.

Clinically Applicable Homogeneous Assay for Serological Diagnosis of Alpha-Fetoprotein by Impact Electrochemistry

Tumor protein quantification with high specificity, sensitivity, and efficiency is of great significance to enable early diagnosis and effective treatment. The existing methods for protein analysis usually suffer from high cost, time-consuming operation, and insufficient sensitivity, making them not clinically friendly. In this work, a label-free homogeneous sensor based on the nano-impact electroanalytic (NIE) technique was proposed for the detection of tumor protein marker alpha-fetoprotein (AFP). The detection principle is based on the recovery of current of single PtNP catalyzed hydrazine oxidation due to the release of the pre-adsorbed passivating aptamers on PtNPs from the competition of the stronger binding between the specific interaction of the AFP aptamer and AFP. The intrinsic one-by-one analytical ability of NIE allows highly sensitive detection, which can be further improved by reducing the reaction/incubation volume. Meanwhile, the current sensor avoids a laborious labeling procedure as well as the separation and washing steps due to the in situ characteristic of NIE. Accordingly, the current sensor enables efficient, highly sensitive, and specific AFP analysis. More importantly, the reliable detection of AFP in diluted real sera from hepatocellular carcinoma (HCC) patients is successfully achieved, indicating that the impact electrochemistry-based sensing platform has great potential to be applied in point-of-care devices for HCC liquid biopsy.

Programmable mismatch-fueled high-efficiency DNA signal amplifier

Herein, by introducing mismatches, a high-efficiency mismatch-fueled catalytic multiple-arm DNA junction assembly (M-CMDJA) with high-reactivity and a high-threshold is developed as a programmable DNA signal amplifier for rapid detection and ultrasensitive intracellular imaging of miRNA. Compared with traditional nucleic acid signal amplification (NASA) with a perfect complement, the M-CMDJA possesses larger kinetic and thermodynamic favorability owing to the more negative reaction standard free energy (ΔG) as driving force, resulting in much higher efficiency and rates. Once traces of the input initiator react with the mismatched substrate DNA, it could be converted into amounts of output multiple-arm DNA junctions via the M-CMDJA as the functional DNA conversion nanodevice. Impressively, the mismatch-fueled catalytic four-arm DNA junction assembly (M-CFDJA) exhibits high conversion efficiency up to 1.05 × 108 in 30 min, which is almost ten times more than those of conventional methods. Therefore, the M-CMDJA could easily address the challenges of traditional methods: slow rates and low efficiency. In application, the M-CFDJA as a DNA signal amplifier was successfully used to develop a biosensing platform for rapid miRNA detection with a LOD of 6.11 aM and the ultrasensitive intracellular imaging of miRNA, providing a basis for the next-generation of versatile DNA signal amplification methods for ultimate applications in DNA nanobiotechnology, biosensing assay, and clinical diagnoses.

Magnetic Rolling Circle Amplification-Assisted Single-Particle Collision Immunosensor for Ultrasensitive Detection of Cardiac Troponin I

Owing to its simplicity, high throughput, and ultrasensitivity, single-particle collision electrochemistry (SPCE) has attracted great attention in biosensing, especially labeled SPCE. However, the low signal conversion efficiency and much interference from complex samples limit its wide application. Here, a new and robust SPCE immunosensor was proposed for ultrasensitive cardiac troponin I (cTnI) detection by combining target-driven rolling circle amplification (RCA) with magnetic beads (MBs). Antibody-modified MBs have good stability, dispersity, and magnetic response capacity in complex samples, enabling efficient capture and separation of cTnI with high specificity and anti-interference ability. The presence of cTnI could specifically drive the formation of magnetic immunocomplexes followed by triggering RCA and enzyme digestion reaction. By using Pt nanoparticles (Pt NPs)-modified ssDNA as signal probes, one cTnI molecule could induce the release of 4.5 × 10⁴ Pt NPs for collision experiments, greatly enhancing signal conversion efficiency and detection sensitivity. Based on the integration of MBs with RCA, the SPCE immunosensor realized 0.57 fg/mL cTnI detection with a wide linear range of 1 fg/mL to 50 ng/mL. Furthermore, cTnI detection in serum samples of myocardial infarction patients was successfully performed, demonstrating great application prospect of the SPCE immunosensor in clinical diagnosis.

Ring Ultramicroelectrodes for Current-Blockade Particle-Impact Electrochemistry

In current-blockade impact electrochemistry, insulating particles are detected amperometrically as they impinge upon a micro- or nanoelectrode via a decrease in the faradaic current caused by a redox mediator. A limit of the method is that analytes of a given size yield a broad distribution of response amplitudes due to the inhomogeneities of the mediator flux at the electrode surface. Here, we overcome this limitation by introducing microfabricated ring-shaped electrodes with a width that is significantly smaller than the size of the target particles. We show that the relative step size is somewhat larger and exhibits a narrower distribution than at a conventional ultramicroelectrode of equal diameter.

A Versatile Electrochemical Biosensor for the Detection of Circulating MicroRNA toward Non-Small Cell Lung Cancer Diagnosis

Circulating microRNAs (miRNAs) can be used as noninvasive biomarkers and are also found circulating in body fluids such as blood. Dysregulated miRNA expression is associated with many diseases, including non-small cell lung cancer (NSCLC), and the miRNA assay is helpful in cancer diagnosis, prognosis, and monitoring. In this work, a versatile electrochemical biosensing system is developed for miRNA detection by DNAzyme-cleavage cycling amplification and hybridization chain reaction (HCR) amplification. With cleavage by Mn²⁺ targeted DNAzyme, DNA-walker can move along the predesigned DNA tracks and contribute to the transduction and enhancement of signals. For the electrochemical process, the formation of multiple G-quadruplex-incorporated long double-stranded DNA (dsDNA/G-quadruplex) structures is triggered through HCR amplification. The introduction of G-quadruplex allows sensitive measurement of miRNA down to 5.68 fM with good specificity. Furthermore, by profiling miRNA in the NSCLC cohort, this designed strategy shows high efficiency (area under the curve (AUC) of 0.879 using receiver operating characteristic (ROC) analysis) with the sensitivity of 80.0% for NSCLC early diagnosis (stage I). For the discrimination of NSCLC and benign disease, the assay displays an AUC of 0.907, superior to six clinically-acceptable protein tumor markers. Therefore, this platform holds promise in clinical application toward NSCLC diagnosis and prognosis.

Stochastic Collision Electrochemistry from Single Pt Nanoparticles: Electrocatalytic Amplification and MicroRNA Sensing

Single-particle collisions have made many achievements in basic research, but challenges still exist due to their low collision frequency and selectivity in complex samples. In this work, we developed an "on-off-on" strategy based on Pt nanoparticles (PtNPs) that catalyze N₂H₄ collision signals on the surface of carbon ultramicroelectrodes and established a new method for the detection of miRNA21 with high selectivity and sensitivity. PtNPs catalyze the reduction of N₂H₄ on the surface of carbon ultramicroelectrodes to generate a stepped collision signal, which is in the "on" state. The single-stranded DNA paired with miRNA21 is coupled with PtNPs to form the complex DNA/PtNPs. Because PtNPs are covered by DNA, the electrocatalytic collision of N₂H₄ oxidation is inhibited. At this time, the signal is in the "off" state. When miRNA21 is added, the strong complementary pairing between miRNA21 and DNA destroys the electrostatic adsorption of DNA/PtNP conjugates and restores the electrocatalytic performance of PtNPs, and the signal is in the "on" state again. Based on this, a new method for detecting miRNA21 was established. It provides a new way for small-molecule sensing and has a wide range of applications in electroanalysis, electrocatalysis, and biosensing.

Mismatch-fueled catalytic hairpin assembly mediated ultrasensitive biosensor for rapid detection of MicroRNA

Herein, a mismatch-fueled catalytic hairpin assembly (MCHA) was rationally engineered, which possessed higher amplification efficiency and faster rate than catalytic hairpin assembly (CHA). Once input target microRNA-21(miRNA-21) triggers the MCHA, the hairpin DNA H1 will be opened to form the duplex H1-miRNA-21, then the mismatched hairpin DNA H2 could easily hybridize with H1-miRNA-21 to generate duplex H1-H2 and the miRNA-21 could be released to enter next cycle, thus generating amounts of output products. Impressively, the MCHA realizes a pretty shorter complete reaction time of 40 min and quite higher amplification efficiency of 9.56 × 10⁶, which dramatically transcended the barrier: low amplification times and long reaction time in traditional CHA. As a proof of the concept, the elaborated MCHA as a hyper-efficiency and high-speed DNA signal-magnifier was successfully applied in ultrasensitive and rapid detection of miRNA-21 with the detection limit of 0.17 fM, which exploited an ingenious nucleic acid signal amplification technique for sensitive and fast detection of biomarkers in biosensing assay and clinic diagnose.

A general controllable release amplification strategy of liposomes for single-particle collision electrochemical biosensing

As an important component of the COVID-19 mRNA vaccines, liposomes play a key role in the efficient protection and delivery of mRNA to cells. Herein, due to the controllable release amplification strategy of liposomes, a reliable and robust single-particle collision electrochemical (SPCE) biosensor was constructed for H9N2 avian influenza virus (H9N2 AIV) detection by combining liposome encapsulation-release strategy with immunomagnetic separation. The liposomes modified with biotin and loaded with platinum nanoparticles (Pt NPs) were used as signal probes for the first time. Biotin facilitated the coupling of biomolecules (DNA or antibodies) through the specific reaction of biotin-streptavidin. Each liposome can encapsulate multiple Pt NPs, which were ruptured under the presence of 1 × PBST (phosphate buffer saline with 0.05% Tween-20) within 2 min, and the encapsulated Pt NPs were released for SPCE experiment. The combination of immunomagnetic separation not only improved the anti-interference capabilities but also avoided the agglomeration of Pt NPs, enabling the SPCE biosensor to realize ultrasensitive detection of 18.1 fg/mL H9N2 AIV. Furthermore, the reliable SPCE biosensor was successfully applied in specific detection of H9N2 AIV in complex samples (chicken serum, chicken liver and chicken lung), which promoted the universality of SPCE biosensor and its application prospect in early diagnosis of diseases.

Programmable High-Speed and Hyper-Efficiency DNA Signal Magnifier

Herein, a programmable dual-catalyst hairpin assembly (DCHA) for realizing the synchronous recycle of two catalysts is developed, displaying high reaction rate and outstanding conversion efficiency beyond traditional nucleic acid signal amplifications (NASA). Once catalyst I interacts with the catalyst II, the DCHA can be triggered to realize the simultaneous recycle of catalysts I and II to keep the highly concentrated intermediate product duplex I-II instead of the steadily decreased one in typical NASA, which can accomplish in about only 16 min and achieves the outstanding conversion efficiency up to 4.54 × 108 , easily conquering the main predicaments of NASA: time-consuming and low-efficiency. As a proof of the concept, the proposed DCHA as a high-speed and hyper-efficiency DNA signal magnifier is successfully applied in the rapid and ultrasensitive detection of miRNA-21 in cancer cell lysates, which exploits the new generation of universal strategy for the applications in biosensing assay, clinic diagnose, and DNA nanobiotechnology.

An electrochemical biosensor based on ARGET ATRP with DSN-assisted target recycling for sensitive detection of tobacco mosaic virus RNA

Herein, an electrochemical biosensor for detecting tobacco mosaic virus (TMV) RNA is constructed by activator regenerated by electron transfer atom transfer radical polymerization (ARGET ATRP) combined with duplex-specific nuclease (DSN)-assisted target recycling. First, the captured DNA (cDNA) is self-assembled on the electrode surface and hybridizes with the TMV RNA (tRNA) to form cDNA/tRNA hybrids. And then the initiator of ARGET ATRP (α-bromoisobutyric acid, BMP) is attached to the cDNA via an amide bond and later triggers ARGET ATRP. Many electroactive monomers (ferrocenylmethyl methacrylate, FMMA) are polymerized and a remarkable electrical signal response of ferrocene (Fc) is obtained. However, with the present of DSN, DSN cleaves the cDNA/tRNA hybrid and releases tRNA to hybridize with another cDNA, thereby causing significant shortening of the length of the cDNA. The number of polymer chains on the electrode surface is drastically reduced, which is followed by a noticeable reduction in the signal of Fc. The method shows high sensitivity, superior selectivity, excellent stability and good reproducibility under optimal conditions with the limit of detection (LOD) of 2.9 fM. Furthermore, the biosensor showed satisfactory applicability in detecting tRNA in real samples, thereby demonstrating the potential of the method for practical TMV RNA detection.

A dual-signaling electrochemical ratiometric strategy combining "signal-off" and "signal-on" approaches for detection of MicroRNAs

A dual-signaling electrochemical ratio metric strategy was developed for detection microRNA-18a based on the duplex-specific nuclease-assisted target recycling and electrochemical atom transfer radical polymerization signal amplification. In the presence of target microRNA, RNA/DNA duplexes are formed, which become the substrate of the duplex-specific nuclease-assisted target recycling. Hence only the DNA strand is cleaved by duplex-specific nuclease enzyme, resulting in the throw away of methylene blue (MB) from the electrode (signal off) accompanied by releasing of target microRNA, which can be recycled in the next hybridization. The remaining piece of capture DNAs on the electrode surface hybridize with the Azide labeled-signal DNAs. "Click reactions" were carried out between 3-Butynyl-2-bromoisobutyrate and Azide to initiate the electrochemical atom transfer radical polymerization reaction. This process could bring a great number of ferrocenylmethyl methacrylate (FMMA) on the surface of electrode (signal on). The I_FMMA/I_MB value was proportionate to the microRNA-18a concentration and measured by square wave voltammetry. The promising potential of the proposed biosensor in clinical analyses was exhibited by its remarkable features such as strong performance, high specificity, agreeable storage stability, and notable selectivity in real sample evaluation with no pretreatment or amplification. Finally, our biosensing method offers such an application to be used for the early clinical diagnosis of Pancreatic Cancer.

Dual 3D DNA Nanomachine-Mediated Catalytic Hairpin Assembly for Ultrasensitive Detection of MicroRNA

Herein, we designed a dual 3D DNA nanomachine (DDNM)-mediated catalytic hairpin assembly (DDNM-CHA) to construct an electrochemical biosensor for ultrasensitive detection of miRNA, which possesses quite a faster reaction rate and much higher amplification efficiency than those of traditional catalytic hairpin assembly (CHA). Impressively, since the DDNM skillfully increases the local concentration of reactants and decreases the steric hindrance of substrates simultaneously, the DDNM-CHA could be endowed with higher collision efficiency and more effective reaction compared with traditional CHA, resulting in a hyper conversion efficiency up to 2.78 × 10⁷ only in 25 min. This way, the developed DDNM-CHA could easily conquer the main predicaments: long reaction time and low efficiency. As a proof of the concept, we adopt the gold nanoparticles (AuNPs) and the magnetic nanoparticle (Fe₃O₄) as the kernel of DNM-A and DNM-B, respectively, and harness the magnetic electrode to directly adsorb the products H1-H2/Fe₃O₄ for constructing an immobilization-free biosensor for high-speed and ultrasensitive detection of miRNA with a detection limit of 0.14 fM. As a result, the DDNM-CHA we developed carves out a new insight to design a functional DNA nanomachine and evolve the analysis method for practical amplification in the sensing area and promotes the deeper exploration of the nucleic acid signal amplification strategy and DNA nanobiotechnology.

Anti-Fouling Magnetic Beads Combined with Signal Amplification Strategies for Ultra-Sensitive and Selective Electrochemiluminescence Detection of MicroRNAs in Complex Biological Media

Herein, an electrochemiluminescence (ECL) microRNA biosensor based on anti-fouling magnetic beads (MBs) and two signal amplification strategies was developed. The newly designed anti-fouling dendritic peptide was wrapped on the surfaces of MBs to make them resistant to nonspecific adsorption of biomolecules in complex biological samples so as to realize accurate and selective target recognition. One of the amplification strategies was achieved through nucleic acid cycle amplification based on the DNAzyme on the surfaces of MBs. Then, the output DNA generated by the nucleic acid cycle amplification program stimulated the hybrid chain reaction (HCR) process on the modified electrode surface to generate the other amplification of the ECL response. Titanium dioxide nanoneedles (TiO₂ NNs), as a co-reaction accelerator of the Ru(bpy)₂(cpaphen)²⁺ and tripropylamine (TPrA) system, were wrapped with the electrodeposited polyaniline (PANI) on the electrode surface to enhance the ECL intensity of Ru(bpy)₂(cpaphen)²⁺. The conducting polymer PANI can not only immobilize the TiO₂ NNs but also improve the conductivity of the modified electrodes. The biosensor exhibited ultra-high sensitivity and excellent selectivity toward the detection of miRNA 21, with a detection limit of 0.13 fM. More importantly, with the anti-fouling MBs as a unique separation tool, this ECL biosensor was capable of assaying targets in complex biological media such as serum and cell lysate.

Quantification of Tumor Protein Biomarkers from Lung Patient Serum Using Nanoimpact Electrochemistry

Protein quantification with high throughput and high sensitivity is essential in the early diagnosis and elucidation of molecular mechanisms for many diseases. Conventional approaches for protein assay often suffer from high costs, long analysis time, and insufficient sensitivity. The recently emerged nanoimpact electrochemistry (NIE), as a contrast, allows in situ detection of analytes one at a time with simplicity, fast response, high throughput, and the potential of reducing the detection limits down to the single entity level. Herein, we propose a NIE-enabled electrochemical immunoassay using silver nanoparticles (AgNPs) as labels for the detection of CYFRA21-1, a typical protein marker for lung carcinoma. This strategy is based on the measurement of the impact frequency and the charge intensity of the electrochemical oxidation of individual AgNPs before and after they are modified with anti-CYFRA21-1 and in turn immunocomplexed with CYFRA21-1. Both the frequency and intensity modes of single-nanoparticle electrochemistry correlate well with each other, resulting in a self-validated immunoassay that provides linear ranges of two orders of magnitude and a limit of detection of 0.1 ng/mL for CYFRA21-1 analysis. The proposed immunoassay also exhibits excellent specificity when challenged with other possible interfering proteins. In addition, the CYFRA21-1 content is validated by a conventional, well-known enzyme-linked immunosorbent assay and successfully quantified in a diluted healthy serum with a satisfactory recovery. Moreover, CYFRA21-1 detection in serum samples of lung cancer patients is successfully demonstrated, suggesting the feasibility of the NIE-based immunoassay in clinically relevant diagnosis. To the best of our knowledge, this is the first report to construct NIE-based electrochemical immunoassays for the specific detection of tumor protein biomarkers.

Sensitive detection of miRNA based on enzyme-propelled multiple photoinduced electron transfer strategy

A method is presented that uses photoinduced electron transfer (PET) for the determination of microRNAs (miRNAs) in clinical serum samples and complicated cell samples by using a smartphone. miRNA-21 is adopted as a model analyte. A 3'-phosphorylated DNA probe containing AgNCs is synthesized and hybridized with miRNA-21. Subsequently, the probe is cleaved specifically by duplex-specific nuclease to form 3'-hydroxylated products, then extended by terminal deoxynucleotidyl transferase (TdT) with superlong G for G-quadruplex/hemin units fabrication. In this way, PET occurred between AgNCs and produced G-quadruplex/hemin units, leading to the fluorescence quenching of AgNCs. Notably, the fluorescence images can be captured and translated into digital information by smartphone, resulting in a direct quantitative determination of miRNA. As a result, our strategy for miRNA assay is achieved with a satisfactory detection limit of 1.43 pM. Interestingly, TdT-propelled G-quadruplex/hemin units as multiple electron acceptors promote the sensitivity of miRNA monitoring. Different miRNAs assays are realized by adjusting the complimentary sequences of DNA probe. These qualities not only broaden the practical application of PET-based strategy, but also provide a new insight into the nucleic acid detection. Schematic representation of AgNCs and enzyme-propelled photoinduced electron transfer strategy. It has been successfully applied for detection of miRNA by image analysis software. The method displays portability and accuracy for miRNA determination, meeting the potential for biochemical and clinical applications in resource-limited settings.

A hybridization-based dual-colorimetric kit for circulating cancer miRNA detection

A dual-colorimetric miRNA detection kit that can simultaneously detect two miRNAs with high sensitivity and selectivity is developed, and the data can be read by the naked eye easily. The kit is able to distinguish the patients from healthy people and achieve lung cancer diagnosis using clinical serum samples in a short time.

Size-Resolved Single Entity Collision Biosensing for Dual Quantification of MicroRNAs in a Single Run

Limited to the accuracy of size resolution, single entity collision biosensing (SECBS) for multiplex immunoassays remains challenging, because it is difficult to get the true value of nanoparticle (NP) sizes based on the current intensity due to the complex movement of NPs on the electrode surface. Considering that the size-dependent movement of NPs meanwhile will generate a characteristic current shape, in this work, the huge difference in the current rise time of 5 and 15 nm Pt NPs colliding on an Au ultramicroelectrode (d = 30 μm) was originally used to develop a size-resolved SECBS for multiplex immunoassays of miRNAs. The limit concentration that can be detected was 0.5 fM. Compared with conventional electrochemical biosensors for multiplex immunoassays, for the size-resolved SECBS, one does not need to worry about potential overlapping. Therefore, the proposed method demonstrates a promising potential for the application of SECBS in multiplex immunoassays.

Single enzyme electroanalysis

Traditional studies of enzymatic activity rely on the combined kinetics of millions of enzyme molecules to produce a product, an experimental approach that may wash out heterogeneities that exist between individual enzymes. Evaluating these properties on an enzyme-by-enzyme basis represents an unambiguous means of elucidating heterogeneities; however, the quantification of enzymatic activity at the single-enzyme level is fundamentally limited by the maximum catalytic rate, k_cat, inherent to a given enzyme. For electrochemical methods measuring current, single enzymes must turn over greater than 10⁷ molecules per second to produce a measurable signal on the order of 10^-12 A. Enzymes with this capability are extremely rare in nature, with typical k_cat values for biologically relevant enzymes falling between 1 and 10 000 s^-1. Thus, clever amplification strategies are necessary to electrochemically detect the vast majority of enzymes. This review details the progress toward the electroanalytical detection and evaluation of single enzyme kinetics largely focused on the nanoimpact method, a chronoamperometric detection strategy that monitors the change in the current-time profile associated with stochastic collisions of freely diffusing entities (e.g., enzymes) onto a microelectrode or nanoelectrode surface. We discuss the experimental setups and methods developed in the last decade toward the quantification of single molecule enzymatic rates. Special emphasis is given to the limitations of measurement science in the observation of single enzyme activity and feasible methods of signal amplification with reasonable bandwidth.

Single-Particle Electrochemical Biosensor with DNA Walker Amplification for Ultrasensitive HIV-DNA Counting

Single-particle electrochemical collision has gained great achievements in fundamental research, but it is challenging to use in practice on account of its low collision frequency and the interference of the complex matrix in actual samples. Here, magnetic separation and DNA walker amplification were integrated to build a robust and sensitive single-particle electrochemical biosensor. Magnetic nanobeads (MBs) can specifically capture and separate targets from complex samples, which not only ensures the anti-interference capability of this method but also avoids the aggregation of platinum nanoparticles (Pt NPs) caused by numerous coexisting substances. A low amount of targets can lead to the release of more Pt NPs and the generation of more collision current transients, realizing cyclic amplification. Compared with simple hybridization, a DNA walker can improve the collision frequency by about 3-fold, greatly enhancing detection sensitivity, and a relationship between collision frequency and target concentration is used to realize quantification. The biosensor realized an ultrasensitive detection of 4.86 fM human immunodeficiency virus DNA (HIV-DNA), which is 1-4 orders of magnitude lower than that of traditional methods. The successful HIV-DNA detection in complex systems (serum and urine) demonstrated a great promising application in real samples and in the development of new single-entity biosensors.

Stochastic Collision Electrochemistry from Single G-Quadruplex/Hemin: Electrochemical Amplification and MicroRNA Sensing

Stochastic collision electrochemistry is a hot topic in single molecule/particle research, which provides an opportunity to investigate the details of the single molecule/particle reaction mechanism that is always masked in ensemble-averaged measurements. In this work, we develop an electrochemical amplification strategy to monitor the electrocatalytic behavior of single G-quadruplex/hemin (GQH) for the reaction between hydrogen peroxide and hydroquinone (HQ) through the collision upon a gold nanoelectrode. The intrinsic peroxidase activities of single GQH were investigated by stochastic collision electrochemical measurements, giving further insights into understanding biocatalytic processes. Based on the unique catalytic activity of GQH, we have also designed a hybridization chain reaction strategy to detect miRNA-15 with good selectivity and sensitivity. This work provided a meaningful strategy to investigate the electrochemical amplification and the broad application for nucleic acid sensing at the single molecule/particle level.

Circular RNAs Sparkle in the Diagnosis and Theranostics of Hepatocellular Carcinoma

Exonic circular RNAs (circRNAs) are a novel subgroup of non-coding RNAs, which are generated by a back-splicing mechanism of the exons or introns. Unlike the linear RNA, circRNA forms a covalently closed loop, and it normally appears more abundant than the linear products of its host gene. Due to the relatively high specificity and stability of circular RNAs in tissues and body fluid, circular RNAs have attracted widely scientific interest for its potential application in cancer diagnosis and as a guide for preclinical therapy, especially for hard-to-treat cancers with high heterogeneity, such as hepatocellular carcinoma (HCC). Thus, we summarize the updated knowledge of circular RNAs, including the mechanism of the generation of endogenous circular RNAs and their regulatory, diagnostic, and therapeutic roles in HCC.

Label-free and enzyme-free fluorescence detection of microRNA based on sulfydryl-functionalized carbon dots via target-initiated hemin/G-quadruplex-catalyzed oxidation

Carbon dots (CDs)-based biosensors have attracted considerable interest in reliable and sensitive detection of microRNA (miRNA) because of their merits of ultra-small size, excellent biosafety and tunable emission, whereas complicated labeling procedure and expensive bioenzyme associated with current strategies significantly limit their practical application. Herein, we developed a label-free and enzyme-free fluorescence strategy based on strand displaced amplification (SDA) for highly sensitive detection of miRNA using sulfydryl-functionalized CDs (CDs-SH) as probe. CDs-SH displayed excellent response to G-quadruplex DNA against other DNAs based on based on the catalytic oxidation of -SH into -S-S- by hemin/G-quadruplex. Further, CDs-SH were employed to detect miRNA, using miRNA-21 as target model, which triggered the SDA reaction of P1 and P2 to generate hemin/G-quadruplex, subsequently making CDs-SH transform from dot to aggresome along with the quenched fluorescence. Therefore, label-free, enzyme-free, and highly sensitive analysis of miRNA-21 was readily acquired with a limit of detection at 0.03 pM. This proposed biosensor couples the advantages of CDs and label-free/enzyme-free strategy, and thus has a significant potential to be used in early and accurate diagnosis of cancer.

A Janus 3D DNA nanomachine for simultaneous and sensitive fluorescence detection and imaging of dual microRNAs in cancer cells

Herein, a Janus three-dimensional (3D) DNA nanomachine was constructed for the simultaneous and sensitive fluorescence detection and imaging of dual microRNAs (miRNAs) in cancer cells, which could effectively eliminate signal interference in a homogeneous nanoparticle-based 3D DNA nanostructure caused by the proximity of the two different signal probes to achieve accurate co-location in the same position of living cancer cells. In this system, the Janus nanoparticles were synthesized as the carrier for immobilizing two different oligonucleotides on two different functionalized hemispheres of the nanoparticles to form a Janus 3D DNA nanostructure, which could convert trace amounts of miRNA-21 and miRNA-155 targets into massive FAM and Cy5-labeled duplexes to induce two remarkable fluorescence emissions by the catalytic hairpin assembly (CHA) and 3D DNA walker cascade nucleic acid amplification strategy, realizing sensitive detection and imaging of miRNA targets in cancer cells. Impressively, in comparison with current miRNA imaging methods based on nanoparticle assemblies, the proposed strategy could efficiently eliminate “false positive” results obtained in single type miRNA detection and distinctly increase the immobilization concentration of two different signal probes using Janus nanoparticles as the carrier to further enhance fluorescence intensity, resulting in accurate co-location in the same position of living cells. Meanwhile, the proposed fluorescence imaging technology makes it possible to visualize low concentrations of miRNAs with tiny change associated with some cancers, which could significantly improve the accuracy and precision compared to those of the conventional fluorescence in situ hybridization (FISH) approach. Therefore, it could serve as persuasive evidence for supplying accurate information to better understand biological processes and investigate mechanisms of various biomolecules and subcellular organelles, resulting in the further validation of their function in tumor proliferation and differentiation. This strategy provided an innovative approach to design new generations of nanomachines with ultimate applications in bioanalysis and clinical diagnoses.

A Janus three-dimensional DNA nanomachine was constructed for the simultaneous and sensitive fluorescent detection and imaging of dual microRNAs in the cancer cells.

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.

Phase imaging of transition from classical to quantum plasmonic couplings between a metal nanoparticle and a metal surface

When a metal nanoparticle is brought near to a metal surface within electron tunneling distance (∼1 nm), classical electromagnetic coupling between the nanoparticle and the metal is expected to transition to quantum coupling. We show that this transition can be observed as a drastic phase change in the surface plasmon resonance (SPR) images of the gold nanoparticles. We study the transition by controlling the distance between the nanoparticles and electrode surface, modeling the impact of the transition on the SPR image in terms of a phase shift and demonstrating detection of microRNA based on the transition from classical to quantum coupling. The work shows that the quantum coupling can be directly visualized in SPR, and the extremely sensitive dependence of the transition on distance leads to a biosensing principle with SPR.

Rapid DNA detection and one-step RNA detection catalyzed by Bst DNA polymerase and narrow-thermal-cycling

We reported a novel detection method named accelerated strand exchange amplification by employing Bst DNA polymerase and narrow-thermal-cycling for the first time, achieving direct detection of 120 copies of DNA within 15 min and 1.2 × 10⁵ copies of RNA within 20 min and sparking the revolution of the use of routine isothermal polymerases for diverse applications.

Light-Controlled Nanoparticle Collision Experiments

Electrochemical monitoring of catalytically amplified collisions of individual metal nanoparticles (NP) with ultramicroelectrodes (UME) has been extensively used to study electrocatalysis, mass-transport, and charge-transfer processes at the single NP level. More recently, photoelectrochemical collision experiments were carried out with semiconductive NPs. Here, we introduce two new types of light-controlled nanoimpact experiments. The first experiment involves localized photodeposition of catalyst (Pt) on TiO₂ NPs with a glass-sheathed carbon fiber simultaneously serving as the light guide and collector UME. The collisions of in situ prepared Pt@TiO₂ NPs with the carbon surface produced blips of water oxidation current, while the activity of pristine TiO₂ NPs was too low to yield measurable signal. In another experiment, collisions of catalytic (Ir oxide) NPs with the semiconductor (Nb doped n-type TiO₂ rutile single crystal) electrode are monitored by measuring the photocurrent of water oxidation.