Label-Free Ratiometric Homogeneous Electrochemical Strategy Based on Exonuclease III-Aided Signal Amplification for Facile and Rapid Detection of miR-378

MiR-378 is abnormally expressed in various cancers, such as hepatocellular carcinoma, renal cell carcinoma, and nonsmall cell lung cancer. Here, we developed a label- and immobilization-free ratiometric homogeneous electrochemical strategy based on exonuclease III (Exo III) for the facile and rapid determination of miR-378. Two 3'-protruding hairpin DNA probes (HPs) are designed in this strategy. Doxorubicin (DOX) and potassium ferrocyanide (Fe2+) were used as label-free probes to produce a response signal (IDOX) and a reference signal (IFe2+) in the solution phase. When no target was present in the solution, the HP was stable, most of the DOX was intercalated in the stem of the HP, and the diffusion rate of DOX was significantly reduced, resulting in reduced electrochemical signal response. When miR-378 was present, double-cycle signal amplification triggered by Exo III cleavage was initiated, ultimately disrupting the hairpin structures of HP1 and HP2 and releasing a large amount of DOX into the solution, yielding a stronger electrochemical signal, which was low to 50 pM. This detection possesses excellent selectivity, demonstrating high application potential in biological systems, and offers simple and low-cost electrochemical detection for miR-378.

A Novel CRISPR/Cas12a-Mediated Ratiometric Dual-Signal Electrochemical Biosensor for Ultrasensitive and Reliable Detection of Circulating Tumor Deoxyribonucleic Acid

Circulating tumor DNA (ctDNA) holds great promise as a noninvasive biomarker for cancer diagnosis, treatment, and prognosis. However, the accurate and specific quantification of low-abundance ctDNA in serum remains a significant challenge. This study introduced, for the first time, a novel exponential amplification reaction (EXPAR)-assisted CRISPR/Cas12a-mediated ratiometric dual-signal electrochemical biosensor for ultrasensitive and reliable detection of ctDNA. To implement the dual-signal strategy, a signal unit (ssDNA-MB@Fc/UiO-66-NH2) was prepared, consisting of methylene blue-modified ssDNA as the biogate to encapsulate ferrocene signal molecules within UiO-66-NH2 nanocarriers. The presence of target ctDNA KRAS triggered EXPAR amplification, generating numerous activators for Cas12a activation, resulting in the cleavage of ssDNA-P fully complementary to the ssDNA-MB biogate. Due to the inability to form a rigid structure dsDNA (ssDNA-MB/ssDNA-P), the separation of ssDNA-MB biogate from the UiO-66-NH2 surface was hindered by electrostatic interactions. Consequently, the supernatant collected after centrifugation exhibited either no or only a weak presence of Fc and MB signal molecules. Conversely, in the absence of the target ctDNA, the ssDNA-MB biogate was open, leading to the leakage of Fc signal molecules. This clever ratiometric strategy with Cas12a as the "connector", reflecting the concentration of ctDNA KRAS based on the ratio of the current intensities of the two electroactive signal molecules, enhanced detection sensitivity by at least 60-300 times compared to single-signal strategies. Moreover, this strategy demonstrated satisfactory performance in ctDNA detection in complex human serum, highlighting its potential for cancer diagnosis.

A sensitive "off-on" electrochemiluminescence DNA sensor based on signal cascade amplification circuit and distance-dependent energy transfer

A sensitive "off-on" electrochemiluminescence (ECL) DNA sensor was constructed based on Exo III-assisted cascade amplification system. In the cascade amplification circuit, target DNA and Exo III cutting substrate were designed into an inverted T-shaped binding mode to form a stable DNA junction, thus effectively triggering Exo III digestion cycle. During the biosensor assembly process, ferrocene (Fc) and distance-dependent ECL resonance energy transfer (ECL-RET) and surface plasmon resonance (SPR) effects were introduced to regulate the ECL of semiconductor quantum dots (QDs). Carboxylated ZnCdSe/ZnS QDs were used as ECL signal probes and K2S2O8 was coreactant, and the initial cathodic ECL signal of QDs was efficiently quenched through electron and energy transfer with Fc and ECL-RET with Au NPs, leaving the system in "off" state. After the products of cascade amplification were introduced into the electrode surface, the single-stranded DNA modified with Fc was displaced, and the distance between Au NPs and QDs became farther, resulting in a transition from ECL-RET to SPR, and then a significant ECL signal boost was achieved, turning the system into "on" state. The combination of efficient cascade amplification system and sensitive "off-on" ECL signal change mode enabled the biosensing platform to detect target DNA with high selectivity (able to distinguish single-base mutated DNA) and ultra-high sensitivity (limit of detection was 31.67 aM, S/N = 3), providing a new perspective for designing highly sensitive and programmable ECL biosensors.

Ratiometric electrochemical biosensor based on lateral movement of multi-pedal DNA tetrahedron machine on biomimetic interface

In this work, a lateral moving multi-pedal DNA tetrahedron machine (MTM) is designed and coupled with dual-signal output system to construct a biomimetic electrochemical ratiometric strategy for ultrasensitive target DNA analysis. The tetrahedral structure provided rigid support for the pedal, ensuring efficient replacement of the rail chain modified with ferrocene. By conjugating cholesterol molecules to one vertex of MTM, it is decorated on a lipid bilayer. This molecular architecture confers lateral movement of MTM on an electrode surface while prevents its detachment from the system. The methylene blue tagged hairpin probe provides constant power to support MTM swim on lipid bilayer. Compared with the conventional motion mode, the lateral moving mechanism has the fastest reaction rate and the highest signal-to-noise ratio. Additionally, the dual-signal reporting system further improves the accuracy of target detection on the basis of ensuring motion efficiency. The work improved movement efficiency and shortened time fragment. A linear relationship between the ratio value of two reporters and target DNA concentration was observed from 0.5 fM to 50 pM with a detection limit of 28 aM. The lateral motion mode of DNA machine coalescing with ratiometric system made this sensing platform ultrasensitive and accurate, which holds new avenue of early diagnosis.

Controllable self-assembled DNA nanomachine enable homogeneous rapid electrochemical one-pot assay of lung cancer circulating tumor cells

A homogeneous rapid (45 min) one-pot electrochemical (EC) aptasensor was established to quantitatively detect circulating tumor cells (CTCs) in lung cancer patients using mucin 1 as a marker. The core of this study is that the three single-stranded DNA (Y1, Y2, and Y3) could be hybridized to form Y-shaped DNA (Y-DNA) and further self-assemble to form DNA nanosphere. The aptamer of mucin 1 could be complementary and paired with Y1, thus disrupting the conformation of the DNA nanosphere. When mucin 1 was present, the aptamer combined specifically with mucin 1, thus preserving the DNA nanosphere structure. Methylene blue (MB) acted as a signal reporter, which could be embedded between two base pairs in the DNA nanosphere to form a DNA nanosphere-MB complex, reducing free MB and resulting in a lower electrochemical signal. The results demonstrated that the linear ranges for mucin 1 and A549 cells were 1 ag/mL-1 fg/mL and 1-100 cells/mL, respectively, with minimum detectable concentrations were 1 ag/mL and 1 cell/mL, respectively. The quantitative analysis of CTCs in 44 clinical blood samples was performed, and the results were consistent with the computerized tomography (CT) images, pathological findings and folate receptor-polymerase chain reaction (FR-PCR) kits. The receiver operating characteristic (ROC) curve exhibited an area under the curve (AUC) value of 0.970. The assay revealed 100% specificity and 94.1% sensitivity. It is believed that this electrochemical aptasensor could provide a new approach to detect CTCs.

"Three-in-one" Zr-MOF Multifunctional Carrier-mediated Fluorescent and Colorimetric Dual-signal Readout Biosensing Platform to Enhance Analytical Performance

To address the urgent demand for sensitive and stable detection applications, significant efforts have been made in the development of dual-signal readout assays for precise target detection and timely health risk control. Here, a new nanomaterial, Pt@PCN-224-HRP-initiator DNA (PP-HRP-iDNA), was exploited to construct a dual-signal readout biosensing platform. Zr-MOF (PCN-224) was loaded with as many Pt nanoparticles (NPs) and as much horseradish peroxidase (HRP) as possible to enhance the brightness of the colorimetric signal recognizable to the naked eye while also acting as a gatekeeper to protect the enzyme activity and ensuring the stability of the assay process. Moreover, the Pt NPs and HRP displayed a synergistic catalytic effect, which promoted the sensitivity of detection. Further, the formation of the Zr-O-P bond eliminated the instability of the interactions between PCN-224 and iDNA in a controllable manner. After the immunoreaction, iDNA stimulated a hybridization chain reaction, resulting in a significant reduction of the fluorescent DNA in the supernatant and a fluorescent signal change. Subsequently, the PP-HRP-iDNA probe implemented UV-light response (450 nm) where 3,3',5,5'-tetramethylbenzidine was used as a substrate for the colorimetric signal readout. By virtue of the nanomaterial-modulated transduction mechanism and the antigen-antibody interactions, this dual-signal biosensor displays high sensitivity, with a limit of detection of 0.65 pg/mL for aflatoxin B₁ and 4 CFU/mL for Salmonella enteritidis, suggesting the detection potential of the biosensing platform for analyzing various targets.

Label-free ratiometric homogeneous electrochemical aptasensor based on hybridization chain reaction for facile and rapid detection of aflatoxin B1 in cereal crops

Aflatoxin B1 (AFB1) contamination has raised global concerns in agricultural and food industry; thus, sensitive, accurate and rapid AFB1 sensors are essential in many circumstances. Herein, we developed a label-free and immobilization-free ratiometric homogeneous electrochemical aptasensor based on hybridization chain reaction (HCR) for facile and rapid determination of AFB1. Methylene blue (MB) and ferrocene (Fc) were used as label-free probes to produce a response signal (I_MB) and a reference signal (I_Fc) in solution phase, respectively. The ratio of I_MB/I_Fc was used as a yardstick to quantify AFB1. HCR was exploited to enlarge the intensity of I_MB as well as ratiometric signal. By combining label-free homogeneous assay and ratiometric strategy, the resulting aptasensor offered sensitive, rapid, and reliable determinations of AFB1 with a detection limit of 38.8 pg mL^-1. The aptasensor was then used to determine AFB1 in cereal samples with comparable reliability as HPLC-MS.

A label-free and modification-free ratiometric electrochemical strategy for enhanced natural enzyme detection using a bare electrode and nanozymes system

Ratiometric electrochemical assays have been demonstrated to be more sensitive and selective in various sensing events, mainly due to their affordable built-in correction and good self-reference capability. But it is known that complicated modification and labeling operations usually are necessary for the construction of ratiometric electrochemical assays, therefore is a hot and important issue needing consideration carefully. We herein report a new yet simple bare electrode-based ratiometric electrochemical bioassay to achieve sensitive and selective analysis of alkaline phosphatase (ALP), using a liquid phase system that contains CoOOH nanozymes and commercially available indicator substrate. This proposed bioassay works based on the ratiometric change of dual electrochemical signals, arising from an exclusive target ALP-triggered hydrolysis of electrochemical substrate p-nitrophenyl phosphate (PNPP). In this design, the two hydrolyzed products of electrochemically active p-nitrophenol (PNP) and electrochemically inactive phosphate anion (PO₄^3-) are responsible together for the ratiometric electrochemical analysis of ALP. PNP exhibits a straightforward current response toward ALP content; however, PO₄^3- cannot show a direct electrochemical signal thus is rationally designed to offer an alternative response by linking it with the specific CoOOH nanozyme-catalyzed reaction of 3,3',5,5'-tetramethylbenzidine (TMB) and H₂O₂, in which the nanozyme-catalyzed product oxTMB shows a direct reduction current at the GCE, and significantly decreases with increasing PO₄^3- species due to the good inhibition of PO₄^3- toward CoOOH nanozyme activity. As a result, a ratiometric electrochemical strategy for ALP analysis with a low limit of detection of 0.366 U/L (S/N = 3) was successfully achieved by integrating the above direct and indirect dual electrochemical responses. This developed bioassay can allow the quantitative diagnosis of ALP activity especially with a label-free and modification-free merit, therefore paving the way for simple, convenient, and portable electroanalytical tools in biosensing design and application.

Contrary Logic Pair Library, Parity Generator/Checker and Various Concatenated Logic Circuits Engineered by a Label-Free and Immobilization-Free Electrochemiluminescence Resonance Energy Transfer System

Herein, a label-free and immobilization-free electrochemiluminescence resonance energy transfer (ECL-RET) system based on graphitic carbon nitride nanosheets (GCNNs)/Ru(phen)32+ donor/acceptor pair is developed, in which the ECL-RET is regulated by regulating the diffusivity of Ru(phen)32+ molecules toward the negatively charged GCNNs through logically programmed DNA hybridization reactions. The two optical signals of GCNNs (445 nm) and Ru(phen)32+ (593 nm) show completely opposite changes through the same one-time DNA hybridization reaction. Based on this ECL-RET system, a contrary logic pair (CLP) library, a parity generator/checker system for differentiating the erroneous bits during data transmission, the parity checker to identify the even/odd natural numbers from 0 to 9, and a series of concatenated logic circuits including a six-input logic gate capable of implementing of 64 input combinations for meeting the needs of computational complexity are developed. The ECL-RET-based molecular logic system avoids the time-consuming, costly and inefficient labeling procedures and the laborious processes of immobilization, presenting great potential for building more complicated and advanced logic gates, and providing a refreshing inspiration for the construction of combinatorial logic circuits based on ECL method.

Electrochemical-Based DNA Logic Devices Regulated by the Diffusion and Intercalation of Electroactive Dyes

Electrochemical-based logic gates are simple to operate, sensitive, controllable, and easy to integrate with silicon-based semiconductor logic devices, showing great application prospects and remaining largely unexplored. Herein, an immobilization-free dual-output electrochemical molecular logic system based on the different diffusivity of electroactive dyes ferrocene (Fc) and methylene blue (MB) toward an indium tin oxide (ITO) electrode under different DNA hybridization reactions was developed. In this system, the hybridization of the catalytic strand IN1 with Fc-modified hairpin DNA H1 triggered an exonuclease III (Exo III) cleavage cycle to obtain free Fc and produce a large number of long double-stranded DNAs via the hybridization chain reaction for intercalating MB, which was previously in the free state. Such a hybridization reaction caused a significant change in the diffusion capacity of MB and Fc toward the ITO electrode, resulting in two electrochemical signals with opposite changes. On this basis, a contrary logic pair library, a parity generator/checker system for differentiating the erroneous bits during data transmission, a parity checker to identify the even/odd natural numbers from 0 to 9, and a series of concatenated logic circuits for meeting the needs of computational complexity were developed. The proposed electrochemical-based molecular logic system greatly expanded the application of the electrochemical method in the construction of logic circuits and provided a conceptual prototype for the development of more advanced and complicated logic devices.

A ratiometric fluorescence assay for bleomycin based on dual-emissive chameleon DNA-templated silver nanoclusters

The authors design dual-emissive DNA-templated silver nanoclusters (DNA-AgNCs) for ratiometric fluorescence sensing bleomycin (BLM) for the first time. A hairpin probe containing two different C-rich DNA templates at two terminals is used to synthesize chameleon DNA-AgNCs, which possess two emission peaks when they are in close proximity. A strong emission is founded at 622 nm (λex = 570 nm) while a weak one is located at 572 nm (λex = 504 nm). Meanwhile, the loop of this probe contains the scission site (5'-GC-3') of BLM. The loop can be cleaved into two parts by BLM-Fe(II) complex, inducing the two DNA-AgNCs away from each other. The fluorescence intensity at 572 nm and 622 nm increases and decreases, respectively. Such chameleon DNA-AgNCs exhibit an obvious fluorescence discoloration from orange to yellow. Therefore, a sensitive ratiometric fluorescent strategy for BLM detection has been proposed with the detection limit of 67 pM. Finally, this ratiometric method is used to detect BLM in serum samples.

Ratiometric Electrochemistry: Improving the Robustness, Reproducibility and Reliability of Biosensors

Electrochemical biosensors are an increasingly attractive option for the development of a novel analyte detection method, especially when integration within a point-of-use device is the overall objective. In this context, accuracy and sensitivity are not compromised when working with opaque samples as the electrical readout signal can be directly read by a device without the need for any signal transduction. However, electrochemical detection can be susceptible to substantial signal drift and increased signal error. This is most apparent when analysing complex mixtures and when using small, single-use, screen-printed electrodes. Over recent years, analytical scientists have taken inspiration from self-referencing ratiometric fluorescence methods to counteract these problems and have begun to develop ratiometric electrochemical protocols to improve sensor accuracy and reliability. This review will provide coverage of key developments in ratiometric electrochemical (bio)sensors, highlighting innovative assay design, and the experiments performed that challenge assay robustness and reliability.

G-quadruplex based biosensor: A potential tool for SARS-CoV-2 detection

G-quadruplex is a non-canonical nucleic acid structure formed by the folding of guanine rich DNA or RNA. The conformation and function of G-quadruplex are determined by a number of factors, including the number and polarity of nucleotide strands, the type of cations and the binding targets. Recent studies led to the discovery of additional advantageous attributes of G-quadruplex with the potential to be used in novel biosensors, such as improved ligand binding and unique folding properties. G-quadruplex based biosensor can detect various substances, such as metal ions, organic macromolecules, proteins and nucleic acids with improved affinity and specificity compared to standard biosensors. The recently developed G-quadruplex based biosensors include electrochemical and optical biosensors. A novel G-quadruplex based biosensors also show better performance and broader applications in the detection of a wide spectrum of pathogens, including SARS-CoV-2, the causative agent of COVID-19 disease. This review highlights the latest developments in the field of G-quadruplex based biosensors, with particular focus on the G-quadruplex sequences and recent applications and the potential of G-quadruplex based biosensors in SARS-CoV-2 detection.

An efficient electrochemical assay for miR-3675-3p in human serum based on the nanohybrid of functionalized fullerene and metal-organic framework

Idiopathic pulmonary fibrosis (IPF) is an interstitial lung disease with unclear pathogenesis, for which diagnosis has been a great challenge. Recent researches have revealed that miR-3675-3p is a promising biomarker for IPF diagnosis. Herein, the present work describes a novel electrochemical microRNA biosensor for rapid and sensitive detection of miR-3675-3p based on multiple signal amplification strategies. First of all, fullerene (C₆₀) is doped with poly(amidoamine) (PAMAM)-functionalized metal-organic framework (MOF) to form a new nanohybrid of C₆₀@PAMAM-MOF, which exhibits more remarkable redox activity compared with the other two synthesized C₆₀-based nanohybrids when triggered by tetraoctylammonium bromide (TOAB). C₆₀@PAMAM-MOF also possesses a large specific surface area and abundant amino groups to anchor Au nanoparticles (AuNPs) for the immobilization of signal probe (SP) to form tracer label and enhance the electrochemical response signal. In addition, core@shell Au-Pt nanoparticles (Au@PtNPs) are absorbed on chitosan-acetylene black (CS-AB) to act as sensing platform, which can promote electron transfer and increase the loading of capture probe (CP). Under optimum conditions, the proposed biosensor displays a wide linear range for miR-3675-3p from 10 fM to 10 nM, with a limit of detection (LOD) as low as 2.99 fM. More significantly, this biosensor shows a lower LOD and wider linear range than that of qRT-PCR, and its trial application in human serum shows favorable results, which exhibits a promising prospect for IPF diagnosis.

One-Step Synthesis of Methylene Blue-Encapsulated Zeolitic Imidazolate Framework for Dual-Signal Fluorescent and Homogeneous Electrochemical Biosensing

In vitro diagnosis requires target biomarkers to be reliably detected at an ultralow level. A dual-signal strategy permits self-calibration to overcome the interferences of experimental and environmental factors, and thus is regarded as a promising approach. However, currently reported works mainly concentrated on the same forms of energy of output signals. Herein, we propose a one-step strategy for synthesis of methylene blue-encapsulated zeolitic imidazolate framework-90 (MB@ZIF-90) with high loading, unique dual-signal property, exceptional recognition capability, and good stability, and we further pioneer MB@ZIF-90 as a dual-signal biosensor for label-free, enzyme-free, and ultrasensitive detection of adenosine triphosphate (ATP) by integration of fluorescence and homogeneous electrochemical techniques. The recognition of MB@ZIF-90 by target ATP spurs the decomposition of ZIF-90, subsequently permitting MB to be released into a supernatant. As compared to the case where ATP does not exist, obviously increased intensities in fluorescence and differential pulse voltammetry current are observed and both signals are directly proportional to ATP concentrations. Thus, the MB@ZIF-90-based biosensor achieved dual-signal detection of ATP in an ultrasensitive manner and displayed a more reliable diagnosis result than previously reported ATP biosensors. This dual-signal strategy provides a new opportunity to develop high-performance biosensors for in vitro diagnosis and demonstrates great potential for future applications in bioinformatics and clinical medicine.

Dual-output toehold-mediated strand displacement amplification for sensitive homogeneous electrochemical detection of specie-specific DNA sequences for species identification

The determination of specie-specific DNA sequences is a key factor for identification of animal species and detection of meat adulteration. Herein, a simple homogeneous electrochemical biosensor was developed for sensitive detection of specie-specific DNA sequences from meat products based on high efficient and specific dual-output toehold-mediated strand displacement (TMSD). After incubation with target DNA, large amount of methylene blue (electrochemical signal molecule) labeled probes (MB-P) were released from preformed DNA duplex structures by the process of dual-output TMSD amplification. The free MB-P could be further digested by Exonuclease I, and the enzymatic products contain little negative charge could diffuse to the surface of indium tin oxide electrode, generating significantly electrochemical signal. As a result, the designed biosensor showed a broad dynamic range from 0.01 pM to 100 pM, with a low detection limit of 8.2 fM, and ideal selectivity and reproducibility. Meanwhile, the approach exhibited acceptable accuracy for the detection of specie-specific DNA sequences, and possessed the potential application for the identification of animal species from meat products.

Donor/Acceptor-Induced Ratiometric Photoelectrochemical Paper Analytical Device with a Hollow Double-Hydrophilic-Walls Channel for microRNA Quantification

Integrating ratiometric photoelectrochemical (PEC) techniques with paper microfluidics to construct a ratiometric PEC paper analytical device for practical application is often restricted by the grave dependence of ratiometric assay on photoactive materials and low mass-transfer rates of the paper channel. Herein, a universal donor/acceptor-induced ratiometric PEC paper analytical device with a hollow double-hydrophilic-walls channel (HDHC) was fabricated for high-performance microRNA-141 (miRNA-141) quantification. Concretely, a photoanode and photocathode were integrated on the paper-based sensing platform in which the photocathode served as a biosensing site for the pursuit of higher selectivity. For formulation of a cascading signal amplification strategy, a unique duplex-specific nuclease-induced target recycling reaction was engineered for the output of a double amount of all useful DNA linkers instead of conventional output of only one available DNA product, which could guarantee the output of abundant DNA linkers with the initiation of a cascade of hybridization chain reaction on both the trunk and branch in the presence of miRNA-141. Then the formed dendriform polymeric DNA duplex structures were further decorated with glucose oxidase (GOx)-mimicking gold nanoparticles by the electrostatic interaction to form a branchy gold tree (BGT). Profiting from the perfect GOx-mimicking activity of BGT and high mass-transfer rates of HDHC, the cathodic photocurrent from Ag₂S/Cu₂O hybrid structure was in a "signal off" state while the anodic photocurrent from graphene quantum dots (GQDs) and Ag₂Se QDs cosensitized ZnO nanosheets was in a "signal on" state because BGT-catalyzed glucose oxidation reaction evoked the consumption of dissolved O₂ as an electron acceptor and the generation of H₂O₂ as an electron donor. With calculation of the ratio of two photocurrent intensities, the quantitative detection of miRNA-141 was achieved with high sensitivity, accuracy, and reliability.