Ratiometric electrochemical proximity assay for sensitive one-step protein detection

Triblock PolyA-Mediated Protein Biosensor Based on a Size-Matching Proximity Hybridization Analysis

The antibodies in the natural biological world utilize bivalency/multivalency to achieve a higher affinity for antigen capture. However, mimicking this mechanism on the electrochemical sensing interface and enhancing biological affinity through precise spatial arrangement of bivalent aptamer probes still pose a challenge. In this study, we have developed a novel self-assembly layer (SAM) incorporating triblock polyA DNA to enable accurate organization of the aptamer probes on the interface, constructing a "lock-and-key-like" proximity hybridization assay (PHA) biosensor. The polyA fragment acts as an anchoring block with a strong affinity for the gold surface. Importantly, it connects the two DNA probes, facilitating one-to-one spatial proximity and enabling a controllable surface arrangement. By precisely adjusting the length of the polyA fragment, we can tailor the distance between the probes to match the molecular dimensions of the target protein. This design effectively enhances the affinity of the aptamers. Notably, our biosensor demonstrates exceptional specificity and sensitivity in detecting PDGF-BB, as confirmed through successful validation using human serum samples. Overall, our biosensor presents a novel and versatile interface for proximity assays, offering a significantly improved surface arrangement and detection performance.

Extended Review Concerning the Integration of Electrochemical Biosensors into Modern IoT and Wearable Devices

Electrochemical biosensors include a recognition component and an electronic transducer, which detect the body fluids with a high degree of accuracy. More importantly, they generate timely readings of the related physiological parameters, and they are suitable for integration into portable, wearable and implantable devices that are significant relative to point-of-care diagnostics scenarios. As an example, the personal glucose meter fundamentally improves the management of diabetes in the comfort of the patients' homes. This review paper analyzes the principles of electrochemical biosensing and the structural features of electrochemical biosensors relative to the implementation of health monitoring and disease diagnostics strategies. The analysis particularly considers the integration of the biosensors into wearable, portable, and implantable systems. The fundamental aim of this paper is to present and critically evaluate the identified significant developments in the scope of electrochemical biosensing for preventive and customized point-of-care diagnostic devices. The paper also approaches the most important engineering challenges that should be addressed in order to improve the sensing accuracy, and enable multiplexing and one-step processes, which mediate the integration of electrochemical biosensing devices into digital healthcare scenarios.

Proximity hybridization induced bipedal DNA walker and rolling circle amplification for label-free electrochemical detection of apolipoprotein A4

Apolipoprotein A4 (Apo-A4) is considered as a prospective molecular biomarker for diagnosis of depression due to its neurosynaptic toxicity. We develop a proximity hybridization-induced DNAzyme-driven bipedal DNA walker strategy for Apo-A4 quantification based on rolling circle amplification (RCA) triggered by poly adenine binding to Ag nanoparticles (AgNPs). With the help of DNAzyme, the free-running bipedal DNA walker can quickly and sequentially shear a molecular beacon that acts as a primer to initiate the RCA process, producing a large number of long DNA strands containing numerous adenines. The long repetitive adenine strands then absorb large amounts of AgNPs on the electrode interface, which is then electrochemically stripped of the AgNPs. The method has a linear detection range of 0.001 ∼ 100 ng mL-1 and a detection limit of 0.46 pg mL-1. The presented detection strategy is label-free, which allows high sensitivity and selectivity for detection of a wide range of protein targets by corresponding DNA-based affinity probes, which have potential applications in bioanalysis.

Rationally Designed DNA-Based Scaffolds and Switching Probes for Protein Sensing

The detection of a protein analyte and use of this type of information for disease diagnosis and physiological monitoring requires methods with high sensitivity and specificity that have to be also easy to use, rapid and, ideally, single step. In the last 10 years, a number of DNA-based sensing methods and sensors have been developed in order to achieve quantitative readout of protein biomarkers. Inspired by the speed, specificity, and versatility of naturally occurring chemosensors based on structure-switching biomolecules, significant efforts have been done to reproduce these mechanisms into the fabrication of artificial biosensors for protein detection. As an alternative, in scaffold DNA biosensors, different recognition elements (e.g., peptides, proteins, small molecules, and antibodies) can be conjugated to the DNA scaffold with high accuracy and precision in order to specifically interact with the target protein with high affinity and specificity. They have several advantages and potential, especially because the transduction signal can be drastically enhanced. Our aim here is to provide an overview of the best examples of structure switching-based and scaffold DNA sensors, as well as to introduce the reader to the rational design of innovative sensing mechanisms and strategies based on programmable functional DNA systems for protein detection.

Synthesis of Site-Specific Antibody-[60]Fullerene-Oligonucleotide Conjugates for Cellular Targeting

An ideal therapeutic antibody-oligonucleotide conjugate (AOC) would be a uniform construct, contain a maximal oligonucleotide (ON) payload, and retain the antibody (Ab)-mediated binding properties, which leads to an efficient delivery of the ON cargo to the site of therapeutic action. Herein, [60]fullerene-based molecular spherical nucleic acids (MSNAs) have been site-specifically conjugated to antibodies (Abs), and the Ab-mediated cellular targeting of the MSNA-Ab conjugates has been studied. A well-established glycan engineering technology and robust orthogonal click chemistries yielded the desired uniform MSNA-Ab conjugates (MW ∼ 270 kDa), with an oligonucleotide (ON):Ab ratio of 24:1, in 20-26% isolated yields. These AOCs retained the antigen binding properties (Trastuzumab's binding to human epidermal growth factor receptor 2, HER2), studied by biolayer interferometry. In addition, Ab-mediated endocytosis was demonstrated with live-cell fluorescence and phase-contrast microscopy on BT-474 breast carcinoma cells, overexpressing HER2. The effect on cell proliferation was analyzed by label-free live-cell time-lapse imaging.

Recent advances in electrochemical proximity ligation assay

Proximity ligation assay (PLA) is a vigorously developed homogeneous immunoassay assisted by DNA combining dual recognition of target protein by pairs of proximity probes, in which the detection of protein is tactfully converted to the detection of DNA. The booming developments in PLA have enabled a variety of ultrasensitive assays for the detection of protein and this concept of PLA is also extended to the detection of nucleic acids and some small molecule. The association between PLA and electrochemical method, defined as electrochemical proximity ligation assay (ECPLA), has gained much interests in disease diagnosis, food safety and environmental assays with the advantages, such as broad range of targets, simplicity, low cost and rapid response. In this review, we took a different perspective to present the history of PLA, the classical ECPLA biosensing methodology as well as the developments of ECPLA based on several key parameters, such as sensitivity, selectivity, reusability and generalization. In addition, the developments of PLA with electrochemiluminescence as readout are also presented. Finally, perspective and some unresolved challenges in ECPLA that can potentially be addressed have also been discussed.

Device integration of electrochemical biosensors

Electrochemical biosensors incorporate a recognition element and an electronic transducer for the highly sensitive detection of analytes in body fluids. Importantly, they can provide rapid readouts and they can be integrated into portable, wearable and implantable devices for point-of-care diagnostics; for example, the personal glucose meter enables at-home assessment of blood glucose levels, greatly improving the management of diabetes. In this Review, we discuss the principles of electrochemical biosensing and the design of electrochemical biosensor devices for health monitoring and disease diagnostics, with a particular focus on device integration into wearable, portable and implantable systems. Finally, we outline the key engineering challenges that need to be addressed to improve sensing accuracy, enable multiplexing and one-step processes, and integrate electrochemical biosensing devices in digital health-care pathways.

Optimization of biofilm conductance measurement with two-electrode microbial electrochemical cells (MECs)

This study was conducted to develop a standardized and consistent method for biofilm conductance measurement for an improved comprehension of extracellular electron transfer. Biofilm conductance (2.12 ± 0.25 × 10^-4 S) with and without a fixed anode potential did not show significant difference. The conductance showed a sigmoidal relationship with anode potential. The current-voltage profile of the tested biofilm at applied voltage larger than 100 mV showed deviation from Ohm's law. Up to 69% decrease in biofilm conductance and deviation from Ohm's law were observed in the current-voltage profile when the measurement time increased. By choosing the voltage range (0- 100 mV) and step (25 mV), measurement time (100-s at each voltage step), and anode control mode, these operation settings were found more suitable for consistent and accurate biofilm conductance measurement in the 2-Au MEC system. This represents the first study that comprehensively evaluated the environmental and instrumental parameters for biofilm conductance measurement.

Ratiometric Electrochemical Biosensing of Methyltransferase Activity

In this work, a novel ratiometric electrochemical readout platform was proposed and developed for the fast and flexible analysis of M.SssI methyltransferase (MTase) activity. In this platform, two hairpin DNAs (H1 and H2) were designed. H1 contains the palindromic sequence of 5′-CCGG-3′ in its stem which could be methylated and hybridize with H2 labeled by methylene blue (MB) as one of the signal reporters on a gold electrode (GE) in the presence of M.SssI MTase. Additionally, a specific immunoreaction was introduced by conjugating an anti-5-methylcytosine antibody, a DNA CpG methylation recognition unit, with 1,3-ferrocenedicarboxylic acid (Fc) as the second signal reporter. The results showed that when the Fc tag approaches, the MB tag was far from the gold electrode surface, resulting in a decrease in the oxidation peak current of MB (IMB) and an increase in the oxidation peak current of Fc (IFc). The ratiometric electrochemical method above shows the linear range of detection was 0 U/mL 40 U/mL with a detection limit of 0.083 U/mL (the mean signal of blank measures þ3s).

Proximity binding induced nucleic acid cascade amplification strategy for ultrasensitive homogeneous detection of PSA

In this work, based on the powerful cycle amplification cascades of proximity hybridization-induced hybridization chain reaction and catalyzed hairpin assembly, we engineered a nonenzymatic and ultrasensitive method which combined the Mg²⁺-DNAzyme recycling signal amplification for the analysis of the human prostate specific antigen. Herein, we adopted PSA-conjugates as triggers in the self-assembly process of two hairpin DNAs (H1, H2) into the products of the CHA which could activate the HCR to induce repeated hybridization. And both ends of each adjacent sequence of the HCR products could form a unit of Mg²⁺-DNAzyme which in presence of cofactor Mg²⁺ could recognize and cyclically cleave the hairpin probes in the solution and thus generate observably enhanced fluorescent signal. Benefit from the nucleic acid circuit amplification strategy, PSA of concentration low to 0.73 pg mL^-1 was detected in this system. This homogeneous sensing method in solution avoid the use of the sophisticated equipment and complex operation, as well as addition of artificial enzyme, thus greatly reducing the constraints and complexity of experimental conditions. Moreover, considering most protein biomarkers in serum don't have their corresponding aptamers, this sensing method provide a general sensing approach for homogeneous sensitive detection of these important protein biomarkers which transfer rough antigen-antibody interactivity to smart signal amplification sensing strategies, thus exhibiting a remarkable prospect in clinical application.

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.

Nonenzymatic Electrochemical Sensor with Ratiometric Signal Output for Selective Determination of Superoxide Anion in Rat Brain

There is still an urgent need to develop reliable analytical methods of O₂^•- in vivo for deeply elucidating the roles of O₂^•- playing in the brain. Herein, a nonenzymatic electrochemical sensor with ratiometric signal output was developed for an in vivo analysis of O₂^•- in the rat brain. Diphenylphosphonate-2-naphthol ester (ND) was designed and synthesized as a specific recognition molecule for the selective determination of O₂^•-. An anodic peak ascribed to the oxidation of 2-naphthol was generated via the nucleophilic substitution between ND and O₂^•- and was increased with the increasing concentration of O₂^•-. Meanwhile, the inner reference of methylene blue (MB) was co-assembled at the electrode surface to enhance the determination accuracy of O₂^•-. The anodic peak current ratio between 2-naphthol and MB exhibited a good linear relationship with the concentration of O₂^•- from 2 to 200 μM. Because of the stable molecule character of ND and its specific reaction with O₂^•-, the developed electrochemical sensor demonstrated excellent selectivity toward various potential interferences in the brain and good stability even after storage for 7 days. Accordingly, the present electrochemical sensor with high selectivity, high stability, and high accuracy was successfully exploited in monitoring the levels of O₂^•- in the rat brain and that of the diabetic model followed by cerebral ischemia.

Semi-quantitative and quantitative detection of ochratoxin A in agricultural by-products using a self-assembling immunochromatographic strip

BACKGROUND

The toxicity and health risks of mycotoxins have encouraged increased awareness and strict monitoring of these contaminants in agricultural by-products. In this paper, we developed and tested a sensitive, selective, and self-assembling immunochromatographic (IC) strip for on-site detection of ochratoxin A (OTA). We were able to demonstrate semi-quantitative and quantitative detection of OTA in agricultural by-product samples.

RESULTS

The optimized IC strip had a limit of detection (LOD) of 0.5 ng mL^-1 OTA using the naked eye for semi-quantitative detection. When a digitized strip reader was used to achieve quantitative results, the LOD for OTA was reduced to 0.1 ng mL^-1 with a linear detection range of 0.1-10 ng mL^-1 . We also evaluated the specificity, stability, accuracy, and precision of the IC strip and demonstrated high performance in all of these areas. We then confirmed the ability of the IC strip to visually detect OTA contamination in authentic agricultural by-product samples from the markets in China. Furthermore, quantitative detection of OTA using the IC strip showed that the concentration of OTA ranged from 1.7 to 101.3 ng g^-1 in the positive agricultural by-product samples, correlating well with the measurements obtained via liquid chromatography with tandem mass spectrometry.

CONCLUSION

The results indicated that this proposed IC strip was capable of sensitive, semi-quantitative, quantitative, and on-site detection of OTA contamination in agricultural by-product samples. © 2020 Society of Chemical Industry.

Electrochemical prostate-specific antigen biosensors based on electroconductive nanomaterials and polymers

Prostate cancer (PCa), the second most malignant neoplasm in men, is also the fifth leading cause of cancer-related deaths in men globally. Unfortunately, this malignancy remains largely asymptomatic until late-stage emergence when treatment is limited due to the lack of effective metastatic PCa therapeutics. Due to these limitations, early PCa detection through prostate-specific antigen (PSA) screening has become increasingly important, resulting in a more than 50% decrease in mortality. Conventional assays for PSA detection, such as enzyme-linked immunosorbent assay (ELISA), are labor intensive, relatively expensive, operator-dependent and do not provide adequate sensitivity. Electrochemical biosensors overcome these limitations because they are rapid, cost-effective, simple to use and ultrasensitive. This article reviews electrochemical PSA biosensors using electroconductive nanomaterials such as carbon-, metal-, metal oxide- and peptide-based nanostructures, as well as polymers to significantly improve conductivity and enhance sensitivity. Challenges associated with the development of these devices are discussed thus providing additional insight into their analytic strength as well as their potential use in early PCa detection.

An electrochemical aptasensor for amyloid-β oligomer based on double-stranded DNA as "conductive spring"

In order to overcome the antibody-based sensor's shortcomings, an electrochemical aptamer (Apt)-based sensor was developed for amyloid-β₄₀ oligomer (Aβ_40-O). The aptasensor was constructed by locating Apt and ferrocence (Fc) on streptavidin-modified gold (SA-gold) nanoparticles. The obtained AptFc@SA-gold nanoparticles were linked onto the Au electrode via the connection of double-stranded DNA (dsDNA) as a "conductive spring." The determination of Aβ_40-O was performed with square-wave voltammetry (SWV). Upon bio-recognition between Apt and Aβ_40-O, the conformation of Apt changed and the formed Apt/Aβ_40-O complex separated from the SA-gold surface. As a result, the surface charge of SA-gold positively shifted, weakening the electrostatic attraction between the SA-gold and the positively charged Au electrode surface (at potential range of 0.1~0.5 V, corresponding to the Fc redox transformation), and stretching the dsDNA chain. Based on the exponential decay of dsDNA's electron transfer efficiency on its chain stretching, the oxidation current density from Fc decreased and displayed linear correlation to the concentration of Aβ_40-O. A wide linear range of 0.100 nM to 1.00 μM with a low detection limit of 93.0 pM was obtained. The aptasensor displayed excellent selectivity toward Aβ_40-O in contrast to other possible interfering analogs (Aβ₄₀ monomer, Aβ₄₂ monomer, and oligomer) at × 100 higher concentrations. The recoveries for Aβ_40-O-spiked artificial cerebrospinal fluid and healthy human serum were 94.0~104% and 92.8~95.4%, respectively. The electrochemical aptasensor meets the demands of clinic determination of Aβ_40-O, which is significant for the early diagnosis of AD. Graphical abstract Schematic representation of the electrochemical aptasensor for amyloid-β oligomer based on the surface charge change induced by target binding.

Nonfaradaic Current Suppression in DNA-Based Electrochemical Assays with a Differential Potentiostat

One of the key factors limiting sensitivity in many electrochemical assays is the nonfaradaic or capacitive current. This is particularly true in modern assay systems based on DNA monolayers at gold electrode surfaces, which have shown great promise for bioanalysis in complex milieu such as whole blood or serum. While various changes in analytical parameters, redox reporter molecules, DNA structures, probe coverage, and electrode surface area have been shown useful, background reduction by hardware subtraction has not yet been explored for these assays. Here, we introduce new electrochemistry hardware that considerably suppresses nonfaradaic currents through real-time analog subtraction during current-to-voltage conversion in the potentiostat. This differential potentiostat (DiffStat) configuration is shown to suppress or remove capacitance currents in chronoamperometry, cyclic voltammetry, and square-wave voltammetry measurements applied to nucleic acid hybridization assays at the electrode surface. The DiffStat makes larger electrodes and higher sensitivity settings accessible to the user, providing order-of-magnitude improvements in sensitivity, and it also significantly simplifies data processing to extract faradaic currents in square-wave voltammetry (SWV). Because two working electrodes are used for differential measurements, unique arrangements are introduced such as converting signal-OFF assays to signal-ON assays or background drift correction in 50% human serum. Overall, this new potentiostat design should be helpful not only in improving the sensitivity of most electrochemical assays, but it should also better support adaptation of assays to the point-of-care by circumventing complex data processing.

Antibody-Oligonucleotide Conjugates as Therapeutic, Imaging, and Detection Agents

Antibody-oligonucleotide conjugates (AOCs) are a novel class of synthetic chimeric biomolecules that has been continually gaining traction in different fields of modern biotechnology. This is mainly due to the unique combination of the properties of their two constituents, exceptional targeting abilities and antibody biodistribution profiles, in addition to an extensive scope of oligonucleotide functional and structural roles. Combining these two classes of biomolecules in one chimeric construct has therefore become an important milestone in the development of numerous biotechnological applications, including imaging (DNA-PAINT), detection (PLA, PEA), and therapeutics (targeted siRNA/antisense delivery). Numerous synthetic approaches have been developed to access AOCs ranging from stochastic chemical bioconjugation to site-specific conjugation with reactive handles, introduced into antibody sequences through protein engineering. This Review gives a general overview of the current status of AOC applications with a specific emphasis on the synthetic methods used for their preparation. The reported synthetic techniques are discussed in terms of their practical aspects and limitations. The importance of the development of novel methods for the facile generation of AOCs possessing a defined constitution is highlighted as a priority in AOC research to ensure the advance of their new applications.

Cellular interface supported toehold strand displacement cascade for amplified dual-electrochemical signal and its application for tumor cell analysis

In this work, toehold strand displacement cascade (TSDC) has been delicately designed and carried out on the cellular interface for the amplification and output of dual-electrochemical signal. Specifically, antibody cross-linked T strand can recognize cell which is linked with immune-magnetic bead. Subsequently, T strand on the cellular interface can mediate the occurrence of TSDC, resulting the change of SN₃/S1-MB to SN₃/S2-Fc ratio in the supernatant after magnetic separation. The resultant SN₃/S1-MB and SN₃/S2-Fc can be immobilized on the electrode interface through click chemistry and give the amplified double electrochemical signal. So the tumor cell amount can closely correlate with the change of the double signal. Except for output of the double signal for improvement of analytical accuracy, the double magnetic separation not only eliminate the interference of the complicated substances in serum, but also remove the influence of cell on click reaction on the electrode interface. So based on cellular interface supported TSDC for amplified dual-electrochemical signal, the established method has been successfully applied to analyze the tumor cells in serum accurately and sensitively.

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

BACKGROUND

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

METHODS

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

RESULTS

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

CONCLUSION

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

Development of the covalent antibody-DNA conjugates technology for detection of IgE and IgM antibodies by immuno-PCR

Immuno-PCR (iPCR) is one of the methods used for the detection of a wide range of analytes and features the high sensitivity of the polymerase chain reaction (PCR) method. iPCR uses antibodies coupled to DNA, followed by the amplification of the attached DNA using RT-PCR. Two major types of antibody-DNA conjugates are currently used, which are obtained as a result of non-covalent (biotin-streptavidin) or covalent interactions. Using a strain-promoted azide-alkyne cycloaddition (SPAAC), we synthesized covalent DNA-antibody conjugates, optimized the reaction conditions, and developed an efficient protocol for the purification of conjugates, with which all unreacted antibodies and oligonucleotides are separated. Covalent DNA-antibody conjugates were tested with iPCR assays that were previously developed for the detection of IgE and IgM antibodies with the use of the supramolecular complex of 5'- and 3'-biotinylated DNA and streptavidin. The results show that the modification of antibodies with amino groups did not allow us to obtain monolabeled antibodies or antibodies with a strictly defined number of DNA-labels. The degree of labeling determined by the dyes introduced through the azido group reflects the actual labeling degree statistically. If the average labeling degree for azido groups is 1.1, the conjugates contain 25% mono-labeled antibodies, 50% double-labeled antibodies, and 25% unlabeled ones. The specificity of the monoclonal antibody to human IgE (BE5) changed after conjugation with the oligonucleotide. The sensitivity of iPCR in the detection of IgM antibodies produced against the Le^C disaccharide using a covalent conjugate was similar to that of a supramolecular complex of 5'- and 3'-biotinylated DNA and streptavidin, but the new procedure is two steps shorter.

An ultrasensitive electrochemical immunoassay based on a proximity hybridization-triggered three-layer cascade signal amplification strategy

An ultrasensitive electrochemical immunoassay based on a proximity hybridization-triggered three-layer cascade signal amplification strategy.

A new electrochemical aptasensor for sensitive assay of a protein based on the dual-signaling electrochemical ratiometric method and DNA walker strategy

Herein, a new electrochemical aptamer-based biosensor for highly sensitive assay of thrombin has been developed based on the dual-signaling electrochemical ratiometric method and the DNA walker strategy, and shows a low detection limit of about 56 fM.

Electrochemical screening of single nucleotide polymorphisms with significantly enhanced discrimination factor by an amplified ratiometric sensor

The detection of single nucleotide polymorphisms (SNPs) is of great clinical significance to the diagnosis of various genetic diseases and cancers. In this work, the development of an ultrasensitive ratiometric electrochemical sensor for screening SNP with a significantly enhanced discrimination factor is reported. The ferrocene (Fc) and methylene blue (MB) dual-tagged triple helix complex (THC) probes are self-assembled on the gold electrode to construct the sensing interface. The addition of the mutant p53 gene causes the disassembly of the THC probes with the release of the Fc-tagged sequence and the folding of the MB-labeled sequence into a hairpin structure, causing the change in the current response ratio of MB to Fc for monitoring the mutant p53 gene. Such ratio is dramatically enhanced by the toehold-mediated displacement reaction-assisted target recycling amplification with the presence of an assistance hairpin sequence. With the significant signal amplification and the advantageous specificity of the THC probes, sub-femtomolar detection limit and a highly enhanced SNP discrimination factor for the mutant p53 gene can be obtained. Besides, the proof-of-demonstration application of the sensor for diluted real samples has been verified, offering such sensor new opportunities for monitoring various genetic related diseases.

Molecular Machine Powered Surface Programmatic Chain Reaction for Highly Sensitive Electrochemical Detection of Protein

A bipedal molecular machine powered surface programmatic chain reaction was designed for electrochemical signal amplification and highly sensitive electrochemical detection of protein. The bipedal molecular machine was built through aptamer-target specific recognition for the binding of one target protein with two DNA probes, which hybridized with surface-tethered hairpin DNA 1 (H1) via proximity effect to expose the prelocked toehold domain of H1 for the hybridization of ferrocene-labeled hairpin DNA 2 (H2-Fc). The toehold-mediated strand displacement reaction brought the electrochemical signal molecule Fc close to the electrode and meanwhile released the bipedal molecular machine to traverse the sensing surface by the surface programmatic chain reaction. Eventually, a large number of duplex structures of H1-H2 with ferrocene groups facing to the electrode were formed on the sensor surface to generate an amplified electrochemical signal. Using thrombin as a model target, this method showed a linear detection range from 2 pM to 20 nM with a detection limit of 0.76 pM. The proposed detection strategy was enzyme-free and allowed highly sensitive and selective detection of a variety of protein targets by using corresponding DNA-based affinity probes, showing potential application in bioanalysis.

Biomacromolecular nanostructures-based interfacial engineering: from precise assembly to precision biosensing

Biosensors are a type of important biodevice that integrate biological recognition elements, such as enzyme, antibody and DNA, and physical or chemical transducers, which have revolutionized clinical diagnosis especially under the context of point-of-care tests. Since the performance of a biosensor depends largely on the bio–solid interface, design and engineering of the interface play a pivotal role in developing quality biosensors. Along this line, a number of strategies have been developed to improve the homogeneity of the interface or the precision in regulating the interactions between biomolecules and the interface. Especially, intense efforts have been devoted to controlling the surface chemistry, orientation of immobilization, molecular conformation and packing density of surface-confined biomolecular probes (proteins and nucleic acids). By finely tuning these surface properties, through either gene manipulation or self-assembly, one may reduce the heterogeneity of self-assembled monolayers, increase the accessibility of target molecules and decrease the binding energy barrier to realize high sensitivity and specificity. In this review, we summarize recent progress in interfacial engineering of biosensors with particular focus on the use of protein and DNA nanostructures. These biomacromolecular nanostructures with atomistic precision lead to highly regulated interfacial assemblies at the nanoscale. We further describe the potential use of the high-performance biosensors for precision diagnostics.

Engineering Biosensors with Dual Programmable Dynamic Ranges

Although extensively used in all fields of chemistry, molecular recognition still suffers from a significant limitation: host-guest binding displays a fixed, hyperbolic dose-response curve, which limits its usefulness in many applications. Here we take advantage of the high programmability of DNA chemistry and propose a universal strategy to engineer biorecognition-based sensors with dual programmable dynamic ranges. Using DNA aptamers as our model recognition element and electrochemistry as our readout signal, we first designed a dual signaling "signal-on" and "signal-off" adenosine triphosphate (ATP) sensor composed of a ferrocene-labeled ATP aptamer in complex to a complementary, electrode-bound, methylene-blue labeled DNA. Using this simple "dimeric" sensor, we show that we can easily (1) tune the dynamic range of this dual-signaling sensor through base mutations on the electrode-bound DNA, (2) extend the dynamic range of this sensor by 2 orders of magnitude by using a combination of electrode-bound strands with varying affinity for the aptamers, (3) create an ultrasensitive dual signaling sensor by employing a sequestration strategy in which a nonsignaling, high affinity "depletant" DNA aptamer is added to the sensor surface, and (4) engineer a sensor that simultaneously provides extended and ultrasensitive readouts. These strategies, applicable to a wide range of biosensors and chemical systems, should broaden the application of molecular recognition in various fields of chemistry.

Dual-signal ratiometric electrochemiluminescence assay for detecting the activity of human methyltransferase

A ratiometric electrochemiluminescence assay using CdS:Eu NCs and luminol as signal emitters was fabricated for detecting the human methyltransferase activity.

A reusable ratiometric electrochemical biosensor on the basis of the binding of methylene blue to DNA with alternating AT base sequence for sensitive detection of adenosine

We develop a reusable ratiometric electrochemical biosensor on the basis of the binding of methylene blue (MB) to DNA with alternating AT base sequence for sensitive detection of adenosine. We design a strand 1 with MB-modified thymine (T) base in the proximal 3' termini as the capture probe for its immobilization on the gold electrode and a 3' termini ferrocene (Fc)-modified aptamer for the recognition of adenosine. The hybridization of strand 1 with the aptamer leads to the formation of a double-stranded DNA (dsDNA) and consequently the away of MB from the electrode surface and the close of Fc to the electrode surface, generating a small value of I_MB/I_Fc (I_MB and I_Fc are the peak currents of MB and Fc, respectively). In the presence of adenosine, its binding with the aptamer induces the release of Fc from the electrode surface and the close of MB to the electrode surface, generating a large value of I_MB/I_Fc. As a result, adenosine may be accurately quantified by the measurement of ratiometric signal (I_MB/I_Fc). This ratiometric electrochemical biosensor can be simply fabricated and exhibits high sensitivity with a limit of detection of as low as 90.8pM and a large dynamic range from 0.1nM to 100μM. Moreover, this biosensor demonstrates good performance with excellent selectivity, regeneration capability, high reliability and good reproducibility, and may become a universal platform for the detection of various biomolecules which can be recognized by aptamers, holding great potential for further applications in biomedical research and clinical diagnosis.

Highly sensitive electrochemical nuclear factor kappa B aptasensor based on target-induced dual-signal ratiometric and polymerase-assisted protein recycling amplification strategy

In this work, an amplified electrochemical ratiometric aptasensor for nuclear factor kappa B (NF-κB) assay based on target binding-triggered ratiometric signal readout and polymerase-assisted protein recycling amplification strategy is described. To demonstrate the effect of "signal-off" and "signal-on" change for the dual-signal electrochemical ratiometric readout, the thiol-hairpin DNA (SH-HD) hybridizes with methylene blue (MB)-modified protection DNA (MB-PD) to form capture probes, which is rationally introduced for the construction of the assay platform. On the interface, the probes can specifically bind to target NF-κB and expose a toehold region which subsequently hybridizes with the ferrocene (Fc)-modified DNA strand to take the Fc group to the electrode surface, accompanied by displacing MB-PD to release the MB group from the electrode surface, leading to the both "signal-on" of Fc (I_Fc) and "signal-off" of MB (I_MB). In order to improve the sensitivity of the electrochemical aptasensor, phi29-assisted target protein recycling amplification strategy was designed to achieve an amplified ratiometric signal. With the above advantages, the prepared aptasensor exhibits a wide linear range of 0.1pgmL^-1 to 15ngmL^-1 with a low detection limit of 0.03pgmL^-1. This strategy provides a simple and ingenious approach to construct ratiometric electrochemical aptasensor and shows promising potential applications in multiple disease marker detection by changing the recognition probe.

Electro-Grafted Electrode with Graphene-Oxide-Like DNA Affinity for Ratiometric Homogeneous Electrochemical Biosensing of MicroRNA

This work demonstrated for the first time a simple and rapid approach to endow the electrode with the excellent discrimination ability over single-stranded DNA (ssDNA) and double-stranded DNA (dsDNA) through the robust electrochemical grafting of in situ generated 1-naphthalenesulfonate (NS^-) diazonium salt onto the surface of indium tin oxide (ITO) electrode. On the basis of understanding the influence of sequence and length on the binding affinity of ssDNA and dsDNA toward NS^- grafted ITO (NS^--ITO) electrode, these interesting findings were successfully employed to rationally develop a ratiometric homogeneous electrochemical biosensing platform for microRNA based on the affinity-mediated signal transduction. The achievement of ultrasensitive detection of microRNA lies in a compatibly designed T7 exonuclease-assisted isothermal amplification strategy, in which the presence of target microRNA initiated the continual and opposite affinity inversion of two rationally engineered electrochemical signal reporters, methylene blue (MB) labeled hairpin reporter and ferrocene (Fc) labeled dsDNA reporter, toward NS^--ITO electrode, thereby providing the ratiometric transduction and amplification of the homogeneous electrochemical output signal. By measuring the distinct variation in the peak current intensity ratios of Fc and MB tags, this ratiometric homogeneous electrochemical microRNA biosensing platform showed a detection limit of 25 aM, which is much lower than that of the reported homogeneous electrochemical biosensors. Therefore, we envision that the proposed approach will find useful applications in disease molecular diagnoses and biomedicine.

Double-loop hairpin probe and doxorubicin-loaded gold nanoparticles for the ultrasensitive electrochemical sensing of microRNA

An electrochemical microRNA (miRNA) analysis platform by combining double-loop hairpin probe (DHP) and doxorubicin-loaded gold nanoparticles (AuNPs@Dox) for ultrasensitive miRNA detection is proposed. Firstly, we here report a DHP that is simultaneously engineered to incorporate a miRNA recognition sequence, an output segment and output's complementary fragment. The important aspect of this hairpin probe is that it would not be degraded by duplex specific nuclease (DSN) and circumvents elaborately chemical modification disadvantages encountered by classic molecular beacon. For the DHP-based DSN signal amplification system, DHP hybridizes with target miRNA to form DNA-miRNA heteroduplexes, and the DSN can hydrolyze the DNA in the heteroduplexes structure selectively, while released target miRNA strand can initiate another cycle resulting in a significant signal amplification and the accumulated output segments could be responsible for strand displacement on the electrode directly. Furthermore, a great deal of doxorubicin (Dox) are loaded on the gold nanoparticles (AuNPs) to fabricate the AuNPs@Dox biocomposites that could magnify the electrochemical signal and enable the ultrasensitive analysis of miRNA. As a result, the miRNA was capable of being detected in a limit of 0.17pM and other kinds of miRNA were discriminated facilely by this method. The described DHP as a toolbox and the nano-biocomposites as a novel signal material would not only promote the design of electrochemical biosensors but also open a good way to promote the establishment of test method in malignant tumors.

Integrated signal probe based aptasensor for dual-analyte detection

For the multi-analyte detection, although the sensitivity has commonly met the practical requirements, the reliability, reproducibility and stability need to be further improved. In this work, two different aptamer probes labeled with redox tags were used as signal probe1 (sP1) and signal probe2 (sP2), which were integrated into one unity DNA architecture to develop the integrated signal probe (ISP). Comparing with the conventional independent signal probes for the simultaneous multi-analyte detection, the proposed ISP was more reproducible and accurate. This can be due to that ISP in one DNA structure can ensure the completely same modification condition and an equal stoichiometric ratio between sP1 and sP2, and furthermore the cross interference between sP1 and sP2 can be successfully prevented by regulating the complementary position of sP1 and sP2. The ISP-based assay system would be a great progress for the dual-analyte detection. Combining with gold nanoparticles (AuNPs) signal amplification, the ISP/AuNPs-based aptasensor for the sensitive dual-analyte detection was explored. Based on DNA structural switching induced by targets binding to aptamer, the simultaneous dual-analyte detection was simply achieved by monitoring the electrochemical responses of methylene blue (MB) and ferrocene (Fc) This proposed detection system possesses such advantages as simplicity in design, easy operation, good reproducibility and accuracy, high sensitivity and selectivity, which indicates the excellent application of this aptasensor in the field of clinical diagnosis or other molecular sensors.

Aptamer/Protein Proximity Binding-Triggered Molecular Machine for Amplified Electrochemical Sensing of Thrombin

The development of convenient and sensitive methods without involving any enzymes or complex nanomaterials for the monitoring of proteins is of great significance in disease diagnostics. In this work, we describe the validation of a new aptamer/protein proximity binding-triggered molecular machinery amplification strategy for sensitive electrochemical assay of thrombin in complex serum samples. The sensing interface is prepared by self-assembly of three-stranded DNA complexes on the gold electrode. The association of two distinct functional aptamers with different sites of thrombin triggers proximity binding-induced displacement of one of the short single-stranded DNAs (ssDNAs) from the surface-immobilized three-stranded DNA complexes, exposing a prelocked toehold domain to hybridize with a methylene blue (MB)-tagged fuel ssDNA strand (MB-DNA). Subsequent toehold-mediated strand displacement by the MB-DNA leads to the release and recycling of the aptamer/protein complexes and the function of the molecular machine. Eventually, a large number of MB-DNA strands are captured by the sensor surface, generating drastically amplified electrochemical responses from the MB tags for sensitive detection of thrombin. Our signal amplified sensor is completely enzyme-free and shows a dynamic range from 5 pM to 1 nM with a detection limit of 1.7 pM. Such sensor also has a high specificity for thrombin assay in serum samples. By changing the affinity probe pairs, the developed sensor can be readily expanded as a more general platform for sensitive detection of different types of proteins.

An electrochemical method for sensitive and rapid detection of FAM134B protein in colon cancer samples

Despite the excellent diagnostic applications of the current conventional immunoassay methods such as ELISA, immunostaining and Western blot for FAM134B detection, they are laborious, expensive and required a long turnaround time. Here, we report an electrochemical approach for rapid, sensitive, and specific detection of FAM134B protein in biological (colon cancer cell extracts) and clinical (serum) samples. The approach utilises a differential pulse voltammetry (DPV) in the presence of the [Fe(CN)₆]^3-/4- redox system to quantify the FAM134B protein in a two-step strategy that involves (i) initial attachment of FAM134B antibody on the surface of extravidin-modified screen-printed carbon electrode, and (ii) subsequent detection of FAM134B protein present in the biological/clinical samples. The assay system was able to detect FAM134B protein at a concentration down to 10 pg μL^-1 in phosphate buffered saline (pH 7.4) with a good inter-assay reproducibility (% RSD = <8.64, n = 3). We found excellent sensitivity and specificity for the analysis of FAM134B protein in a panel of colon cancer cell lines and serum samples. Finally, the assay was further validated with ELISA method. We believe that our assay could potentially lead a low-cost alternative to conventional immunological assays for target antigens analysis in point-of-care applications.

Ratiometric electrochemical detection of hydrogen peroxide and glucose

Hydrogen peroxide (H₂O₂) detection is of high importance as it is a versatile (bio)marker whose detection can indicate the presence of explosives, enzyme activity and cell signalling pathways. Herein, we demonstrate the rapid and accurate ratiometric electrochemical detection of H₂O₂ using disposable screen-printed electrodes through a reaction-based indicator assay. Ferrocene derivatives equipped with self-immolative linkers and boronic acid ester moieties were synthesised and tested, and, through a thorough assay optimisation, the optimum probe showed good stability, sensitivity and selectivity towards H₂O₂. The optimised conditions were then applied to the indirect detection of glucose via an enzymatic assay, capable of distinguishing 10 μM from the background within minutes.

A sensitive ratiometric electrochemical biosensor based on DNA four-way junction formation and enzyme-assisted recycling amplification

We develop a ratiometric electrochemical biosensor for DNA assay based on DNA four-way junction formation and enzyme-assisted recycling amplification.

A potentiometric resolved ratiometric photoelectrochemical aptasensor

A novel ratiometric photoelectrochemical aptasensor based on the potentiometric resolved photocurrents generated from different PEC active materials was designed for the first time.

Target-induced cyclic DNAzyme formation for colorimetric and chemiluminescence imaging assay of protein biomarkers

A target-induced cyclic strategy for DNAzyme formation was developed for simple and sensitive colorimetric and chemiluminescence detection of protein biomarkers.