Bacterial Analysis Using an Electrochemical DNA Biosensor with Poly-Adenine-Mediated DNA Self-Assembly

Electrochemical biosensor for sensitive detection of SARS-CoV-2 gene fragments using Bi2Se3 topological insulator

In this study, we have designed an electrochemical biosensor based on topological material Bi2Se3 for the sensitive detection of SARS-CoV-2 in the COVID-19 pandemic. Flake-shaped Bi2Se3 was obtained directly from high-quality single crystals using mechanical exfoliation, and the single-stranded DNA was immobilized onto it. Under optimal conditions, the peak current of the differential pulse voltammetry method exhibited a linear relationship with the logarithm of the concentration of target-complementary-stranded DNA, ranging from 1.0 × 10-15 to 1.0 × 10-11 M, with a detection limit of 3.46 × 10-16 M. The topological material Bi2Se3, with Dirac surface states, enhanced the signal-to-interference plus noise ratio of the electrochemical measurements, thereby improving the sensitivity of the sensor. Furthermore, the electrochemical sensor demonstrated excellent specificity in recognizing RNA. It can detect complementary RNA by amplifying and transcribing the initial DNA template, with an initial DNA template concentration ranging from 1.0 × 10-18 to 1.0 × 10-15 M. Furthermore, the sensor also effectively distinguished negative and positive results by detecting splitting-synthetic SARS-CoV-2 pseudovirus with a concentration of 1 copy/μL input. Our work underscores the immense potential of the electrochemical sensing platform based on the topological material Bi2Se3 in the detection of pathogens during the rapid spread of acute infectious diseases.

Triblock polyadenine-based electrochemical aptasensor for ultra-sensitive detection of carcinoembryonic antigen via exonuclease III-assisted target recycling and hybridization chain reaction

Carcinoembryonic antigen (CEA), a key colon biomarker, demands a precise detection method for cancer diagnosis and prognosis. This study introduces a novel electrochemical aptasensor using a triblock polyadenine probe for ultra-sensitive detection of CEA. The method leverages Exonuclease III (Exo III)-assisted target recycling and hybridization chain reaction. The triblock polyadenine probe self-assembles on the bare gold electrode through the strong affinity between adenine and gold electrode, blocking CEA diffusion and providing a large immobilization surface. CEA binding to hairpin probe 1 (HP1), followed by the hybridization between HP1 and hairpin probe 2 (HP2), triggers DNA cleavage by Exo III, amplifying the signal via a hybridization chain reaction and producing numerous dsDNA walkers that generates a dramatic electrochemical impedance signal. Under optimized conditions, the aptasensor achieved two ultra-low detection limits: 0.39 ag∙mL-1 within the concentration range of 5 ag∙mL-1 to 5 × 106 ag∙mL-1, and 1.5 ag∙mL-1 within the concentration range of 5 × 106 ag∙mL-1 to 1 × 1010 ag∙mL-1. Its performance in human serum samples meets the practical standards, offering a promising new tool for ultrasensitive tumor marker detection, potentially revolutionizing early cancer diagnosis.

A multi-channel electrochemical biosensor based on polyadenine tetrahedra for the detection of multiple drug resistance genes

Antimicrobial resistance poses a serious threat to human health due to the high morbidity and mortality caused by drug-resistant microbial infections. Therefore, the development of rapid, sensitive and selective identification methods is key to improving the survival rate of patients. In this paper, a sandwich-type electrochemical DNA biosensor based on a polyadenine-DNA tetrahedron probe was constructed. The key experimental conditions were optimized, including the length of polyadenine, the concentration of the polyadenine DNA tetrahedron, the concentration of the signal probe and the hybridization time. At the same time, poly-avidin-HRP80 was used to enhance the electrochemical detection signal. Finally, excellent biosensor performance was achieved, and the detection limit for the synthetic DNA target was as low as 1 fM. In addition, we verified the practicability of the system by analyzing E. coli with the MCR-1 plasmid and realized multi-channel detection of the drug resistance genes MCR-1, blaNDM, blaKPC and blaOXA. With the ideal electrochemical interface, the polyA-based biosensor exhibits excellent stability, which provides powerful technical support for the rapid detection of antibiotic-resistant strains in the field.

Strategy, Design, and Fabrication of Electrochemical Biosensors: A Tutorial

Advanced healthcare requires novel technologies capable of real-time sensing to monitor acute and long-term health. The challenge relies on converting a real-time quantitative biological and chemical signal into a desired measurable output. Given the success in detecting glucose and the commercialization of glucometers, electrochemical biosensors continue to be a mainstay of academic and industrial research activities. Despite the wealth of literature on electrochemical biosensors, reports are often specific to a particular application (e.g., pathogens, cancer markers, glucose, etc.), and most fail to convey the underlying strategy and design, and if it is transferable to detection of a different analyte. Here we present a tutorial review for those entering this research area that summarizes the basic electrochemical techniques utilized as well as discusses the designs and optimization strategies employed to improve sensitivity and maximize signal output.

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.

Development of Optical Differential Sensing Based on Nanomaterials for Biological Analysis

The discrimination and recognition of biological targets, such as proteins, cells, and bacteria, are of utmost importance in various fields of biological research and production. These include areas like biological medicine, clinical diagnosis, and microbiology analysis. In order to efficiently and cost-effectively identify a specific target from a wide range of possibilities, researchers have developed a technique called differential sensing. Unlike traditional "lock-and-key" sensors that rely on specific interactions between receptors and analytes, differential sensing makes use of cross-reactive receptors. These sensors offer less specificity but can cross-react with a wide range of analytes to produce a large amount of data. Many pattern recognition strategies have been developed and have shown promising results in identifying complex analytes. To create advanced sensor arrays for higher analysis efficiency and larger recognizing range, various nanomaterials have been utilized as sensing probes. These nanomaterials possess distinct molecular affinities, optical/electrical properties, and biological compatibility, and are conveniently functionalized. In this review, our focus is on recently reported optical sensor arrays that utilize nanomaterials to discriminate bioanalytes, including proteins, cells, and bacteria.

Construction of an Enzyme Cascade Based on the Accurate Adjacent Arrangement of Coupled Enzymes Using a Triblock PolyA DNA Probe

Intracellular enzyme cascades are essential for various biological processes, and mimicking their functions in artificial systems has attracted significant research attention. However, achieving convenient and efficient spatial organization of enzymes on interfaces remains a critical challenge. In this work, we designed a simple single-DNA scaffold using triblock polyA single-stranded DNA for the arrangement of coupled enzymes. The scaffold was assembled onto a gold electrode through the affinity of polyA-Au, and two enzymes (glucose oxidase and horseradish peroxidase) were captured through hybridization. The molecular distance between the enzymes was regulated by changing the length of the polyA fragment. As a proof of concept, a glucose biosensor was constructed based on the enzyme cascade amplification. The biosensor exhibited excellent detection capability for glucose in human serum samples with a limit of detection of 1.6 μM. Additionally, a trienzyme cascade reaction was successfully activated, demonstrating the potential scalability of our approach for multienzyme reactions. This study provides a promising platform for the development of easy-to-operate, highly efficient, and versatile enzyme cascade systems using DNA scaffolds.

Poly-adenine-mediated tetrahedral DNA nanostructure with multiple target-recognition sites for ultrasensitive and rapid electrochemical detection of Aflatoxin B1

Tetrahedral DNA nanostructures (TDNs) are widely used in the development of electrochemical biosensors due to their structural stability, programmability, and strong interfacial orderliness. However, the complex modifications on the electrode and the single vertex target recognition of the TDNs limit their applications in electrochemical biosensing. Herein, we developed a universal detection system based on a novel polyadenine-based tetrahedral DNA nanostructure (ATDN) using Aflatoxin B1 (AFB1) as the model target for analysis. In the absence of target AFB1, the signal probes (SP) modified with ferrocene would be anchored by five aptamers on ATDN. The target capture by aptamers led to a release of SP from the electrode surface, resulting in a significant reduction of the electrochemical signal. This new nanostructure was not only dispensed with multi-step electrode modifications and strong mechanical rigidity but also had five modification sites which enhanced the detection sensitivity for the target. As a result, this biosensor shows good analytical performance in the linear range of 1 fg mL-1 to 1 ng mL-1, exhibiting a low detection limit of 0.33 fg mL-1. Satisfactory accuracy has also been demonstrated through good recoveries (95.2%-98.9%). The proposed new tetrahedral DNA nanostructure can provide a more rapid and sensitive alternative to previous electrochemical sensors based on the conventional TDN. Since DNA sequences can be designed flexibly, the sensing platform in this strategy can be extended to detect various targets in different fields.

Electrochemical nucleic acid sensors: Competent pathways for mobile molecular diagnostics

Electrochemical nucleic acid biosensor has demonstrated great promise in clinical diagnostic tests, mainly because of its flexibility, high efficiency, low cost, and easy integration for analytical applications. Numerous nucleic acid hybridization-based strategies have been developed for the design and construction of novel electrochemical biosensors for diagnosing genetic-related diseases. This review describes the advances, challenges, and prospects of electrochemical nucleic acid biosensors for mobile molecular diagnosis. Specifically, the basic principles, sensing elements, applications in diagnosis of cancer and infectious diseases, integration with microfluidic technology and commercialization are mainly included in this review, aiming to provide new insights and directions for the future development of electrochemical nucleic acid biosensors.

Rose bengal-mediated photoinduced atom transfer radical polymerization for high sensitivity detection of target DNA

Convenient and sensitive detection of biomolecules is of utmost importance in the field of early disease screening. In this study, a Rose Bengal-Mediated photoinduced atom transfer radical polymerization (photoATRP) method was used to achieve highly sensitive detection of target DNA (tDNA). The tDNA was specifically recognized using PNA with terminal modified sulfhydryl groups, and the initiator α-bromophenylacetic acid (BPAA) was attached to the electrode surface via a phosphate-Zr⁴⁺-carboxylate acid structure. Under the excitation of blue light, rose bengal (RB) acts as a photocatalyst, β-nicotinamide adenine dinucleotide (NADH) as an electron donor, and ferrocenylmethyl methacrylate (FMMA) as a monomer to activate the photoATRP reaction and generate a large number of electroactive polymer chains on the electrode surface. Under optimal conditions, the method can be used for the quantitative analysis of tDNA in the concentration range of 1-10⁵ fM (R² = 0.994) with a limit of detection (LOD) of 0.115 fM. This metal-free mediated photoATRP biosensor, with low cost and environmental friendliness, has great potential in the field of highly sensitive biomolecule detection.

Electrochemical Detection of Femtomolar DNA via Boronate Affinity-Mediated Decoration of Polysaccharides with Electroactive Tags

In view of their high efficiency and cost-effectiveness, polymers are of great promise as carriers for signal tags in amplified detection. Herein, we present a polysaccharide-amplified method for the electrochemical detection of a BRCA1 breast cancer gene-derived DNA target at the femtomolar levels. Briefly, peptide nucleic acid (PNA) with a complementary sequence was tethered as the capture probe for the DNA target, to which carboxyl group-containing polysaccharides were then attached via facile phosphate-Zr(IV)-carboxylate crosslinking, followed by the decoration of polysaccharide chains with electroactive ferrocene (Fc) signal tags via affinity coupling between a cis-diol site and phenylboronic acid (PBA) group. As the polysaccharide chain contains hundreds of cis-diol sites, boronate affinity can enable the site-specific decoration of each polysaccharide chain with hundreds of Fc signal tags, efficiently transducing each target capture event into the decoration of many Fc signal tags. As polysaccharides are cheap, renewable, ubiquitous, and biodegradable natural biopolymers, the use of polysaccharides for signal amplification offers the benefits of high efficiency, cost-effectiveness, excellent biocompatibility, and environmental friendliness. The linear range of the polysaccharide-amplified method for DNA detection was demonstrated to be from 10 fM to 10 nM (R² = 0.996), with the detection limit as low as 2.9 fM. The results show that this method can also discriminate single base mismatch with satisfactory selectivity and can be applied to DNA detection in serum samples. In view of these merits, the polysaccharide-amplified PNA-based electrochemical method holds great promise in DNA detection with satisfactory sensitivity and selectivity.

Rapid detection of miRNA via development of consecutive adenines (polyA)-based electrochemical biosensors

Herein, we report rapid electrochemical detection of miRNA let-7a based on a DNA probe consisting of a polyA and Fc-co-labeled harpin structure (the polyA-H probe). The polyA-H probe could be facilely immobilized on Au surfaces through the interactions between polyA and Au, followed by its pre-hybridization with a single strand (S1). The probe's surface density could be optimized for minimizing steric hindrance via changing the polyA block length. The target let-7a could be rapidly amplified via loop-mediated isothermal amplification (LAMP) with four simplified primers, followed by inducing the formation of dimeric i-motif (DIM) structure via H⁺-induced rapid folding of two C-rich sequences of motif strand 1 and strand 2. It was found that, after introducing the as-formed DIM to hybridize the S1, the immobilized polyA₂₀-H probe could rapidly revert to its hairpin structure, sending out a turn-on electrochemical signal of the Fc. The total time for detecting the let-7a was around 80 min, obviously less than that of most of electrochemical DNA sensors reported previously. The biosensor showed a linear relationship of the current response to the let-7a in the range of 10 fM to 50 nM with a limit of detection (LOD) of 5.1 fM. Our biosensors were further tested using human serum spiked with the let-7a and the extracts of the breast adenocarcinoma cells spiked with and without the let-7a, respectively. Satisfied results were obtained. This study shows a potential promising future of development of electrochemical biosensors for rapid detection of miRNAs in the application of clinical practice.

Aptamer-Target Recognition-Promoted Ratiometric Electrochemical Strategy for Evaluating the Microcystin-LR Residue in Fish without Interferences

Given the significance of food safety, it is highly urgent to develop a sensitive yet reliable sensor for the practical analysis of algal toxins. As most of the developed sensors are disturbed by interfering substances and the target toxin is detected in a single-signal manner based on the immunoassay technology. Herein, we developed an aptamer-based dual-signal ratiometric electrochemical sensor for the sensitive and accurate analysis of microcystin-LR (MC-LR), using it as a proof-of-concept analyte. Methylene blue-tagged ssDNA (MB-ssDNA) was immobilized at the gold electrode surface accompanied with the absence of ferrocene-tagged ssDNA (Fc-ssDNA), resulting in a high differential pulse voltammetry (DPV) current of MB and a low DPV current of Fc. The recognition of MB-ssDNA by MC-LR stimulated the formation of MC-LR@MB-ssDNA, which induced the removal of MB-ssDNA from the electrode and the exposure of SH-ssDNA, enabling Fc-ssDNA to be captured at the electrode surface via nucleic acid hybridization. In comparison with MC-LR deficiency, the DPV signal of MB dropped along with an improved DPV signal of Fc, contributing to the ratiometric detection of MC-LR, with the limit of detection down to 0.0015 nM. Furthermore, this ratiometric electrochemical sensor was successfully explored to assess the bioaccumulated amount of MC-LR in the liver and meat of fish. The aptamer-based ratiometric strategy to develop an electrochemical MC-LR assay will offer a promising avenue to develop high-performance sensors, and the sensor will find more useful application in MC-LR-related aquatic product safety studies.

Coenzyme-catalyzed electroinitiated reversible addition fragmentation chain transfer polymerization for ultrasensitive electrochemical DNA detection

Ultrasensitive detection of biomarkers at an early stage is generally limited by external influence factors such as high reaction temperature, complex operations, and sophisticated instruments. Here, we circumvent these problems by using nicotinamide adenine dinucleotide (NAD⁺) to control electroinitiated reversible addition fragmentation chain transfer (electro-RAFT) polymerization for biosensing that enables the detection of a few molecules of target DNA. In this coenzyme-catalyzed electro-RAFT polymerization, numerous ferrocenylmethyl methacrylate (FCMMA) as monomer with electrochemistry signal were linked to the biomarker on Au electrode. Afterwards, a strong oxidation peak appears at the potential of about 0.3 V that represents a typical oxidation potential of FCMMA. The sensitivity of this methodology was presented by detecting DNA from 10^-1 to 10⁴ fM concentration and detection limit (LOD) being down to 4.39 aM in 10 μL samples. This is lower by factors than detection limits of most other ultra-sensitive electrochemical DNA assays.

Development of pattern recognition based on nanosheet-DNA probes and an extendable DNA library

Pattern recognition, also called "array sensing," is a recognition strategy with a wide and expandable analysis range, based on high-throughput analysis data. In this work, we constructed a sensor array for the identification of targets including bacterial pathogens and proteins by using FAM-labeled DNA probes and 2D nanosheet materials. We designed an ordered and extendible DNA library for the collection of recognition probes. Unlike traditional DNA probes with random and massive sequences, our DNA library was constructed following a 5-digit binary number (00000-11111, 0 = CCC, and 1 = TTT), and especially, 8 special symmetry sequences were chosen from the library. Two different nanosheet materials were used as the quencher. When targets were added, the interaction between DNA and the nanosheets was competitively affected, and as a result, the fluorescence signal changed accordingly. Finally, by using our fluorescent sensor array, 17 bacteria and 8 proteins were precisely recognized. We believe that our work has provided a simple and valuable strategy for the improvement of the recognition range and discrimination precision for the development of pattern recognition.

Electrochemical Analysis of Target-Induced Hairpin-Mediated Aptamer Sensors

The state of probe DNA at the biosensing interface greatly affects the detection performance of electrochemical DNA biosensors. Herein, we constructed a target-induced hairpin-mediated biosensing interface to study the effect of probe DNA on the analytical performance of adenosine triphosphate aptamer (ATPA) and adenosine triphosphate (ATP) detection. Moreover, we also explored the electrochemical contribution of the coexisting hairpin and double-stranded DNA (dsDNA) to this sensing interface. Experimental results suggested that the molecular recognition ability and detection performance of the biosensing interface were majorly dependent on the surface density of methylene blue (MB)-labeled probe hairpin DNA and partly affected by the spatial state of the formed dsDNA. When the surface density of hairpin DNA was moderate (5.72 pmol cm^-2), this sensing interface determined as low as 0.74 fM ATPA and 5.04 pM ATP with high selectivity and excellent regeneration, respectively. Furthermore, we calculated that the formed dsDNA had a 31.87% contribution in the total electrochemical signal for 10 pM ATPA detection. Based on the above results, we designed an XOR logic gate based on the biosensing interface for ATPA and ATP detection.

Efficient immobilization of aptamers on the layered double hydroxide nanohybrids for the electrochemical proteins detection

Despite the use of layered double hydroxides (LDH) in different electrochemical (bio)sensors, the construction of aptasensors using LDH-based surfaces was not reported to the best of our knowledge. This may be due to the lack of a suitable linker to attach aptamers to the LDH-modified surface. LDH-based aptasensors are established here as very sensitive and reliable devices in serum and cerebrospinal fluid (CSF) analysis. 5'-NH₂ DNA aptamer probes were immobilized on the LDH-based surfaces in a vertical conformation without any linker materials. Due to the low electron conductivity of the LDH, carbon nanotubes (CNT) with high electronic conductivity and high surface area were combined with LDH. Thrombin was used as a model protein for aptasensing. The sensor shows a linear range of 0.005-12,000 pmol L^-1 and a limit of detection of 0.1 fmol L^-1. Moreover, the aptasensor was used for the sensing of thrombin in CSF and serum samples acquired from both healthy and patients with different disease.

DNA/RNA Electrochemical Biosensing Devices a Future Replacement of PCR Methods for a Fast Epidemic Containment

Pandemics require a fast and immediate response to contain potential infectious carriers. In the recent 2020 Covid-19 worldwide pandemic, authorities all around the world have failed to identify potential carriers and contain it on time. Hence, a rapid and very sensitive testing method is required. Current diagnostic tools, reverse transcription PCR (RT-PCR) and real-time PCR (qPCR), have its pitfalls for quick pandemic containment such as the requirement for specialized professionals and instrumentation. Versatile electrochemical DNA/RNA sensors are a promising technological alternative for PCR based diagnosis. In an electrochemical DNA sensor, a nucleic acid hybridization event is converted into a quantifiable electrochemical signal. A critical challenge of electrochemical DNA sensors is sensitive detection of a low copy number of DNA/RNA in samples such as is the case for early onset of a disease. Signal amplification approaches are an important tool to overcome this sensitivity issue. In this review, the authors discuss the most recent signal amplification strategies employed in the electrochemical DNA/RNA diagnosis of pathogens.

A dual signal amplification strategy combining thermally initiated SI-RAFT polymerization and DNA-templated silver nanoparticles for electrochemical determination of DNA

A highly sensitive method is described for determination of DNA. It is based on dual signal amplification, viz. (a)DNA-templated metal deposition, and (b) thermally initiated surface-initiated reversible addition-fragmentation chain transfer (SI-RAFT) polymerization. A peptide nucleic acid (PNA) with a terminal thiol group was grasped onto a gold electrode by self-assembly. The modified electrode serves as a probe to selectively capture target DNA (tDNA). In the next step, Zr(IV) ions are bound to the phosphate groups of the tDNA. A chain-transfer agent (CTA) for thermally initiated SI-RAFT polymerization, 4-cyano-4-(phenylcarbonothioylthio)pentanoic acid (CPAD), was immobilized on tDNA by conjugation of the carboxy group to Zr(IV) ions. Subsequently, numerous monomers of glycosyloxyethyl methacrylate (GEMA) were connected to the CPAD by thermally initiated SI-RAFT polymerization with azobisisobutyronitrile (AIBN) serving as the free-radical thermal initiator. Afterwards, hydroxyl groups of the GEMA were oxidized to aldehyde groups reacting with sodium periodate, and silver nanoparticles were further introduced on the surface of electrode via "silver mirror reaction". This results in a large electrochemical signal amplification. Under optimized conditions, the electrochemical signal (best measured at a working potential of 0 V vs. SCE (KCl; 3 M)) increases linearly with the logarithm of tDNA concentration in the 10 to 10⁶ aM concentration range. The detection limit is as low as 5.6 aM (~34 molecules in a 10 μL sample). This is lower by factors between 2 and 1800 times than detection limits of most other ultra-sensitive electrochemical DNA assays. Graphical abstractSchematic representation of a dual signal amplification strategy combining thermally initiated surface-initiated reversible addition-fragmentation chain transfer polymerization (SI-RAFT) and DNA-templated silver nanoparticles for electrochemical determination of DNA.

Ultrasensitive Electrochemical DNA Biosensor Based on a Label-Free Assembling Strategy Using a Triblock polyA DNA Probe

Multiblock DNA probe attracted a large amount of scientific attention, for the development of multitarget biosensor and improved specificity/sensitivity. However, the development of multiblock DNA probes highly relied on the chemical synthesis of organic linkers or nanomaterials, which limited their practicability and biological compatibility. In this work, we developed a label-free assembling strategy using a triblock DNA capture probe, which connects two DNA probes with its intrinsic polyA fragment (probe-PolyA-probe, PAP). The middle polyA segment has a high affinity to the gold electrode surface, leading to excellent reproducibility, stability, and regeneration of our biosensor. Two flanking capture probes were tandemly co-assembled on the electrode surface with consistent spatial relationship and exactly the same amount. When combined with the target DNA, the hybridization stability was improved, because of the strong base stacking effect of two capture probes. The sensitivity of our biosensor was proved to be 10 fM, with a wide analysis range between 10 fM to 1 nM. Our PAP-based biosensor showed excellent specificity when facing mismatched DNA sequences. Even single nucleotide polymorphisms can be distinguished by each probe. The excellent practicability of our biosensor was demonstrated by analyzing genomic DNA both with and without PCR amplification.

Ultrasensitive Electrochemical Biosensor of Bacterial 16S rRNA Gene Based on polyA DNA Probes

Traditional microbiology analysis is usually hindered by the long time-cost and lack of portability in many urgent situations. In this work, we developed a novel electrochemical DNA biosensor (E-biosensor) for sensitive analysis of the 16S rRNA gene of five bacteria, using a consecutive adenine (polyA) probe. The polyA probe consists of a polyA tail and a recognition part. The polyA tail can combine onto the gold surface with improved controllability of the surface density, by conveniently changing the length of polyA. The recognition part of the capture probe together with two biotin-labeled reporter probes hybridize with the target DNA and form a stable DNA-tetramer sandwich structure, and then avidin-HRP enzyme was added to produce a redox current signal for the following electrochemical detection. Finally, we realized sensitive quantification of artificial target DNA with a limit of detection (LOD) of 10 fM, and excellent selectivity and reusability were also demonstrated. Importantly, the detection capability was equally good when facing bacterial genomic DNA, due to the base-stacking force of our multireporter-probe system, which can help to break the second structure and stabilize the probe-target complexes. Our biosensor was constructed on a 16-channel electrode chip without any polymerase chain reaction (PCR) process needed, which took a significant step toward a portable bacteria biosensor.

Electrochemical biosensor for methyl parathion based on single-walled carbon nanotube/glutaraldehyde crosslinked acetylcholinesterase-wrapped bovine serum albumin nanocomposites

Semiconducting single-walled carbon nanotubes (s-SWCNTs) have been demonstrated as an excellent material for transistors, miniaturized devices and sensors due to their high carrier mobility, stability, scattering-free ballistic transport of carriers etc. Herein, we have designed a biosensor to selectively detect methyl parathion (MP, organophosphorus pesticide) using glutaraldehyde (Glu) cross-linked with acetylcholinesterase (AChE) immobilized on s-SWCNTs wrapped with bovine serum albumin (BSA). The fabricated biosensor was characterized and confirmed by Fourier-transform infrared spectroscopy (FT-IR), cyclic voltammetry (CV), electrochemical impedance spectroscopy (EIS) and square wave voltammetry (SWV). In the presence of MP, the effective interaction between AChE and MP favours the accumulation of MP-AChE complex on the glassy carbon electrode (GCE) surface which reduces the electron transfer property. Based on this interaction, detection of various concentration of MP was demonstrated by SWV using BSA/AChE-Glu-s-SWCNTs composite modified electrode. The proposed biosensor exhibited a wide linear range (WLR) for MP target in 100 mM phosphate buffered saline solution (PBS) (pH 7.4) from 1 × 10^-10 M to 5 × 10^-6 M with a limit of detection (LOD) of 3.75 × 10^-11 M. In addition, the BSA/AChE-Glu-s-SWCNTs/GCE biosensor showed good repeatability and reproducibility for MP detection. Moreover, the proposed biosensor showed better electrode stability when stored at 4 °C. This new electrochemical biosensor is also exhibited high selectivity and sensitivity for MP, which made it possible to test MP in real strawberry and apple juices. Furthermore, the BSA/AChE-Glu-s-SWCNTs/GCE offered a favourable electron transfer between the acetylthiocholine chloride (ATCl) and electrode interface than BSA/AChE-s-SWCNTs/GCE, s-SWCNTs/GCE and bare GCE.

Constructing Submonolayer DNA Origami Scaffold on Gold Electrode for Wiring of Redox Enzymatic Cascade Pathways

Advances in biomimetic microelectronics offer a range of patterned assemblies of proteins and cells for in vitro metabolic engineering where coordinated biochemical pathways allow cell metabolism to be characterized and potentially controlled on a chip. To achieve these goals, developing new methods for interfacing biological systems to microelectronic devices has been in urgent demand. Here, we report the assembly of a DNA origami-templated enzymatic cascade (glucose oxidase and horseradish peroxidase) on gold electrodes, where a monolayer of DNA origami is anchored on gold electrodes via Au-S chemistry, to create programmable, electrochemically driven biomimetic device containing both biochemical and electronic components. Upon the posing of a specific electrical potential, substrates/products flow through the enzyme pair and the end product transfers electrons to the electrode. The steady state flux of the distance-dependent enzymatic cascade reactions is translated into a steady state current signal that records the overall enzyme activity. This biological system can be finely tuned by varying the distance between the enzyme pair, which opens new routes to interface microelectronic devices to biological functions.

Redox Engineering of Cytochrome c using DNA Nanostructure-Based Charged Encapsulation and Spatial Control

Three-dimensional (3D) DNA nanostructures facilitate the directed self-assembly of various objects with designed patterns with nanometer scale addressability. Here, we report the enhancement of cytochrome c (cyt c) redox activity by using a designed 3D DNA nanostructure attached to a gold electrode to spatially control the position of cyt c within the tetrahedral framework. Charged encapsulation and spatial control result in the significantly increased redox potential and enhanced electron transfer of this redox protein when compared to cyt c directly adsorbed on the gold surface. Two different protein attachment sites on one double stranded edge of a DNA tetrahedron were used to position cyt c inside and outside of the cage. Cyt c at both binding sites show similar redox potential shift and only slight difference in the electron transfer rate, both orders of magnitude faster than the cases when the protein was directly deposited on the gold electrode, likely due to an effective electron transfer pathway provided by the stabilization effect of the protein created by the DNA framework. This study shows great potential of using structural DNA nanotechnology for spatial control of protein positioning on electrode, which opens new routes to engineer redox proteins and interface microelectronic devices with biological function.

Facilely prepared low-density DNA monolayer-based electrochemical biosensor with high detection performance in human serum

Presently, most reported electrochemical biosensors, for highly sensitive and selective detection of nucleic acid, still require multiple, time-consuming assembly steps and high-consumption DNA probes as well as lack good performance in human serum, which greatly limit their applicability. Herein, an easy-to-fabricate electrochemical DNA biosensor constructed by assembly of bovine serum albumin (BSA) followed with direct incubation of amplified products has been proposed. This method combined terminal deoxynucleoside transferase (TdTase)-mediated isothermal amplification and polyHRP catalysis to achieve dual-signal enhancement, and was featured with low-density DNA monolayer for its employment of only 2 nM capture probes. Surprisingly, based on the low-density DNA monolayer, the steric hindrance effect of polyHRP could effectively restrain the background compared with HRP, which further pushes the signal-to-noise (S/N) ratio to 70 than that of most currently available methods. Additionally, this strategy also showed favorable specificity and powerful anti-interference in human serum, and thus potentially attractive for diagnosis of diseases.

In situ electron microscopy of the self-assembly of single-stranded DNA-functionalized Au nanoparticles in aqueous solution

Solution-phase self-assembly of DNA-functionalized nanoparticles into mesoscale structures is a promising strategy for creating functional materials from nanocrystal building blocks. The predominant approach has been the use of Watson-Crick base pairing between complementary bases in designated 'sticky ends' to trigger programmable self-assembly into ordered superlattices. Here we demonstrate the ordered self-assembly of Au nanoparticles conjugated with single-stranded (ss) DNA in acidic solutions. Au nanoparticles functionalized with thiolated ssDNA are protected against coalescence and the DNA conformation undergoes significant modifications at low pH, which can be associated with the protonation of adenine bases and the formation of a parallel poly-adenine duplex, which govern the interaction between ssDNA-Au nanoparticle conjugates. In situ liquid cell electron microscopy enables real-time imaging of the self-assembly process and the identification of key characteristics, such as the preferred structural motifs and interparticle separations in the native solution environment. Our results highlight alternatives to conventional base-pairing interactions for building DNA-directed nanoparticle superlattices.

A label-free electrochemical aptasensor based on magnetic biocomposites with Pb2+-dependent DNAzyme for the detection of thrombin

Herein, a novel magnetic biocomposite (Fe₃O₄@Au-S1/S2) was applied to analyze thrombin. The Fe₃O₄@Au-S1/S2 consisted of Fe₃O₄@Au nanoparticles (Fe₃O₄@Au NPs) as carriers for magnetic separation and magnetic field-induced self-assembly, thiolated complementary strand (S1) anchored based on Au-S bond and thrombin binding aptamer (S2) as a recognition element. As a redox indicator, methylene blue (MB) can be adsorbed to DNA anchored on the surface of Fe₃O₄@Au NPs by electro-static interaction. In the absence of thrombin, MB were adsorbed on double-stranded DNA (S1/S2) which anchored on Fe₃O₄@Au NPs and a high electrochemical signal of MB was recorded by Differential pulse voltammetry. Conversely, the complementary strand (S1) exposed after thrombin competitively bonded with aptamer. The introduction of Pb²⁺-dependent DNAzyme (S3) split S1 at specific rA site, resulting in the significantly decreased adsorption capacity of MB. Thus, the thrombin detection could be recorded by monitoring the electrochemical signal reduction of MB through incubation of thrombin with S3. This method exhibited a high sensitivity toward thrombin with a broad linear range from 5 pmol L^-1 to 5 nmol L^-1 and a limit of detection of 1.8 pmol L^-1.