Sequence-Specific Detection of Femtomolar DNA via a Chronocoulometric DNA Sensor (CDS): Effects of Nanoparticle-Mediated Amplification and Nanoscale Control of DNA Assembly at Electrodes

Hybridization-driven synchronous regeneration of biosensing interfaces for Listeria monocytogenes based on recognition of fullerol to single- and double-stranded DNA

A novel sensitive and reusable electrochemical biosensor for Listeria monocytegenes DNA has been constructed based on the recognition of water-soluble hydroxylated fullerene (fullerol) to single- and double-stranded DNA. First, the fullerol was electrodeposited on glassy carbon electrode (GCE), acting as a matrix for non-covalent adsorption of single-stranded probe DNA. Upon hybridization with the target DNA, the double helix structure was formed and desorbed from the electrode surface, driving synchronous regeneration of the biosensing interfaces. The biosensor showed a probe DNA loading density of 144 pmol∙cm-2 with the hybridization efficiency of 72.2%. The biosensor is applicable for the analysis of target DNA in actual milk samples with recoveries between 101.0% and 104.0%. This sensing platform provides a simple method for the construction of sensitive and reusable biosensor to monitor Listeria monocytogenes-related food pollution.

Electrocatalysis in MOF Films for Flexible Electrochemical Sensing: A Comprehensive Review

Flexible electrochemical sensors can adhere to any bendable surface with conformal contact, enabling continuous data monitoring without compromising the surface's dynamics. Among various materials that have been explored for flexible electronics, metal-organic frameworks (MOFs) exhibit dynamic responses to physical and chemical signals, offering new opportunities for flexible electrochemical sensing technologies. This review aims to explore the role of electrocatalysis in MOF films specifically designed for flexible electrochemical sensing applications, with a focus on their design, fabrication techniques, and applications. We systematically categorize the design and fabrication techniques used in preparing MOF films, including in situ growth, layer-by-layer assembly, and polymer-assisted strategies. The implications of MOF-based flexible electrochemical sensors are examined in the context of wearable devices, environmental monitoring, and healthcare diagnostics. Future research is anticipated to shift from traditional microcrystalline powder synthesis to MOF thin-film deposition, which is expected to not only enhance the performance of MOFs in flexible electronics but also improve sensing efficiency and reliability, paving the way for more robust and versatile sensor technologies.

Sensing of gene expression in live cells using electrical impedance spectroscopy and DNA-functionalized gold nanoparticles

A novel electrical impedance spectroscopy-based method for non-destructive sensing of gene expression in living cells is presented. The approach used takes advantage of the robustness and responsiveness of electrical impedance spectroscopy and the highly specific and selective nature of DNA hybridization. The technique uses electrical impedance spectroscopy and gold nanoparticles functionalized with single-stranded DNA complementary to an mRNA of interest to provide reliable, real-time, and quantifiable data on gene expression in live cells. The system was validated by demonstrating specific detection of the uidA mRNA, which codes for the β-glucuronidase (GUS) enzyme, in Solanum lycopersicum MsK8 cells. Gold nanoparticles were functionalized with single-stranded DNA oligonucleotides consisting of either a sequence complementary to uidA mRNA or an arbitrary sequence. The DNA-functionalized gold nanoparticles were mixed with cell suspensions, allowing the gold nanoparticles to penetrate into the cells. The impedance spectra of suspensions of cells with gold nanoparticles inserted within them were then studied. In suspensions of uidA-expressing cells and gold nanoparticles functionalized with the complementary single-stranded DNA oligonucleotide, the impedance magnitude in the frequency range of interest was significantly higher (146 %) in comparison to all other controls. Due to its highly selective nature, the methodology has the potential to be used as a precision agricultural sensing system for accurate and real-time detection of markers of stress, viral infection, disease, and normal physiological activities.

A flash signal amplification approach for ultrasensitive and rapid detection of single nucleotide polymorphisms in tuberculosis

In recent years, the demand for rapid, sensitive, and simple methods for diagnosing deoxyribonucleic acid (DNA) has grown due to the increase in the variation of infectious diseases. This work aimed to develop a flash signal amplification method coupled with electrochemical detection for polymerase chain reaction (PCR)-free tuberculosis (TB) molecular diagnosis. We exploited the slightly miscible properties of butanol and water to instantly concentrate a capture probe DNA, a single-stranded mismatch DNA, and gold nanoparticles (AuNPs) to a small volume to reduce the diffusion and reaction time in the solution. In addition, the electrochemical signal was enhanced once two strands of DNA were hybridized and bound to the surface of the gold nanoparticle at an ultra-high density. To eliminate non-specific adsorption and identify mismatched DNA, the self-assembled monolayers (SAMs) and Muts proteins were sequentially modified on the working electrode. This sensitive and specific approach can detect as low as attomolar levels of DNA targets (18 aM) and is successfully applied to detecting tuberculosis-associated single nucleotide polymorphisms (SNPs) in synovial fluid. More importantly, as this biosensing strategy can amplify the signal in only a few seconds, it possesses a great potential for point-of-care and molecular diagnosis applications.

Multi-Walled Carbon Nanotube Array Modified Electrode with 3D Sensing Interface as Electrochemical DNA Biosensor for Multidrug-Resistant Gene Detection

Drug resistance in cancer is associated with overexpression of the multidrug resistance (MDR1) gene, leading to the failure of cancer chemotherapy treatment. Therefore, the establishment of an effective method for the detection of the MDR1 gene is extremely crucial in cancer clinical therapy. Here, we report a novel DNA biosensor based on an aligned multi-walled carbon nanotube (MWCNT) array modified electrode with 3D nanostructure for the determination of the MDR1 gene. The microstructure of the modified electrode was observed by an atomic force microscope (AFM), which demonstrated that the electrode interface was arranged in orderly needle-shaped protrusion arrays. The electrochemical properties of the biosensor were characterized by cyclic voltammetry (CV), differential pulse voltammetry (DPV), and electrochemical impedance spectroscopy (EIS). Chronocoulometry (CC) was used for the quantitative detection of the MDR1 gene. Taking advantage of the good conductivity and large electrode area of the MWCNT arrays, this electrochemical DNA sensor achieved a dynamic range from 1.0 × 10-12 M to 1.0 × 10-8 M with a minimal detection limit of 6.4 × 10-13 M. In addition, this proposed DNA biosensor exhibited high sensitivity, selectivity, and stability, which may be useful for the trace analysis of the MDR1 gene in complex samples.

Nanotechnology‐based electrochemical biosensors for monitoring breast cancer biomarkers

Breast cancer is categorized as the most widespread cancer type among women globally. On-time diagnosis can decrease the mortality rate by making the right decision in the therapy procedure. These features lead to a reduction in medication time and socioeconomic burden. The current review article provides a comprehensive assessment for breast cancer diagnosis using nanomaterials and related technologies. Growing use of the nano/biotechnology domain in terms of electrochemical nanobiosensor designing was discussed in detail. In this regard, recent advances in nanomaterial applied for amplified biosensing methodologies were assessed for breast cancer diagnosis by focusing on the advantages and disadvantages of these approaches. We also monitored designing methods, advantages, and the necessity of suitable (nano) materials from a statistical standpoint. The main objective of this review is to classify the applicable biosensors based on breast cancer biomarkers. With numerous nano-sized platforms published for breast cancer diagnosis, this review tried to collect the most suitable methodologies for detecting biomarkers and certain breast cancer cell types.

One-click investigation of shape influence of silver nanostructures on SERS performance for sensitive detection of COVID-19

Sensitive and accurate detection of SARS-CoV-2 methods is meaningful for preventing and controlling the novel coronavirus. The detection techniques supporting portable, onsite, in-time, and online data transfer are urgently needed. Here, we one-click investigated the shape influence of silver nanostructures on SERS performance and their applications in the sensitive detection of SARS-CoV-2. Such investigation is achieved by adjusting multiple parameters (concentration, potential, and time) on the integrated electrochemical array, thus various morphologies (e.g., bulk, dendritic, globular, and spiky) can be one-click synthesized. The SERS performance results indicated that dendritic nanostructures are superior to the other three with an order of magnitude signal enhancement. Such on-electrode dendritic silver substrate also represents high sensitivity (LOD = 7.42 × 10⁻¹⁴ M) and high reproducibility (RSD = 3.67%) toward the SARS-CoV-2 RNA sequence detection. Such approach provides great potentials for rapid diagnosis and prevention of diverse infectious diseases.

Various types of electrochemical biosensors for leukemia detection and therapeutic approaches

Leukemia often initiates following dysfunctions in hematopoietic stem cells lineages. Various types of leukemia, including acute lymphoblastic leukemia (ALL), chronic myelogenous leukemia (CML), acute promyelocytic leukemia (APL), and human T-cell leukemia/lymphoma virus type 1 (HTLV-1) can thus call for different diagnosis and treatment options. One of the most important subjects in leukemia is the early detection of the disease for effective therapeutic purposes. In this respect, biosensors detecting the molecules of deoxyribonucleic acid (DNA) as analytes are called genosensors or DNA biosensors. Electrochemical sensors, as the most significant approach, also involve reacting of chemical solutions with sensors to generate electrical signals proportional to analyte concentrations. Biosensors can further help detect cancer cells in the early stages of the disease. Moreover, electrochemical biosensors, developed based on various nanomaterials (NMs), can increase sensitivity to the detection of leukemia-related genes, e.g., BCR/ABL as a fusion gene and promyelocytic leukemia/retinoic acid receptor alpha (PML/RARα). Therefore, the present review reflects on previous studies recruiting different NMs for leukemia detection.

Electrochemical DNA synthesis and sequencing on a single electrode with scalability for integrated data storage

DNA has been considered as a compelling candidate for digital data storage due to advantages such as high coding density, long retention time, and low energy consumption. Despite many works reported, the development of a DNA-based database of full integration, high efficiency, and practical applicability is still challenging. In this work, we report the synthesis and sequencing of DNA on a single electrode with scalability for an integrated DNA-based data storage system. The synthesis of DNA is based on phosphoramidite chemistry and electrochemical deprotection. The sequencing relies on charge redistribution originated from polymerase-catalyzed primer extension, leading to a measurable current spike. By regeneration of the electrode after sequencing, repeated sequencing can be achieved to improve the accuracy. A SlipChip device is developed to simplify the liquid introduction involved in DNA synthesis and sequencing. As the proof-of-concept experiment, text information is stored in the system and then accurately retrieved.

Application strategies of peptide nucleic acids toward electrochemical nucleic acid sensors

Peptide nucleic acids (PNAs) have attracted tremendous interest in the fabrication of highly sensitive electrochemical nucleic acid biosensors due to their higher stability and increased sensitivity than common DNA probes. The neutral pseudopeptide backbone of PNAs not only makes the PNA/DNA duplexes more stable but also provides many opportunities to construct ultrasensitive nucleic acid sensors. This review presents the details of various protocols for the construction of PNA-based electrochemical nucleic acid sensors. The crucial factors, origin, and development of PNA, immobilization methods of PNA probes and signal generation mechanisms, are discussed. This review aims to provide a reference for ultrasensitive PNA electrochemical biosensor preparation.

Nucleic Acid Tests for Clinical Translation

Nucleic acids, including deoxyribonucleic acid (DNA) and ribonucleic acid (RNA), are natural biopolymers composed of nucleotides that store, transmit, and express genetic information. Overexpressed or underexpressed as well as mutated nucleic acids have been implicated in many diseases. Therefore, nucleic acid tests (NATs) are extremely important. Inspired by intracellular DNA replication and RNA transcription, in vitro NATs have been extensively developed to improve the detection specificity, sensitivity, and simplicity. The principles of NATs can be in general classified into three categories: nucleic acid hybridization, thermal-cycle or isothermal amplification, and signal amplification. Driven by pressing needs in clinical diagnosis and prevention of infectious diseases, NATs have evolved to be a rapidly advancing field. During the past ten years, an explosive increase of research interest in both basic research and clinical translation has been witnessed. In this review, we aim to provide comprehensive coverage of the progress to analyze nucleic acids, use nucleic acids as recognition probes, construct detection devices based on nucleic acids, and utilize nucleic acids in clinical diagnosis and other important fields. We also discuss the new frontiers in the field and the challenges to be addressed.

Single-Molecule FRET-Based Dynamic DNA Sensor

Selective and sensitive detection of nucleic acid biomarkers is of great significance in early-stage diagnosis and targeted therapy. Therefore, the development of diagnostic methods capable of detecting diseases at the molecular level in biological fluids is vital to the emerging revolution in the early diagnosis of diseases. However, the vast majority of the currently available ultrasensitive detection strategies involve either target/signal amplification or involve complex designs. Here, using a p53 tumor suppressor gene whose mutation has been implicated in more than 50% of human cancers, we show a background-free ultrasensitive detection of this gene on a simple platform. The sensor exhibits a relatively static mid-FRET state in the absence of a target that can be attributed to the time-averaged fluorescence intensity of fast transitions among multiple states, but it undergoes continuous dynamic switching between a low- and a high-FRET state in the presence of a target, allowing a high-confidence detection. In addition to its simple design, the sensor has a detection limit down to low femtomolar (fM) concentration without the need for target amplification. We also show that this sensor is highly effective in discriminating against single-nucleotide polymorphisms (SNPs). Given the generic hybridization-based detection platform, the sensing strategy developed here can be used to detect a wide range of nucleic acid sequences enabling early diagnosis of diseases and screening genetic disorders.

Organic and inorganic mixed phase modification of a silver surface for functionalization with biomolecules and stabilization of electromotive force

A solid-state potentiometric biosensor based on the organic and inorganic mixed phase modification of a silver surface is proposed. Stabilization of the electromotive force and functionalization with biomolecules on the sensing surface were simultaneously achieved using silver chloride chemically deposited with 1,3-diaminopropanetetraacetic acid ferric ammonium salt monohydrate and a self-assembled monolayer with oligonucleotide probes, respectively. The formation of silver chloride and adsorption of alkanethiol on the silver surface were confirmed with X-ray photoelectron spectroscopy. The resulting modified surface reduced the nonspecific binding of interfering biomolecules and achieved a high signal to noise ratio. The electromotive forces of the modified silver thin film electrodes were stable under constant chloride ion concentrations. Hybridization assays were performed to detect microRNA 146. The lower limit of detection was 0.1 pM because of the small standard deviation. The proposed biosensor could be useful as a disposable single-use sensor in medical fields such as liquid biopsies.

The organic and inorganic mixed phase modification of a silver surface is proposed for solid-state potentiometric biosensors.

Elementary processes of DNA surface hybridization resolved by single-molecule kinetics: implication for macroscopic device performance

Direct monitoring of single-molecule reactions has recently become a promising means of mechanistic investigation. However, the resolution of reaction pathways from single-molecule experiments remains elusive, primarily because of interference from extraneous processes such as bulk diffusion. Herein, we report a single-molecule kinetic investigation of DNA hybridization on a metal surface, as an example of a bimolecular association reaction. The tip of the scanning tunneling microscope (STM) was functionalized with single-stranded DNA (ssDNA), and hybridization with its complementary strand on an Au(111) surface was detected by the increase in the electrical conductance associated with the electron transport through the resulting DNA duplex. Kinetic analyses of the conductance changes successfully resolved the elementary processes, which involve not only the ssDNA strands and their duplex but also partially hybridized intermediate strands, and we found an increase in the hybridization efficiency with increasing the concentration of DNA in contrast to the knowledge obtained previously by conventional ensemble measurements. The rate constants derived from our single-molecule studies provide a rational explanation of these findings, such as the suppression of DNA melting on surfaces with higher DNA coverage. The present methodology, which relies on intermolecular conductance measurements, can be extended to a range of single-molecule reactions and to the exploration of novel chemical syntheses.

Hybridization of a single DNA molecule on a surface was investigated by electrical conductance measurements. The hybridization efficiency increases with increasing the DNA concentration, in contrast to preceding studies with ensemble studies.

Nucleic Acids Analysis

Nucleic acids are natural biopolymers of nucleotides that store, encode, transmit and express genetic information, which play central roles in diverse cellular events and diseases in living things. The analysis of nucleic acids and nucleic acids-based analysis have been widely applied in biological studies, clinical diagnosis, environmental analysis, food safety and forensic analysis. During the past decades, the field of nucleic acids analysis has been rapidly advancing with many technological breakthroughs. In this review, we focus on the methods developed for analyzing nucleic acids, nucleic acids-based analysis, device for nucleic acids analysis, and applications of nucleic acids analysis. The representative strategies for the development of new nucleic acids analysis in this field are summarized, and key advantages and possible limitations are discussed. Finally, a brief perspective on existing challenges and further research development is provided.

Ultrasensitive Electrochemical Impedance Detection of Mycoplasma agalactiae DNA by Low-Cost and Disposable Au-Decorated NiO Nanowall Electrodes

Nanostructured electrodes detecting bacteria or viruses through DNA hybridization represent a promising method, which may be useful in on-field applications where PCR-based methods are very expensive, time-consuming, and require trained personnel. Indeed, electrochemical sensors combine disposability, fast response, high sensitivity, and portability. Here, a low-cost and high-surface-area electrode, based on Au-decorated NiO nanowalls, demonstrates a highly sensitive PCR-free detection of a real sample of Mycoplasma agalactiae (Ma) DNA. NiO nanowalls, synthesized by aqueous methods, thermal annealing, and Au decoration, by electroless deposition, ensure a high-surface-area platform for successful immobilization of Ma thiolated probe DNA. The morphological, chemical, and electrochemical properties of the electrode were characterized, and a reproducible detection of synthetic Ma DNA was observed and investigated by impedance measurements. Electrochemical impedance spectroscopy (EIS) ascribed the origin of impedance signal to the Ma DNA hybridization with its probe immobilized onto the electrode. The electrode successfully discriminates between DNA extracted from healthy and infected sheep milk, showing the ability to detect Ma DNA in concentrations as low as 53 ± 2 copy number μL^-1. The Au-decorated NiO nanowall electrode represents a promising route toward PCR-free, disposable, rapid, and molecular detection.

Optimized DNA-based biosensor for monitoring Leishmania infantum in human plasma samples using biomacromolecular interaction: a novel platform for infectious disease diagnosis

Leishmania parasite identification is very important in clinical studies of leishmaniasis and its diagnosis. Though there are various clinical and epidemiological approaches to identifying Leishmania infantum, due to some limitations of the traditional methods, sensitive and specific techniques are needed and are in great demand. To achieve selective and rapid detection, a sensitive signal transducer with high surface area is necessary. In this work, a new paper sensor was fabricated using silver nanoprisms electrodeposited on the GQD conductive nano-ink (Ag NPr/GQDs nano-ink). A high surface area and suitable interface for anchoring biomolecules was achieved by electrodepositing gold nanoparticles (AuNPs) functionalized with cysteamine (AuNPs-CysA) on the surface of the paper sensor altered by Ag NPr/GQDs nano-ink. To prepare a sensitive and selective bio-device for the recognition of Leishmania in human plasma specimens, a DNA-thiol probe was stabilized on the surface of the platform. Hybridization of DNA was evaluated by chronoamperometry (ChA). The engineered DNA-based paper biosensor showed high sensitivity and selectivity for the identification of Leishmania genomic DNA. Under optimum circumstances, a linear range was obtained using photographic paper from 1 μM to 1 zM and an ivory sheet from 1 nM to 1 zM. The lower limits of quantitation (LLOQ) on the photographic paper and ivory sheet were 1 zM. In addition, the designed DNA-based biosensor revealed well-defined performance in the recognition of mismatched sequences (single base, two base and three base mismatches) and selectivity.

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.

CoAl-layered double hydroxide nanosheet-based fluorescence assay for fast DNA detection

In the study, CoAl-layered double hydroxide (CoAl-LDH) was prepared as a fluorescence quenching agent to detect DNA molecules. Because of its simple preparation for a large scale, excellent surface effect, good biocompatibility and high fluorescence quenching capability, the effective, rapid, and sensitive DNA detection was realized. The fluorescence quenching efficiency of LDH to 5(6)-carboxyfluorescein attached to single stranded DNA (FAM-ssDNA) was as high as 88%, and after FAM-ssDNA hybridized with the complementary DNA oligonucleotide, that to FAM-dsDNA was about 33%. The quenching mechanisms of LDH for ssDNA and dsDNA were discussed. Phosphate exposed of ssDNA played an important role in quenching effect. Compared to dsDNA, more exposed phosphate groups in ssDNA resulted in the stronger electrostatic interaction between ssDNA and LDH, and thus the higher quenching efficiency. Under optimal conditions, the linear equation was y = 38.26 + 3.37x in a linear relationship of 1-50 nM, and the correlation coefficient R² corresponded to 0.999, and the limit of detection was calculated to be 0.79 nM (3σ). Cytotoxicity studies have shown that LDH has good biocompatibility. The study provides an effective, sensitive and safe approach for DNA detection and gives an insight for the design of LDH-based biosensing materials.

Ultrasensitive DNA Detection Based on Inorganic-Organic Nanocomposite Cosensitization and G-Quadruplex/Hemin Catalysis for Signal Amplification

A novel photoelectrochemical (PEC) aptasensor was fabricated for DNA detection based on the coupling of cosensitization and peroxidase-like catalytic activity. Specifically, the surfaces of branched-TiO₂ nanorods (B-TiO₂ NRs) were modified with Cd²⁺ and S²⁺ to obtain B-TiO₂ NRs/CdS hybrid structures, which were subsequently used as matrices to immobilize hairpin DNA (hDNA) probes. CdTe/TCPP (TCPP = meso-tetra(4-carboxyphenyl)-porphine) used for signal amplification was labeled on the terminal of the hDNA probe. Without the target DNA (tDNA) presence, the immobilized hDNA probe with CdTe/TCPP possessed a hairpin form and was located near the B-TiO₂ NRs/CdS electrode surface, forming a cosensitized structure formation and then generating strong photocurrent with H₂O₂ as the electron donor. During detection, the specific recognition of tDNA by the sensing hDNA probe triggered the formation of the G-quadruplex/hemin DNAzyme, which effectively catalyzed the decomposition of H₂O₂. Meanwhile, cosensitization disappeared when the hDNA probe hybridized with tDNA, further reducing the photocurrent. With a double-signal amplification strategy, the sensing platform designed in this work demonstrated a linear detection ability in the 0.5 fM-5 nM range with a detection limit equal to 0.14 fM. Notably, through encoding in the base sequences of the hDNA and marking it, a versatile PEC platform could be structured for the detection of various DNA targets, which could promise applications in point-of-care diagnostic fields.

Gold nanoparticle-engineered electrochemical aptamer biosensor for ultrasensitive detection of thrombin

In order to obtain a lower detection limit in electrochemical detection, the choice of signal amplification strategy is of great importance. In this work, we describe an electrochemical sandwich aptasensor based on a signal amplification system involving two thrombin (TB) aptamers (TBA1 and TBA2), gold nanoparticles (AuNPs) as aptamer carriers, and [Ru(NH₃)₆]³⁺ for signal conversion. In the presence of the target thrombin, TBA1 and TBA2 specifically bind to TB, and the TBA1-TB-TBA2 complexes cause the formation of a sandwich structure, meaning more [Ru(NH₃)₆]³⁺ can be adsorbed on the negatively charged phosphate backbone of the aptamers, resulting in an increase in the differential pulse voltammetry (DPV) current. Under optimal conditions, the aptasensor exhibited a linear range of 1 fM to 6 pM and a limit of detection of 0.1429 fM (S/N = 3) for TB. The proposed aptasensor displayed an excellent selectivity and reproducibility. Importantly, the aptasensor was capable of detecting TB in serum samples successfully.

Ultrasensitive analysis of microRNAs with gold nanoparticle-decorated molybdenum disulfide nanohybrid-based multilayer nanoprobes

The nanoprobe-based signal amplification strategy is a powerful way to ultrasensitively detect biomolecules. Herein, a gold nanoparticle-decorated molybdenum disulfide (MoS₂-AuNP)-based multilayer nanoprobe (MLNP) was designed for ultrasensitive analysis of microRNA-21 (miRNA-21). The MLNP-amplified electrochemical biosensor exhibited an ultrawide dynamic range (10 aM-1 μM) and an ultralow detection limit (38 aM) for target miRNA-21 analysis. Furthermore, this biosensor can determine miRNA-21 expression in cell lysates of 100 human cervical cancer (HeLa) cells. Our results demonstrate that MoS₂-AuNP nanocomposites have great potential in constructing biosensors for target molecule analysis.

A photoelectrochemical aptasensor for the sensitive detection of streptomycin based on a TiO2/BiOI/BiOBr heterostructure

In photoelectrochemical sensor (PEC sensor), sensitivity and selectivity are two essential factors which are determined by photosensitive of materials and identification of elements. Herein, a novel PEC aptamer sensor for streptomycin-specific detection was developed, with which the visible-light-active TiO₂/BiOI/BiOBr heterostructure and aptamers were employed as photoactive material and bio-identification elements, separately. The combination of an appropriate amount of TiO₂ with BiOI/BiOBr enhanced the photocurrent response, and thus is beneficial to the construction of PEC sensors. In addition, the one-pot synthesis of TiO₂/BiOI/BiOBr has the advantage of being environmentally-friendly. Under optimized conditions, the photocurrent response of aptamer/TiO₂/BiOI/BiOBr/ITO is linear with SRT concentration from 0.05 to 150 nM, and the detection limit (S/N = 3) is as low as 0.04 nM. This novel PEC sensing strategy provided an ultra-sensitive sensor with high selectivity and stability for SRT detection.

Stochastic electrochemistry at ultralow concentrations: the case for digital sensors

There is increasing demand, in particular from the medical field, for assays capable of detecting sub-pM macromolecular concentrations with high specificity. Methods for detecting single bio/macromolecules have already been developed based on a variety of transduction mechanisms, which represents the ultimate limit of mass sensitivity. Due to limitations imposed by mass transport and binding kinetics, however, achieving high concentration sensitivity additionally requires the massive parallelization of these single-molecule methods. This leads to a new sort of 'digital' assay based on large numbers of parallel, time-resolved measurements aimed at detecting, identifying and counting discrete macromolecular events instead of reading out an average response. In this Tutorial Review we first discuss the challenges inherent to trace-level detection and the motivations for developing digital assays. We then focus on the potential of recently developed single-entity impact electrochemistry methods for use in digital sensors. These have the inherent advantage of relying on purely electrical signals. They can thus in principle be implemented using integrated circuits to provide the parallelization, readout and analysis capabilities required for digital sensors.

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.

Synergy of Peptide-Nucleic Acid and Spherical Nucleic Acid Enabled Quantitative and Specific Detection of Tumor Exosomal MicroRNA

Exosomal microRNAs are essential in intercellular communications and disease progression, yet it remains challenging to quantify the expression level due to their small size and low abundance in blood. Here, we report a "sandwich" electrochemical exosomal microRNA sensor (SEEmiR) to detect target microRNA with high sensitivity and specificity. In SEEmiR, neutrally charged peptide nucleic acid (PNA) enables kinetically favorable hybridization with the microRNA target relative to negatively charged DNA, particularly in a short sequence (10 nt). More importantly, this property allows PNA to cooperate with a spherical nucleic acid (SNA) nanoprobe that heavily loads with oligonucleotide-adsorbed electroactive tags to enhance detection sensitivity and specificity. Such a PNA-microRNA-SNA sandwich construct is able to minimize the background noise via PNA, thereby maximizing the SNA-mediated signal amplification in electrostatic adsorption-based SEEmiR. The synergy between PNA and SNA makes the SEEmiR sensor able to achieve a broad dynamic range (from 100 aM to 1 nM) with a detection limit down to 49 aM (2 orders of magnitude lower than that without SNA) and capable of distinguishing a single-base mismatch. This ultrasensitive sensor provides label-free and enzyme-independent microRNA detection in cell lysates, unpurified tumor exosomal lysates, cancer patients' blood, and accurately differentiates the patients with breast cancer from the healthy ones, suggesting its potential as a promising tool in cancer diagnostics.

Label-free potentiometric aptasensing platform for the detection of Pb2+ based on guanine quadruplex structure

Potentiometric aptasensors enhanced by integrating advanced nanomaterials are of particular interest for the detection of multiplex species (e.g., proteins, bacteria, micro-organisms) due to their low cost, ease of operation, and low detection limits. However, potentiometric detection of small ionic species aptasensors is still challenging. This article describes the first example of a label-free G-quadruplex-based potentiometric aptasensing platform for the detection of Pb²⁺. Polyion oligonucleotide-labeled gold nanoparticles (AuNPs-DNA) as probes are modified on Au electrode, providing high-density negative charge on the electrode surface. These signal-amplifying probes can selectively form G-quadruplexes with the presence of Pb²⁺ ions and reduce the negative charges on the electrode surface, hence achieving potentiometric detection of Pb²⁺ ions with high selectivity. The AuNPs-DNA-based aptasensor shows an acceptable sensitivity over a wide range from 10^-11 to 10^-6 M with a detection limit of 8.5 pM. Furthermore, confirmed by coupled plasma mass spectrometry, the sensing platform is capable of performing effective and accurate detection of Pb²⁺ level in real water samples. The presented aptasensor offers a fast, convenient, low-maintenance, and highly sensitive alternative for on-site water pollution detections.

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.

Universal DNA biosensing based on instantaneously electrostatic attraction between hexaammineruthenium (III) and DNA molecules

Despite rapid progress in DNA biosensors by employing various materials as well as techniques, most of the reported sensors are based on specific recognition of a DNA fragment, however can not perform universal measurement of DNA molecules (i.e. genomic DNA). In this work, we proposed a novel DNA biosensing method based on instantaneously electrostatic attraction (IEA) between hexaammineruthenium (III) and DNA molecules. The current variation of freely diffused Ru(NH₃)₆³⁺ caused by its quick and strong static interaction with phosphate backbones was employed as a universal probe to detect DNA molecules in solution, with no need for immobilization of capture probes on the electrode. After optimization, 30 μL of 300 μM Ru(NH₃)₆³⁺ solution was added onto the gold electrode with a working electrode diameter of 2 mm, and a detection limit of 3.8 ng/μL was achieved, which is equivalent to NanoDrop™ One spectrometer, the commonly used instrument for DNA quantification. Using reusable and inexpensive gold electrode, the approach provided an easy-operated sequence-independent DNA detection method, and was proved to be able to detect genomic and plasmid DNA directly.

DNA Mini-Barcoding: A Derived Barcoding Method for Herbal Molecular Identification

In recent years, the demand for natural herbal products (NHP) has increased; however, the quality of these products is difficult to confirm due to the lack of a comprehensive quality control system. Traditional methods are not effective in detecting processed ingredients. DNA barcoding is an established technique that has been used for more than 10 years. This technique uses short standard sequences (generally 200-600 bp) to identify species. While a complete DNA barcode is difficult to obtain from NHP due to DNA degradation, mini-barcoding is a complementary tool to identify species in NHP. DNA mini-barcoding uses smaller DNA segments for polymerase chain reaction amplification and can be applied to identify species rapidly. The present review summarizes the development and application of DNA mini-barcodes over recent years and discusses the limitations of this technique. This review also compares mini-barcoding and meta-barcoding, a technique using universal polymerase chain reaction primers to simultaneously amplify multiple DNA barcodes and identify many species in a single environmental sample. Additionally, other detection methods that can be combined with mini-barcodes, such as nucleotide signatures, high-resolution DNA melting analysis, and gold nanoparticles, are discussed. DNA mini-barcoding can fill the gaps left by other methods in the field of herbal molecular identification.

Integrated Solid-State Nanopore Electrochemistry Array for Sensitive, Specific, and Label-Free Biodetection

Nanopore ionic current measurement is currently a prevailing readout and offers considerable opportunities for bioassays. Extending conventional electrochemistry to nanoscale space, albeit noteworthy, remains challenging. Here, we report a versatile electrochemistry array established on a nanofluidic platform by controllably depositing gold layers on the two outer sides of anodic aluminum oxide (AAO) nanopores, leading to form an electrochemical microdevice capable of performing amperometry in a label-free manner. Electroactive species ferricyanide ions passing through gold-decorated nanopores act as electrochemical indicator to generate electrolytic current signal. The electroactive species flux that dominates current signal response is closely related to the nanopore permeability. Such well-characteristic electrolytic current-species flux correlation lays a premise for quantitative electrochemical analysis. As a proof-of-concept demonstration, we preliminarily verify the analytical utility by detection of nucleic acid and protein at picomolar concentration levels. Universal surface modification and molecule assembly, specific target recognition and reliable signal output in nanopore enable direct electrochemical detection of biomolecules without the need of cumbersome probe labeling and signal amplification.

Control of Probe Density at DNA Biosensor Surfaces Using Poly(l-lysine) with Appended Reactive Groups

Biosensors and materials for biomedical applications generally require chemical functionalization to bestow their surfaces with desired properties, such as specific molecular recognition and antifouling properties. The use of modified poly(l-lysine) (PLL) polymers with appended oligo(ethylene glycol) (OEG) and thiol-reactive maleimide (Mal) moieties (PLL-OEG-Mal) offers control over the presentation of functional groups. These reactive groups can readily be conjugated to, for example, probes for DNA detection. Here we demonstrate the reliable conjugation of thiol-functionalized peptide nucleic acid (PNA) probes onto predeposited layers of PLL-OEG-Mal and the control over their surface density in the preceding synthetic step of the PLL modification with Mal groups. By monitoring the quartz crystal microbalance (QCM) frequency shifts of the binding of complementary DNA versus the density of Mal moieties grafted to the PLL, a linear relationship between probe density and PLL grafting density was found. Cyclic voltammetry experiments using Methylene Blue-functionalized DNA were performed to establish the absolute probe density values at the biosensor surfaces. These data provided a density of 1.2 × 10¹² probes per cm² per % of grafted Mal, thus confirming the validity of the density control in the synthetic PLL modification step without the need of further surface characterization.

Quantum dot-based electrochemical biosensor for stripping voltammetric detection of telomerase at the single-cell level

Human telomerase is responsible for the maintenance of chromosome end structures and is a valuable biomarker for malignant growth. However, the accurate measurement of telomerase activity at the single-cell level has remained a great challenge. Here we develop a simple quantum dot (QD)-based electrochemical biosensor for stripping voltammetric detection of telomerase activity at the single-cell level. We designed a thiol-modified capture DNA which may be immobilized on the gold electrode by the gold-sulfur bond. The presence of telomerase enables the addition of the telomere repeats of (TTAGGG)_n to the 3' end of the primer, accompanied by the incorporation of abundant biotins in the extension product with the assistance of the biotin-tagged dATP. The subsequent hybridization of extension product with the capture DNA and the addition of streptavidin-coated QDs induce the assembly of large amounts of QDs onto the electrode via specific biotin-streptavidin binding. After the acidic dissolution of QDs, the released Cd (II) can be simply quantified by anodic stripping voltammetry (ASV). Due to the introduction of large amounts of QDs by telomerase-induced primer extension reaction and the synergistic signal amplification induced by the release of Cd (II) from the QDs, this biosensor can detect telomerase activity at the single-cell level without the involvement of any thermal cycling and extra enzymes for signal amplification. Moreover, this assay exhibits a large dynamic range over four orders of magnitude and it is very simple without the involvement of specific hairpin probe design and complicated labelling, holding great potential in point-of-need testing.

DNA Nanotechnology-Enabled Interfacial Engineering for Biosensor Development

Biosensors represent biomimetic analytical tools for addressing increasing needs in medical diagnosis, environmental monitoring, security, and biodefense. Nevertheless, widespread real-world applications of biosensors remain challenging due to limitations of performance, including sensitivity, specificity, speed, and reproducibility. In this review, we present a DNA nanotechnology-enabled interfacial engineering approach for improving the performance of biosensors. We first introduce the main challenges of the biosensing interfaces, especially under the context of controlling the DNA interfacial assembly. We then summarize recent progress in DNA nanotechnology and efforts to harness DNA nanostructures to engineer various biological interfaces, with a particular focus on the use of framework nucleic acids. We also discuss the implementation of biosensors to detect physiologically relevant nucleic acids, proteins, small molecules, ions, and other biomarkers. This review highlights promising applications of DNA nanotechnology in interfacial engineering for biosensors and related areas.

DNA Electrochemistry and Electrochemical Sensors for Nucleic Acids

Sensitive, specific, and fast analysis of nucleic acids (NAs) is strongly needed in medicine, environmental science, biodefence, and agriculture for the study of bacterial contamination of food and beverages and genetically modified organisms. Electrochemistry offers accurate, simple, inexpensive, and robust tools for the development of such analytical platforms that can successfully compete with other approaches for NA detection. Here, electrode reactions of DNA, basic principles of electrochemical NA analysis, and their relevance for practical applications are reviewed and critically discussed.

A novel mode of DNA assembly at electrode and its application to protein quantification

Sensitive and specific detection of protein is of great significance for early diagnosis and prognosis of many diseases. However, great challenges remain unsolved including relative low sensitivity, high cost, long testing time, complicated instrument and laborious operation. To improve the performance of protein detection methods, development of fine reaction interface for recognition and signal amplification is of great importance. In this work, we construct a novel mode of DNA assembly at electrode interface based on a tripodal surface anchor and an electrochemical aptasensor for protein assay is developed. The orientation of the immobilized DNA is optimized, which promises the efficiency of protein recognition. In addition, hybridization chain reaction is employed for further signal amplification. Therefore, this detection method shows high sensitivity with excellent specificity. The strategy can be universally applicable by simply modifying the sequences of used DNA probes.

Preparation, Modification, Characterization, and Biosensing Application of Nanoporous Gold Using Electrochemical Techniques

Nanoporous gold (np-Au), because of its high surface area-to-volume ratio, excellent conductivity, chemical inertness, physical stability, biocompatibility, easily tunable pores, and plasmonic properties, has attracted much interested in the field of nanotechnology. It has promising applications in the fields of catalysis, bio/chemical sensing, drug delivery, biomolecules separation and purification, fuel cell development, surface-chemistry-driven actuation, and supercapacitor design. Many chemical and electrochemical procedures are known for the preparation of np-Au. Recently, researchers are focusing on easier and controlled ways to tune the pores and ligaments size of np-Au for its use in different applications. Electrochemical methods have good control over fine-tuning pore and ligament sizes. The np-Au electrodes that are prepared using electrochemical techniques are robust and are easier to handle for their use in electrochemical biosensing. Here, we review different electrochemical strategies for the preparation, post-modification, and characterization of np-Au along with the synergistic use of both electrochemistry and np-Au for applications in biosensing.

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.