Nanoprobe-Initiated Enzymatic Polymerization for Highly Sensitive Electrochemical DNA Detection

Recent Advances in Conductive Polymers-Based Electrochemical Sensors for Biomedical and Environmental Applications

Electrochemical sensors play a pivotal role in various fields, such as biomedicine and environmental detection, due to their exceptional sensitivity, selectivity, stability, rapid response time, user-friendly operation, and ease of miniaturization and integration. In addition to the research conducted in the application field, significant focus is placed on the selection and optimization of electrode interface materials for electrochemical sensors. The detection performance of these sensors can be significantly enhanced by modifying the interface of either inorganic metal electrodes or printed electrodes. Among numerous available modification materials, conductive polymers (CPs) possess not only excellent conductivity exhibited by inorganic conductors but also unique three-dimensional structural characteristics inherent to polymers. This distinctive combination allows CPs to increase active sites during the detection process while providing channels for rapid ion transmission and facilitating efficient electron transfer during reaction processes. This review article primarily highlights recent research progress concerning CPs as an ideal choice for modifying electrochemical sensors owing to their remarkable features that make them well-suited for biomedical and environmental applications.

Electrochemical aptamer biosensor for DNA detection based on label-free aptamers

Electrochemical aptasensor has been broadly advanced for nucleic acid detection. However, it is a long-term goal to design an aptasensor with high specificity, flexibility, and simplicity. In this work, we develop a strategy of triblock DNA probe, which consists of two DNA probes at both ends and ployA fragments in the middle as probe-polyA-probe. PolyA fragment has high affinity to the surface of gold electrode, so it can be assembled on the electrode surface via polyA instead of traditional Au-S bonds. When the target DNA is simultaneously hybridized with the two capture probes, the hybridization stability can be improved due to the strong base stacking effect. [Ru(NH₃)₆]³⁺, as signal probe, can be electrostatically adsorbed on the negatively charged DNA skeleton. A wide linear range (10 pM-10 μM) is obtained with a detection limit of 2.9 pM. Our electrochemical aptasensor has good repeatability, stability, and specificity. More importantly, the electrochemical sensor can successfully detect DNA in human serum samples, which proves its practical value and extensive applicability in complex environment.

Singlet-oxygen generated by a metal-organic framework for electrochemical biosensing

Enzyme-based electrochemical biosensors have been widely employed for analyte detection for several years. However, for wide application, there are many challenges to overcome, such as the sensitivity of the catalytic activity, and the reproducibility and stability of enzymes. In this work, an enzyme-free sensing strategy based on two-dimensional (2D) metal-organic frameworks (MOFs) as photosensitizers and singlet-oxygen (1O2) as the oxidant has been designed via photocatalysis and electrochemical analysis. To be specific, MOF sheets (Zn-ZnMOF) were prepared with Zn as the node and zinc(ii)tetraphenylporphyrin (TCPP(Zn)) as the ligand, which could generate 1O2 from air under light illumination, and sequentially the generated 1O2 could oxidize analytes to form their oxidation state which could be detected and reduced on the electrode, completing a redox cycle and amplifying electrochemical signals. Thanks to the morphology and superior quantum yield of 1O2 of the Zn-ZnMOF, this method could overcome the limitation of enzymes and afford selective detection, such as of hydroquinone with a detection limit of 0.8 μM in 0.1 M PBS (pH = 7.4). Furthermore, the method does not require additional reactive reagents but only with air and on/off light switching. Thirdly, the method detects the target without washing and enzyme-labelled. With these merits, this work provides a new platform for MOFs as photosensitizers for electrochemical sensors and further development of sensitive, selective, and stable electroanalytical devices for bio-application.

Immobilization-free electrochemical DNA sensor based on signal cascade amplification strategy

The development of convenient and efficient strategies without using complex nanomaterials or enzymes for signal amplification is very important for bioanalytical applications. Herein, a novel electrochemical DNA sensor was developed by harnessing the signal amplification efficiency of catalytic hairpin assembly (CHA) and a brand-new signal marker tetraferrocene. The prepared sensor had both ends of the probe H2 labeled with tetraferrocene; both ends have a large number of unhybridized T bases, which cause tetraferrocene to move closer to the electrode surface, generating a high-efficiency amplification signal. In the presence of target DNA, it induced strand exchange reactions promoting the formation of double-stranded DNA and recycling of target DNA. Under optimal conditions, the sensor showed a good linear correlation between the peak currents and logarithm of target DNA concentrations (ranging from 0.1 fM to 0.3125 pM) with a detection limit of 0.06 fM, which is obtained by a triple signal-to-noise ratio. Additionally, the prepared sensor possesses excellent selectivity, reproducibility, and stability, demonstrating efficient and stable DNA detection methodology.

Acoustic Methodology for Selecting Highly Dissipative Probes for Ultrasensitive DNA Detection

The objective of this work is to present a methodology for the selection of nanoparticles such as liposomes to be used as acoustic probes for the detection of very low concentrations of DNA. Liposomes, applied in the past as mass amplifiers and detected through frequency measurement, are employed in the current work as probes for energy-dissipation enhancement. Because the dissipation signal is related to the structure of the sensed nanoentity, a systematic investigation of the geometrical features of the liposome/DNA complex was carried out. We introduce the parameter of dissipation capacity by which several sizes of liposome and DNA structures were compared with respect to their ability to dissipate acoustic energy at the level of a single molecule/particle. Optimized 200 nm liposomes anchored to a dsDNA chain led to an improvement of the limit of detection (LoD) by 3 orders of magnitude when compared to direct DNA detection, with the new LoD being 1.2 fmol (or 26 fg/μL or 2 pM). Dissipation monitoring was also shown to be 8 times more sensitive than the corresponding frequency response. The high versatility of this new methodology is demonstrated in the detection of genetic biomarkers down to 1-2 target copies in real samples such as blood. This study offers new prospects in acoustic detection with potential use in real-world diagnostics.

Terminal-conjugated non-aggregated constraints of gold nanoparticles on lateral flow strips for mobile phone readouts of enrofloxacin

Antibiotics abuse now poses a global threat to public health. Monitoring their residual levels as well as metabolites are of great importance, still challenges remain in in situ tracing during the circulation. Herein, taking the typical antibacterial Enrofloxacin (ENR) as a subject, a paper-based aptasensor was tailored by manipulating a duo of aptameric moieties to "sandwich" the target in a lateral-flow regime. To visualize the tight-binding sandwich motif more vividly, an irregular yet robust DNA-bridged gold nanoparticles (AuNPs) proximity strategy was developed with recourse to terminal deoxynucleotidyl transferase, of which the nonaggregate constraining feature was unveiled via optical absorption and scanning probe topography. This complex performed exceptionally better in the test strip context than single-particle tags, leading to an enhanced on-chip focusing. Rather than qualitative color developing, further efforts were taken to visualize the readouts in a quantitative manner by exploiting the smartphone camera for pattern recognition along with data processing in a professional App. Overall, this prototyped contraption realized a rapid and ultrasensitive quantification of ENR down to 0.1 μg/L along with a broad linear range over 5 orders of magnitude, plus excellent selectivity and precision even for real samples. Such innovative fusion across DNA-structured nanomanufacturing and intelligent perception provides a prospective and invigorating solution to point-of-care inspection.

Study of horseradish peroxidase and hydrogen peroxide bi-analyte sensor with boronate affinity-based molecularly imprinted film

A novel electrochemical horseradish peroxidase (HRP) sensor was developed based on boronate affinity-based electropolymerized polythionine (PTh) molecularly imprinted polymer (MIP) as specific recognition element for HRP on gold nanoparticles (AuNPs) modified glassy carbon electrode, in which PTh acted as the electrochemical probe for the sensor. The sensor was characterized by scanning electron microscopy and electron dispersive spectroscopy. Electrochemical impedance spectroscopy, cyclic voltammetry, and differential pulse voltammetry were exploited for the study of the properties of the MIP sensor. The MIP sensor exhibited excellent linear response over the range of 2.0 × 10−10 mg/mL ∼ 1.0 × 10−7 mg/mL for HRP. In addition, with MIP film as HRP immobilized matrices, the sensor for the detection of H2O2 was developed with the MIP sensor based on the reduction of H2O2 catalyzed by HRP in the presence of electron mediator PTh. The sensor showed linear relationships between the current response and H2O2 concentration from 6.0 × 10−7 to 2.0 × 10−5 mol/L. HRP and H2O2 bi-analyte sensor based on MIP film was successfully developed in this work. The developed method can also be applicable for enzyme and its enzymatic substrate bi-analyte sensor.

Biosensing and Delivery of Nucleic Acids Involving Selected Well-Known and Rising Star Functional Nanomaterials

In the last fifteen years, the nucleic acid biosensors and delivery area has seen a breakthrough due to the interrelation between the recognition of nucleic acid's high specificity, the great sensitivity of electrochemical and optical transduction and the unprecedented opportunities imparted by nanotechnology. Advances in this area have demonstrated that the assembly of nanoscaled materials allows the performance enhancement, particularly in terms of sensitivity and response time, of functional nucleic acids' biosensing and delivery to a level suitable for the construction of point-of-care diagnostic tools. Consequently, this has propelled detection methods using nanomaterials to the vanguard of the biosensing and delivery research fields. This review overviews the striking advancement in functional nanomaterials' assisted biosensing and delivery of nucleic acids. We highlight the advantages demonstrated by selected well-known and rising star functional nanomaterials (metallic, magnetic and Janus nanomaterials) focusing on the literature produced in the past five years.

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.

Terminal deoxynucleotidyl transferase (TdT)-catalyzed homo-nucleotides-constituted ssDNA: Inducing tunable-size nanogap for core-shell plasmonic metal nanostructure and acting as Raman reporters for detection of Escherichia coli O157:H7

Core-shell plasmonic metal nanoparticles with interior nanogaps are superior nanostructures owing to their large signal enhancement for Surface enhanced Raman spectroscopy (SERS). Herein, we incorporated Terminal deoxynucleotidyl transferase (TdT)-catalyzed DNA in the preparation of core-shell nanostructures for the detection of Escherichia coli O157:H7 (E. coli O157:H7) cells. The elongated products-homo-nucleotides-composed of long single DNA strands (hn-D) are used not only to induce tunable-size nanogaps but also as Raman reporters with consistent and uniform signal enhancement. Using this synthetic process of hn-D-embedded core-shell nanoparticles (hn-DENPs), we found that the length of hn-D strands affects the size of the nanogap. In addition, performances of the specific Raman imaging of E. coli O157:H7, high detection sensitivity of 2 CFU/mL, and the recovery of 98.1%-105.2% measured in the real food samples, make hn-DENP a biosensor that will be widely used in biological detection.

A planar and uncharged copper(II)-picolinic acid chelate: Its intercalation to duplex DNA by experimental and theoretical studies and electrochemical sensing application

Using an external redox-active molecule as a DNA hybridization indicator is still a popular strategy in electrochemical DNA biosensors because it is label-free and the multi-site binding can enhance the response signal. A planar and uncharged transition metal complex, Cu(PA)₂ (PA = picolinic acid) with excellent electrochemical activity has been synthesized and its interaction with double-stranded DNA (dsDNA) is studied by experimental electrochemical methods and theoretical molecular docking technology. The experimental results reveal that the copper complex interacts with dsDNA via specific intercalation, which is verified by the molecular docking result. The surface-based voltammetric analysis demonstrates that the planar Cu(PA)₂ can effectively accumulate within the electrode-confined hybridized duplex DNA rather than the single-stranded probe DNA. Based on this phenomenon, the Cu(PA)₂ is utilized as an electrochemical hybridization indicator for the detection of oligonucleotides. The sensing assays show that upon incubation in Cu(PA)₂ solution, the probe electrode does not display any Faraday signal, but the hybridized one has a pair of strong redox peaks corresponding to the electrochemistry of Cu(PA)₂, showing excellent hybridization indicating function of Cu(PA)₂ without background interference. The signal intensity of Cu(PA)₂ is dependent on the concentrations of the target oligonucleotide ranging from 1 fM to 100 nM with an experimental detection limit of 1.0 fM. Due to the specific intercalation of Cu(PA)₂ with dsDNA, the biosensor also exhibits good ability to recognize oligonucleotide with different base mismatching degree.

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.

Label-free and sensitive detection assay for terminal deoxynucleotidyl transferase via polyadenosine-coralyne fluorescence enhancement strategy

Terminal deoxynucleotidyl transferase (TdT) is a unique template-free polymerase that randomly adds multiple deoxyribonucleoside triphosphates (dNTPs) to the 3'-OH terminus of ssDNA. This characteristic makes TdT a versatile enzymatic tool in many fields. Moreover, aberrant TdT expression is a well-recognized biomarker of several leukemic diseases and is related to carcinogenesis. In this study, we developed a facile, rapid, label-free, and convenient assay for TdT detection. TdT-generated poly A tails formed a fluorescent enhancement complex in the presence of coralyne. To achieve a better signal-to-noise ratio, we used potassium thiocyanate (KSCN), instead of other halogen anions (KCl, KBr, KI, NaI) as the quenching agent of dissociate coralyne. Our results demonstrate that this assay is extremely facile, rapid, and label-free; at levels as low as 0.025 U/mL, TdT was distinctly detected within 55 min. And the determination of TdT activity in RBL-2H3 and Reh cells lysates exhibited a good sensing performance, demonstrating its potential applications in biochemical research and clinical diagnosis.

Luminescent magnetic nanoparticles encapsulated in MOFs for highly selective and sensitive detection of ClO-/SCN- and anti-counterfeiting

It is well-known that ClO- and SCN- can cause adverse effects on the environment and organisms; therefore, development of new strategies for detecting ClO- and SCN-, especially in water, are highly desirable. Here, we present luminous Eu(iii) complex-functionalized Fe3O4 nanoparticles encapsulated into zeolitic imidazolate framework materials (nano-ZIF-8) and successfully employ this nano-MOF as a fluorescence probe for selective and sensitive detection of ClO- and SCN-. The introduction of ClO- into nano-ZIF-8 solution induced a significant decrease in the characteristic fluorescence emission of Eu3+ at 613 nm. However, strong fluorescence emission was again observed when SCN- was successively injected into the prepared nano-ZIF-8-ClO-. Thus, a novel fluorescence system for simultaneous detection of free ClO- and SCN- was established. On the basis of the superior adsorption performance of nano-MOF materials, free residual ClO- and SCN- in water was rapidly, sensitively and selectively detected with a detection limit of 0.133 nM and 0.204 nM, respectively. Moreover, nano-ZIF-8 was successfully used for monitoring the concentration levels of ClO- and SCN- in specimens of tap water and Yellow River water. Furthermore, the reversibility and regeneration of nano-ZIF-8 in sensing ClO- and SCN- is advantageous for applications of nano-ZIF-8 in solid-state sensing and anti-counterfeiting. As far as we know, this is the first time that nano-MOFs have been used as a selective fluorescence probe for ClO-/SCN- detection and anti-counterfeiting.

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

The spatial arrangement of DNA probes on the electrode surface is of critical significance for the performance of electrochemical biosensors. However, rational control of the probe surface remains challenging. In this work, we develop a capture probe carrying a poly-adenine anchoring block to construct a programmable self-assembled monolayer for a "sandwich-type" electrochemical biosensor. We show that with a co-assembling strategy using a polyA capture probe and 6-mercapto-1-hexanol, the density of the probes on the gold electrode can be simply adjusted by the length of polyA. The electron-transfer effect and thus the hybridization efficiency can as well be optimized by tuning the polyA length. As a result, we obtained an excellent biosensor performance with a limit of detection as low as 5 fM for a synthetic DNA target. We demonstrate the practicability of this system by analyzing a PCR product from Escherichia coli genomic DNA (0.2 pg/μL). On the basis of the ideal electrochemical interface, our polyA-based biosensor exhibited excellent reusability and stability, which is important for potential applications in the onsite analysis for a wide range of targets.

A surface acoustic wave biosensor synergizing DNA-mediated in situ silver nanoparticle growth for a highly specific and signal-amplified nucleic acid assay

An SAW biosensor harmonizes the surface mass effect for signal-amplified and sequence-specific DNA detection in blood serum.

Aptamer-initiated on-particle template-independent enzymatic polymerization (aptamer-OTEP) for electrochemical analysis of tumor biomarkers

Herein, an aptamer-initiated on-particle template-independent enzymatic polymerization (aptamer-OTEP) strategy for electrochemical aptasensor (E-aptasensor) is developed for analysis of cancer biomarker carcino-embryonic antigen (CEA). A pair of DNA aptamers is employed which can be specifically bond with CEA simultaneously. One of the aptamer is thiolated at 3'-terminal and immobilized onto the gold electrode as a capture probe, while the other one has a thiol group at its 5'-terminal and is modified onto the gold nanoparticles surface to form a nanoprobe. In the present of target, the two aptamers can "sandwich" the target, thus the nanoprobe is attached to the electrode. Then terminal deoxynucleotidyl transferase (TdT) is employed to catalyze the incorporation of biotin labeled dNTPs into the 3'-OH terminals of the DNA aptamer on the nanoprobe. The as-generated long DNA oligo tentacles allow specific binding of numerous avidin modified horseradish peroxidase (Av-HRP), resulting in tens of thousands of HRP catalyzed reduction of hydrogen peroxide and sharply increasing electrochemical signals. Taking advantage of the enzyme based nucleic acid amplification and nanoprobe, this strategy is demonstrated to possess the outstanding amplification efficiency.

Highly sensitive visual detection of mutant DNA based on polymeric nanoparticles-participating amplification

Taking advantage of the nanoparticles' large surface area and structural repeating characteristics, polymeric nanoparticles-participating polymerization-based amplification system was designed to enhance the sensitivity of detection.