Electrochemical nucleic acid detection based on parallel structural dsDNA/recombinant azurin hybrid

Investigation of G-Quadruplex DNA-Mediated Charge Transport for Exploring DNA Oxidative Damage in Telomeres

The human telomeric DNA 3' single-stranded overhang comprises tandem repeats of the sequence d(TTAGGG), which can fold into the stable secondary structure G-quadruplex (G4) and is susceptible to oxidative damage due to the enrichment of G bases. 8-Oxoguanine (8-oxoG) formed in telomeric DNA destabilizes G4 secondary structures and then inhibits telomere functions such as the binding of G4 proteins and the regulation of the length of telomeres. In this work, we developed a G4-DNA self-assembled monolayer electrochemical sensing interface using copper-free click chemistry based on the reaction of dibenzocyclooctyl with azide, resulting in a high yield of DNA tethers with order and homogeneity surfaces, that is more suitable for G-quadruplex DNA charge transport (CT) research. At high DNA coverage density surfaces, G-quadruplex DNA is 4 times more conductive than double-stranded DNA owing to the well-stacked aromatic rings of G-quartets acting as good charge transfer channels. The effect of telomeric oxidative damage on G-quadruplex-mediated CT is investigated. The accommodation of 8-oxoG at G sites originally in the syn or anti conformation around the glycosyl bond in the nonsubstituted hTel G-quadruplex causes structural perturbation and a conformational shift, which disrupts the π-stack, affecting the charge transfer and attenuating the electrochemical signal. The current intensity was found to correlate with the amount of 8-oxodG, and the detection limit was estimated to be approximately one lesion in 286 DNA bases, which can be converted into 64.7 fmol on the basis of the total surface DNA coverage. The improved G4-DNA order and homogeneity sensing interface represent a major step forward in this regard, providing a reliable and controlled electrochemical platform for the accurate measurement and diagnosis of G4-DNA oxidative damage.

Nanomaterials in electrochemical nanobiosensors of miRNAs

Nanomaterial-based biosensors have received significant attention owing to their unique properties, especially enhanced sensitivity. Recent advancements in biomedical diagnosis have highlighted the role of microRNAs (miRNAs) as sensitive prognostic and diagnostic biomarkers for various diseases. Current diagnostics methods, however, need further improvements with regards to their sensitivity, mainly due to the low concentration levels of miRNAs in the body. The low limit of detection of nanomaterial-based biosensors has turned them into powerful tools for detecting and quantifying these biomarkers. Herein, we assemble an overview of recent developments in the application of different nanomaterials and nanostructures as miRNA electrochemical biosensing platforms, along with their pros and cons. The techniques are categorized based on the nanomaterial used.

Combination of specific proteins as markers for accurate detection of extracellular vesicles using proximity ligation-mediated bHCR amplification

As the molecular characteristics of extracellular vesicles (EVs) are closely related to the occurrence and progression of cancer, the detection of tumor-derived EVs provides a promising non-invasive tool for the early diagnosis and treatment of cancer. However, it would be difficult for most of the existing methods to avoid false positives because the obtained result declares the amounts of proteins, but cannot accurately reflect the protein sources, including EV proteins and interfering proteins, in the actual samples. In this manuscript, a robust, accurate, and sensitive fluorescent strategy for profiling EV proteins is developed by using the combination of specific proteins as markers (Co-marker). Our strategy relies on the Co-marker recognition-activated cascade bHCR amplification, which forms numerous G-quadruplex structures that are integrated with fluorescent dyes for signal transduction. Notably, the detection accuracy can be improved owing to the effective avoidance of false positives from interfering proteins or single protein markers. Moreover, by using the double-positive protein recognition mode, unpurified detection can be achieved that avoids time-consuming EVs purification procedures. With its capacities of accuracy, portability, sensitivity, high throughput, and non-purification, the developed strategy might provide a practical tool for EV identification and the related early diagnosis and treatment of cancer.

3D Neural Network Composed of Neurospheroid and Bionanohybrid on Microelectrode Array to Realize the Spatial Input Signal Recognition in Neurospheroid

There have been several studies for demonstration of 2D neural network using living cells or organic/inorganic molecules, but to date, there is no report of development of a 3D neural network in vitro. Based on developed bionanohybrid composed of protein, DNA, molybdenum disulfide nanoparticles, and peptides for controlling electrophysiological states of living cells, here, the in vitro 3D neural network composed of the bionanohybrid, 3D neurospheroid and the microelectrode array (MEA) is developed. After production of the 3D neurospheroid derived from human neural stem cells, the bionanohybrid developed on the MEA successfully semi-penetrates the neurites of the 3D neurospheroid and forms the 3D neural network. The developed 3D neural network successfully exhibited the electrophysiological output signals of the 3D neurospheroid by transmitting the input signal applied by the bionanohybrid. Moreover, by using the selectively immobilized bionanohybrid on the MEA, the spatial input signal recognition in the neurospheroid of 3D neural network is realized for the first time. This newly developed in vitro 3D neural network provides a promising strategy to be applied in brain-on-a-chip, brain disease-related drug efficacy evaluation, bioelectronics, and bioelectronic medicine.

Ultrasensitive Electrochemical Detection of Mutated Viral RNAs with Single-Nucleotide Resolution Using a Nanoporous Electrode Array (NPEA)

The detection of nucleic acids and their mutation derivatives is vital for biomedical science and applications. Although many nucleic acid biosensors have been developed, they often require pretreatment processes, such as target amplification and tagging probes to nucleic acids. Moreover, current biosensors typically cannot detect sequence-specific mutations in the targeted nucleic acids. To address the above problems, herein, we developed an electrochemical nanobiosensing system using a phenomenon comprising metal ion intercalation into the targeted mismatched double-stranded nucleic acids and a homogeneous Au nanoporous electrode array (Au NPEA) to obtain (i) sensitive detection of viral RNA without conventional tagging and amplifying processes, (ii) determination of viral mutation occurrence in a simple detection manner, and (iii) multiplexed detection of several RNA targets simultaneously. As a proof-of-concept demonstration, a SARS-CoV-2 viral RNA and its mutation derivative were used in this study. Our developed nanobiosensor exhibited highly sensitive detection of SARS-CoV-2 RNA (∼1 fM detection limit) without tagging and amplifying steps. In addition, a single point mutation of SARS-CoV-2 RNA was detected in a one-step analysis. Furthermore, multiplexed detection of several SARS-CoV-2 RNAs was successfully demonstrated using a single chip with four combinatorial NPEAs generated by a 3D printing technique. Collectively, our developed nanobiosensor provides a promising platform technology capable of detecting various nucleic acids and their mutation derivatives in highly sensitive, simple, and time-effective manners for point-of-care biosensing.

Biomolecular Electron Controller Composed of Nanobiohybrid with Electrically Released Complex for Spatiotemporal Control of Neuronal Differentiation

In vitro spatiotemporal control of cell differentiation is a critical issue in several biomedical fields such as stem cell therapy and regenerative medicine, as it enables the generation of heterogeneous tissue structures similar to those of their native counterparts. However, the simultaneous control of both spatial and temporal cell differentiation poses important challenges, and therefore no previous studies have achieved this goal. Here, the authors develop a cell differentiation biomolecular electron controller ("Biomoletron") composed of recombinant proteins, DNA, Au nanoparticles, peptides, and an electrically released complex with retinoic acid (RA) to spatiotemporally control SH-SY5Y cell differentiation. RA is only released from the Biomoletron when the complex is electrically stimulated, thus demonstrating the temporal control of SH-SY5Y cell differentiation. Furthermore, by introducing a patterned Au substrate that allows controlling the area where the Biomoletron is immobilized, spatiotemporal differentiation of the SH-SY5Y cell is successfully achieved. Therefore, the proposed Biomoletron-mediated differentiation method provides a promising strategy for spatiotemporal cell differentiation control with applications in regenerative medicine and cell therapy.

Bionanohybrid composed of metalloprotein/DNA/MoS2/peptides to control the intracellular redox states of living cells and its applicability as a cell-based biomemory device

The development of cell-based bioelectronic devices largely depends on the direct control of intracellular redox states. However, most related studies have focused on the accurate measurement of electrical signals from living cells, whereas direct intracellular state control remains largely unexplored. Here, we developed a biocompatible transmembranal bionanohybrid structure composed of a recombinant metalloprotein, DNA, molybdenum disulfide nanoparticles (MoS₂), and peptides to control intracellular redox states, which can be used as a cell-based biomemory device. Using the capacitance of MoS₂ located inside the cell, the bionanohybrid controled the intracellular redox states of living cells by recording and extracting intracellular charges, which inturn was achieved by activating (writing) and deactivating (erasing) the cells. As a proof of concept, cell-based biomemory functions including writing, reading, and erasing were successfully demonstrated and confirmed via electrochemical methods and patch-clamp analyses, resulting in the development of the first in vitro cell-based biomemory device. This newly developed bionanohybrid provides a novel approach to control cellular redox states for cell-based bioelectronic applications, and can be applicable in a wide range of biological fields including bioelectronic medicine and intracellular redox status regulation.

Emerging materials for the electrochemical detection of COVID-19

The SARS-CoV-2 virus is still causing a dramatic loss of human lives worldwide, constituting an unprecedented challenge for the society, public health and economy, to overcome. The up-to-date diagnostic tests, PCR, antibody ELISA and Rapid Antigen, require special equipment, hours of analysis and special staff. For this reason, many research groups have focused recently on the design and development of electrochemical biosensors for the SARS-CoV-2 detection, indicating that they can play a significant role in controlling COVID disease. In this review we thoroughly discuss the transducer electrode nanomaterials investigated in order to improve the sensitivity, specificity and response time of the as-developed SARS-CoV-2 electrochemical biosensors. Particularly, we mainly focus on the results appeard on Au-based and carbon or graphene-based electrodes, which are the main material groups recently investigated worldwidely. Additionally, the adopted electrochemical detection techniques are also discussed, highlighting their pros and cos. The nanomaterial-based electrochemical biosensors could enable a fast, accurate and without special cost, virus detection. However, further research is required in terms of new nanomaterials and synthesis strategies in order the SARS-CoV-2 electrochemical biosensors to be commercialized.

Gold nanoparticle/MXene for multiple and sensitive detection of oncomiRs based on synergetic signal amplification

Multiple and sensitive detection of oncomiRs for accurate cancer diagnostics is still a challenge. Here, a synergetic amplification strategy was introduced by combining a MXene-based electrochemical signal amplification and a duplex-specific nuclease (DSN)-based amplification system for rapid, attomolar and concurrent quantification of multiple microRNAs on a single platform in total plasma. Synthesized MXene-Ti₃C₂T_x modified with 5 nm gold nanoparticles (AuNPs) was casted on a dual screen-printed gold electrode to host vast numbers of DNA probes identically co-immobilized on dedicated electrodes. Interestingly, presence of MXene provided biofouling resistance and enhanced the electrochemical signals by almost 4 folds of magnitude, attributed to its specious surface area and remarkable charge mobility. The 5 nm AuNPs were perfectly distributed within the whole flaky architect of the MXene to give rise to the electrochemical performance of MXene and provide the thiol-Au bonding feature. This synergetic strategy reduced the DSN-based biosensors' assay time to 80 min, provided multiplexability, antifouling activity, substantial sensitivity and specificity (single mutation recognition). The limit of detection of the proposed biosensor for microRNA-21 and microRNA-141 was respectively 204 aM and 138 aM with a wide linear range from 500 aM to 50 nM. As a proof of concept, this newly-developed strategy was coupled with a 96-well adaptive sensing device to successfully profile three cancer plasma samples based on their altered oncomiR abundances.

Single Functionalized pRNA/Gold Nanoparticle for Ultrasensitive MicroRNA Detection Using Electrochemical Surface-Enhanced Raman Spectroscopy

Controlling the selective one-to-one conjugation of RNA with nanoparticles is vital for future applications of RNA nanotechnology. Here, the monofunctionalization of a gold nanoparticle (AuNP) with a single copy of RNA is developed for ultrasensitive microRNA-155 quantification using electrochemical surface-enhanced Raman spectroscopy (EC-SERS). A single AuNP is conjugated with one copy of the packaging RNA (pRNA) three-way junction (RNA 3WJ). pRNA 3WJ containing one strand of the 3WJ is connected to a Sephadex G100 aptamer and a biotin group at each arm (SEPapt/3WJ/Bio) which is then immobilized to the Sephadex G100 resin. The resulting complex is connected to streptavidin-coated AuNP (STV/AuNP). Next, the STV/AuNP-Bio/3WJa is purified and reassembled with another 3WJ to form a single-labeled 3WJ/AuNP. Later, the monoconjugate is immobilized onto the AuNP-electrodeposited indium tin oxide coated substrate for detecting microRNA-155 based on EC-SERS. Application of an optimum potential of +0.2 V results in extraordinary amplification (≈7 times) of methylene blue (reporter) SERS signal compared to the normal SERS signal. As a result, a highly sensitive detection of 60 × 10-18 m microRNA-155 in 1 h in serum based on monoconjugated AuNP/RNA is achieved. Thus, the monofunctionalization of RNA onto nanoparticle can provide a new methodology for biosensor construction and diverse RNA nanotechnology development.

Fabrication of Electrochemical-Based Bioelectronic Device and Biosensor Composed of Biomaterial-Nanomaterial Hybrid

The field of bioelectronics has paved the way for the development of biochips, biomedical devices, biosensors and biocomputation devices. Various biosensors and biomedical devices have been developed to commercialize laboratory products and transform them into industry products in the clinical, pharmaceutical, environmental fields. Recently, the electrochemical bioelectronic devices that mimicked the functionality of living organisms in nature were applied to the use of bioelectronics device and biosensors. In particular, the electrochemical-based bioelectronic devices and biosensors composed of biomolecule-nanoparticle hybrids have been proposed to generate new functionality as alternatives to silicon-based electronic computation devices, such as information storage, process, computations and detection. In this chapter, we described the recent progress of bioelectronic devices and biosensors based on biomaterial-nanomaterial hybrid.

Recent Advances on Electrochemical Biosensing Strategies toward Universal Point-of-Care Systems

A number of very recently developed electrochemical biosensing strategies are promoting electrochemical biosensing systems into practical point-of-care applications. The focus of research endeavors has transferred from detection of a specific analyte to the development of general biosensing strategies that can be applied for a single category of analytes, such as nucleic acids, proteins, and cells. In this Minireview, recent cutting-edge research on electrochemical biosensing strategies are described. These developments resolved critical challenges regarding the application of electrochemical biosensors to practical point-of-care systems, such as rapid readout, simple biosensor fabrication method, ultra-high detection sensitivity, direct analysis in a complex biological matrix, and multiplexed target analysis. This Minireview provides general guidelines both for scientists in the biosensing research community and for the biosensor industry on development of point-of-care system, benefiting global healthcare.

Multifunctional Nanobiohybrid Material Composed of Ag@Bi2Se3/RNA Three-Way Junction/miRNA/Retinoic Acid for Neuroblastoma Differentiation

Nanoparticle-based cell differentiation therapy has attracted increasing research interest as it is a promising substitute for conventional cancer treatment methods. Here, the topological insulator bismuth selenide nanoparticle (Bi₂Se₃ NP) was core-shelled with silver (Ag@Bi₂Se₃) to represent remarkable biocompatibility and plasmonic features (ca. 2.3 times higher than those of Ag nanoparticle). Moreover, a newly developed RNA three-way junction (3WJ) structure was designed for the quad-functionalization of any type of nanoparticle and surface. One leg of the 3WJ was attached to the Ag@Bi₂Se₃, and the other leg harbored a cell-penetrating RNA and a florescence tag. The third leg was designed to inhibit micro-RNA-17 (miR-17) and to further release retinoic acid (RA). A new drug delivery mechanism was developed for the slow release of RA inside the cytosol based on the prerequisite inhibition of miR-17 using a strand displacement strategy. In this paper, we report a simple methodology for resolving the hydrophobicity challenges of RA by its conjugation with a RNA strand (RA/R) through a stimulus-responsive cross-linker. The developed nanobiohybrid material could fully differentiate SH-SY5Y cancer cells into neurons and stop their growth in 6 days without requiring sequential treatments which has not been reported yet. Using a surface-enhanced Raman spectroscopy technique, the RA delivery and the cell differentiation process were monitored nondestructively in real time. The fabricated nanobiohybrid material could open the new horizons in the fabrication of different diagnostic/therapeutic agents.

TiO2 nanowires as an effective sensing platform for rapid fluorescence detection of single-stranded DNA and double-stranded DNA

Numerous nanomaterials have been utilized for novel biosensors with sensitivity and selectivity in the last decades due to their intrinsic unique properties. Herein, a facile fluorescence method for nucleic acid detection was developed by employing TiO₂ nanowires (NWs) as the sensing platform. The quenching effect of TiO₂ NWs to fluorophore-labelled single-stranded DNA (ssDNA) was found to be more significant than that to fluorophore-labelled double-stranded DNA (dsDNA) or triplex DNA probes. More importantly, the whole quenching process was also fast since it just took about ten minutes to reach the equilibrium. Based on the different affinities of TiO₂ NWs to ssDNA, dsDNA and triplex DNA probes, the sequence-specific nucleic acids were detected with sensitivity and specificity. Further investigation has demonstrated that the quenching efficiency of TiO₂ NWs to long ssDNA was apparently superior than that to short ssDNA. Moreover, the fluorescence from various ssDNA probes labelled with a wide spectrum of fluorescent dyes could also be quenched by TiO₂ NWs. These inspiring results reveal that TiO₂ NWs could be an excellent universal nanoquencher used in the next-generation biosensors.

Molecular methods in electrochemical microRNA detection

High-throughput profiling/sensing of nucleic acids has recently emerged as a highly promising strategy for the early diagnosis and improved prognosis of a broad range of pathologies, most notably cancer. Among the potential biomarker candidates, microRNAs (miRNAs), a class of non-coding RNAs of 19-25 nucleotides in length, are of particular interest due to their role in the post-transcriptional regulation of gene expression. Developing miRNA sensing technologies that are quantitative, ultrasensitive and highly specific has proven very challenging because of their small size, low natural abundance and the high degree of sequence similarity among family members. When compared to optical based methods, electrochemical sensors offer many advantages in terms of sensitivity and scalability. This non-comprehensive review aims to break-down and highlight some of the most promising strategies for electrochemical sensing of microRNA biomarkers.

Bifunctional Au@Bi2 Se3 Core-Shell Nanoparticle for Synergetic Therapy by SERS-Traceable AntagomiR Delivery and Photothermal Treatment

For the first time, topological insulator bismuth selenide nanoparticles (Bi₂ Se₃ NP) are core-shelled with gold (Au@Bi₂ Se₃ ) i) to represent considerably small-sized (11 nm) plasmonic nanoparticles, enabling accurate bioimaging in the near-infrared region; ii) to substantially improve Bi₂ Se₃ biocompatibility, iii) water dispersibility, and iv) surface functionalization capability through straightforward gold-thiol interaction. The Au@Bi₂ Se₃ is subsequently functionalized for v) effective targeting of SH-SY5Y cancer cells, vi) disrupting the endosome/lysosome membrane, vii) traceable delivery of antagomiR-152 and further synergetic oncomiR knockdown and photothermal therapy (PTT). Unprecedentedly, it is observed that the Au shell thickness has a significant impact on evoking the exotic plasmonic features of Bi₂ Se₃ . The Au@Bi₂ Se₃ possesses a high photothermal conversion efficiency (35.5%) and a remarkable surface plasmonic effect (both properties are approximately twofold higher than those of 50 nm Au nanoparticles). In contrast to the siRNA/miRNA delivery methods, the antagomiR delivery is based on strand displacement, in which the antagomiR-152 is displaced by oncomiR-152 followed by a surface-enhanced Raman spectroscopy signal drop. This enables both cancer cell diagnosis and in vitro real-time monitoring of the antagomiR release. This selective PTT nanoparticle can also efficiently target solid tumors and undergo in vivo PTT, indicating its potential clinical applications.

Electrochemical Biosensor Composed of Silver Ion-Mediated dsDNA on Au-Encapsulated Bi2 Se3 Nanoparticles for the Detection of H2 O2 Released from Breast Cancer Cells

A newly developed electrochemical biosensor composed of a topological insulator (TI) and metallic DNA (mDNA) is fabricated. The bismuth selenide nanoparticle (Bi₂ Se₃ NP) is synthesized and sandwiched between the gold electrode and another Au-deposited thin layer (Bi₂ Se₃ @Au). Then, eight-silver-ion mediated double-stranded DNA (mDNA) is immobilized onto the substrate (Bi₂ Se₃ @Au-mDNA) for the further detection of hydrogen peroxide. The Bi₂ Se₃ NP acts as the electrochemical-signal booster, while unprecedentedly its encapsulation by the Au thin layer keeps the TI surface states protected, improves its electrochemical-signal stability and provides an excellent platform for the subsequent covalent immobilization of the mDNA through Au-thiol interaction. Electrochemical results show that the fabricated biosensor represents much higher Ag⁺ redox current (≈10 times) than those electrodes prepared without Bi₂ Se₃ @Au. The characterization of the Bi₂ Se₃ @Au-mDNA film is confirmed by atomic force microscopy, scanning tunneling microscopy, and cyclic voltammetry. The proposed biosensor shows a dynamic range of 00.10 × 10^-6 m to 27.30 × 10^-6 m, very low detection limit (10 × 10^-9 m), unique current response (1.6 s), sound H₂ O₂ recovery in serum, and substantial capability to classify two breast cancer subtypes (MCF-7 and MDA-MB-231) based on their difference in the H₂ O₂ generation, offering potential applications in the biomedicine and pharmacology fields.

A highly sensitive and selective fluorescent probe without quencher for detection of Pb2+ ions based on aggregation-caused quenching phenomenon

Lead is a highly toxic heavy metal, and various functional nucleic acid (FNA)-based biosensors have been developed for the detection of Pb²⁺ in environmental monitoring. However, most fluorescence biosensors that have been reported were designed on the basis of a double-labeled (fluorophore and quencher group) DNA sequence, which not only involved an inconvenient organic synthesis but also restricted their wider use in practical applications. Here, we utilized a G-rich DNA sequence as a recognition probe and conjugated fluorene (CF) to develop a fluorescence sensor without a quencher based on the aggregation-caused quenching (ACQ) effect. In the presence of Pb²⁺, the degree of aggregation of CF was reduced because Pb²⁺ induced the formation of a G-quadruplex structure of the CF-DNA probe, and the fluorescence signal increased with the concentration of Pb²⁺ (0–1 μM), with a limit of detection of 0.36 nM. This fluorescent probe without a quencher enables the sensitive and selective detection of Pb²⁺. On the basis of these advantages, the CF-DNA probe represents a promising analytical method for detecting Pb²⁺.

Fluorescent probe with only a fluorophore but no quencher for detecting Pb²⁺ on the basis of the aggregation-caused quenching (ACQ) phenomenon.