Electrochemical single nucleotide polymorphisms genotyping on surface immobilized three-dimensional branched DNA nanostructure

Superlarge, Rigidified DNA Tetrahedron with a Y-Shaped Backbone for Organizing Biomolecules Spatially and Maintaining Their Full Bioactivity

A major impediment to the clinical translation of DNA tiling nanostructures is a technical bottleneck for the programmable assembly of DNA architectures with well-defined local geometry due to the inability to achieve both sufficient structural rigidity and a large framework. In this work, a Y-backbone was inserted into each face to construct a superlarge, sufficiently rigidified tetrahedral DNA nanostructure (called RDT) with extremely high efficiency. In RDT, the spatial size increased by 6.86-fold, and the structural rigidity was enhanced at least 4-fold, contributing to an ∼350-fold improvement in the resistance to nucleolytic degradation even without a protective coating. RDT can be mounted onto an artificial lipid-bilayer membrane with molecular-level precision and well-defined spatial orientation that can be validated using the fluorescence resonance energy transfer (FRET) assay. The spatial orientation of Y-shaped backbone-rigidified RDT is unachievable for conventional DNA polyhedrons and ensures a high level of precision in the geometric positioning of diverse biomolecules with an approximately homogeneous environment. In tests of RDT, surface-confined horseradish peroxidase (HRP) exhibited nearly 100% catalytic activity and targeting aptamer-immobilized gold nanoparticles showed 5.3-fold enhanced cellular internalization. Significantly, RDT exhibited a 27.5-fold enhanced structural stability in a bodily environment and did not induce detectable systemic toxicity.

Emerging ctDNA detection strategies in clinical cancer theranostics

Circulating tumor DNA (ctDNA) is naked DNA molecules shed from the tumor cells into the peripheral blood circulation. They contain tumor-specific gene mutations and other valuable information. ctDNA is considered to be one of the most significant analytes in liquid biopsies. Over the past decades, numerous researchers have developed various detection strategies to perform quantitative or qualitative ctDNA analysis, including PCR-based detection and sequencing-based detection. More and more studies have illustrated the great value of ctDNA as a biomarker in the diagnosis, prognosis and heterogeneity of tumor. In this review, we first outlined the development of digital PCR (dPCR)-based and next generation sequencing (NGS)-based ctDNA detection systems. Besides, we presented the introduction of the emerging ctDNA analysis strategies based on various biosensors, such as electrochemical biosensors, fluorescent biosensors, surface plasmon resonance and Raman spectroscopy, as well as their applications in the field of biomedicine. Finally, we summarized the essentials of the preceding discussions, and the existing challenges and prospects for the future are also involved.

Electrochemical Biosensors for Circulating Tumor DNA Detection

Early diagnosis and treatment have always been highly desired in the fight against cancer, and detection of circulating tumor DNA (ctDNA) has recently been touted as highly promising for early cancer-screening. Consequently, the detection of ctDNA in liquid biopsy is gaining much attention in the field of tumor diagnosis and treatment, which has also attracted research interest from industry. However, it is difficult to achieve low-cost, real-time, and portable measurement of ctDNA in traditional gene-detection technology. Electrochemical biosensors have become a highly promising solution to ctDNA detection due to their unique advantages such as high sensitivity, high specificity, low cost, and good portability. Therefore, this review aims to discuss the latest developments in biosensors for minimally invasive, rapid, and real-time ctDNA detection. Various ctDNA sensors are reviewed with respect to their choices of receptor probes, designs of electrodes, detection strategies, preparation of samples, and figures of merit, sorted by type of electrode surface recognition elements. The development of biosensors for the Internet of Things, point-of-care testing, big data, and big health is analyzed, with a focus on their portable, real-time, and non-destructive characteristics.

Aggregation-Induced Emission Luminogen-Based Dual-Mode Enzyme-Linked Immunosorbent Assay for Ultrasensitive Detection of Cancer Biomarkers in a Broad Concentration Range

The enzyme-linked immunosorbent assay (ELISA) is one of the most commonly used methods for measuring antibodies and antigens in biological samples. However, developing new ELISAs with high detection sensitivity and broad detection dynamic ranges without resorting to complicated signal processing and equipment setups remains a challenge. In this work, we report a strategy to simultaneously improve the detection sensitivity and broaden the dynamic range by replacing the chromogenic reagents used in traditional ELISAs with an aggregation-induced emission luminogen (AIEgen). The developed AIE-ELISA could generate complementary absorbance and fluorescence signals with a linear detection range of 1.6-25,000 pg/mL. The application of this dual-mode AIE-ELISA in the detection of the prostate-specific antigen (PSA) realized a limit of detection of 1.3 pg/mL (3.78 × 10^-14 M) and dynamic range improvement of approximately 2 orders of magnitude compared to a single-mode ELISA, which enabled it to discriminate a minor PSA difference in a patient's serum. The simpler experimental operation, faster enzyme response speed, and better photostability of AIEgen than the traditional chromogenic reagents used in ELISAs showed that our developed AIE-ELISA holds great potential in the fields of immunoassay, immunohistochemistry, and immunocytochemistry.

Coprinus comatus endophytic bacteria characteristics and mechanisms for the cadmium resistance

Characteristics and resistant mechanisms of macro-fungus endophytic bacteria to cadmium (Cd) have not been well defined. Strains L1 and L3 with Cd-resistant capacity were isolated from the fruiting body of Coprinus comatus, which were identified as Bacillus sp. Under the stress of Cd, the morphologies of both L1 and L3 changed to reduce the threat of Cd. The results of Fourier Transform Infrared Spectrometry indicated that functional groups such as -OH, -COOH, and -NH₂ participated in the Cd adsorption process. The contents of Cd adsorbed on the cell wall of L1 were 83.46-174.51% higher than that of L3. On the contrary, the contents of Cd accumulated in L1 cytoplasm were 38.77-74.77% lower than that of L3. As the level of Cd increased from 10 to 30 mg/L, the percentages of Cd distributed on the cell walls of L1 and L3 increased by 42.43% and 26.78%, respectively. The results also revealed that the contents of Cd absorbed by the sterilized strains L1 and L3 were 47.67-64.94% and 8.65-78.63% higher than that of living ones, respectively. In addition, the proline production of L1 was 23.75-109.68% higher than that of L3, while the malondialdehyde (MDA) production of L1 was 0.96-15.60% lower than that of L3. Thus, through the comparison of endophytic bacterial physiological responses, the possible characteristics and resistant mechanisms of macro-fungus endophytic bacteria under Cd stress were firstly reported.

DNA-Tetrahedral-Nanostructure-Based Entropy-Driven Amplifier for High-Performance Photoelectrochemical Biosensing

In virtue of the inherent molecular recognition and programmability, DNA has recently become the most promising for high-performance biosensors. The rationally engineered nucleic acid architecture will be very advantageous to hybridization efficiency, specificity, and sensitivity. Herein, a robust and split-mode photoelectrochemical (PEC) biosensor for miRNA-196a was developed based on an entropy-driven tetrahedral DNA (EDTD) amplifier coupled with superparamagnetic nanostructures. The DNA tetrahedron structure features in rigidity and structural stability that contribute to obtain precise identification units and specific orientations, improving the hybridization efficiency, sensitivity, and selectivity of the as-designed PEC biosensor. Further, superparamagnetic Fe₃O₄@SiO₂@CdS particles integrated with DNA nanostructures are beneficial for the construction of a split-mode, highly selective, and reliable PEC biosensor. Particularly, the enzyme- and hairpin-free EDTD amplifier eliminates unnecessary interference from the complex secondary structure of pseudoknots or kissing loops in typical hairpin DNAs, significantly lowers the background noise, and improves the detection sensitivity. This PEC biosensor is capable of monitoring miRNA-196a in practical settings with additional advantages of efficient electrode fabrication, stability, and reproducibility. This strategy can be extended to various miRNA assays in complex biological systems with excellent performance.

24-Epibrassinolide combined with heavy metal resistant bacteria enhancing phytoextraction of Amaranthus hypochondriacus L. in Cd-contaminated soil

The remediation efficiency of phytoextraction on heavy metal could be influenced by metal bioavailability and plant growth. Hence, we applied a synergistic intensification system with plant hormone (24-Epibrassinolide, EBR) and metal-resistant bacterium (Serratia sp. CTZ4) to enhance Cd extraction of Amaranthus hypochondriacus L. in contaminated soil. Results demonstrated that the combination of CTZ4 and EBR promoted soil microecology through decreasing soil pH, improving soil enzymatic activity (dehydrogenase, invertase, acid phosphate, urease). Besides, microbial community structure was evaluated to understand the diversity and relative abundance of microbe in soil after remediation. Moreover, the maximum extraction of Cd was 5.91 mg kg^-1 and increased about 60.16 % to CK. Meanwhile, the antioxidant system (SOD, CAT activities) of plant was improved significantly as well as plants biomass increasing by 46.02 % with the combination of EBR and CTZ4. Thus, our results proved that the utilization of EBR and CTZ4 is an alternated method to enhance phytoextraction efficiency of A. hypochondriacus in Cd-contaminated soil.

Zippering DNA Tetrahedral Hyperlink for Ultrasensitive Electrochemical MicroRNA Detection

Pluripotency of a DNA tetrahedron (DNA^TT) has made the iconic framework a compelling keystone in biosensors and biodevices. Herein, distinct from the well-tapped applications in substrate fabrication, we focus on exploring their tracing and signaling potentials. A homologous family of four isostructural DNA^TT, i.e., DNA^{TTα/β/γ/δ}, was engineered to form a sensor circuitry, in which a target-specific monolayer of thiolated DNA^TTγ pinned down the analyte jointly with the reciprocal DNA^TTδ into a sandwich complex; the latter further rallied an in situ interdigital relay of biotinylated DNA^TTα/β into a microsized hyperlink dubbed polyDNA^TT. Its scale and growth factors were illuminated rudimentarily in transmission electron microscopy and confocal laser scanning microscopy. Using a nonsmall-cell lung cancer-related microRNA (hsa-miR-193a-3p) as the subject, a compound DNA-backboned construct was synthesized, fusing all building blocks together. Its superb tacticity and stereochemical conformality avail the templating of a horseradish peroxidase train, which boosted the paralleled catalytic surge of proton donors, resulting in an attomolar detection limit and a broad calibration range of more than seven orders of magnitude. Such oligomerization bested the conventional hybridization chain reaction laddering at both biomechanical stability and stoichiometric congruency. More significantly, it demonstrates the flexibility of DNA architectures and their multitasking ability in biosensing.

High-effectively degrade the di-(2-ethylhexyl) phthalate via biochemical system: Resistant bacterial flora and persulfate oxidation activated by BC@Fe3O4

Di-(2-ethylhexyl) phthalate (DEHP) has been classified as a priority pollutant which increased the healthy risk to human and animals dramatically. Hence, a novel biochemical system combined by DEHP-resistant bacterial flora (B) and a green oxidant of persulfate (PS) activated by Nano-Fe₃O₄ was applied to degrade DEHP in contaminated soil. In this study, the resistant bacterial flora was screened from activated sludge and immobilized by sodium alginate (SAB). Nano-Fe₃O₄ was coated on biochar (BC@Fe₃O₄) to prevent agglomerating in soil. X-ray diffraction (XRD) and scanning electron microscope (SEM) were utilized to characterize BC@Fe₃O₄. Results demonstrated that the treatment of biochemical system (SAB + BC@Fe₃O₄ + PS) presented the maximum degradation rate about 92.56% within 24 days of incubation and improved soil microecology. The 16S rDNA sequences analysis of soil microorganisms showed a significantly different abundance and a similar diversity among different treatments. Kyoto Encyclopedia of Genes and Genomes (KEGG) functional genes difference analysis showed that some metabolic pathways, such as metabolism of cofactors and vitamins, energy metabolism, cell growth and death, replication and repair, were associated with the biodegradation of DEHP. Besides, DEHP was converted to MEHP and PA by biodegradation, while DEHP was converted to DBP and PA by persulfate and BC@Fe₃O₄, and then ultimately degraded to CO₂ and H₂O.

Encapsulation and release of living tumor cells using hydrogels with the hybridization chain reaction

Circulating tumor cells (CTCs) enable noninvasive liquid biopsy and identification of cancer. Various approaches exist for the capture and release of CTCs, including microfluidic methods and those involving magnetic beads or nanostructured solid interfaces. However, the concomitant cell damage and fragmentation that often occur during capture make it difficult to extensively characterize and analyze living CTCs. Here, we describe an aptamer-trigger-clamped hybridization chain reaction (atcHCR) method for the capture of CTCs by porous 3D DNA hydrogels. The 3D environment of the DNA networks minimizes cell damage, and the CTCs can subsequently be released for live-cell analysis. In this protocol, initiator DNAs with aptamer-toehold biblocks specifically bind to the epithelial cell adhesion molecule (EpCAM) on the surface of CTCs, which triggers the atcHCR and the formation of a DNA hydrogel. The DNA hydrogel cloaks the CTCs, facilitating quantification with minimal cell damage. This method can be used to quantitively identify as few as 10 MCF-7 cells in a 2-µL blood sample. Decloaking of tumor cells via gentle chemical stimulus (ATP) is used to release living tumor cells for subsequent cell culture and live-cell analysis. We also describe how to use the protocol to encapsulate and release cells of cancer cell lines, which can be used in preliminary experiments to model CTCs. The whole protocol takes ~2.5 d to complete, including downstream cell culture and analysis.

Characteristics and in situ remediation effects of heavy metal immobilizing bacteria on cadmium and nickel co-contaminated soil

Cadmium (Cd) and nickel (Ni) in soil have caused serious environmental problems and increased healthy risks to humans and biota, it is vital important and necessary to develop effective methods to resolve the combined contaminated problems. In this study, strains L5 and L6 with good heavy metal resistant and immobilizing capacities were isolated from Cd and Ni contaminated soil. Bacterial characteristic experiment illustrated that many functional groups (-OH, -NH₂ and -COO et al.) were distributed on the surface of L5 and L6. Under the stress of heavy metals, bacterial appearances were distorted. The pot experiment indicated that the concentrations of HOAc-extractable Cd and Ni in soil reduced 6.26-15.33% and 13.31-19.53% with the inoculation of L5 and L6. In addition, the immobilization rates on Cd and Ni improved 61.27-128.50% and 23.69-39.66% with re-inoculation of strains L5 and L6 at 30 days, respectively. After inoculation of strains L5 and L6 for 60 days, the activities of FDA hydrolysis, acid phosphatase, urease, invertase and dehydrogenase in soil increased obviously. Furthermore, bacterial diversity indexes and community structure of soil were also improved. Thus, given the beneficial remediation effects of the isolated strains, L5 and L6 have great potentials for heavy metals contaminated soil remediation.

Impacts of a novel strain QY-1 allied with chromium immobilizing materials on chromium availability and soil biochemical properties

In-situ passivation of soil chromium (Cr) contamination based on chemical and biological passivators has been widely concerned, however, the cooperative effect of two types of passivators on Cr passivation and soil properties was little investigated. In this study, nano zero valent iron (nZVI) and humic acid (HA) as the chemical passivators were selected and were combined with a novel Cr resistant strain QY-1 to study these two points. Results demonstrated that the combination was more effective in Cr immobilization, among which, HA + QY-1 had the highest passivation rate (82.83%), followed by nZVI + QY-1. HA + QY-1 alleviated soil Cr stress most efficiently as its soil relevant fertility indicators, microbial quantity, respiration and seed gemination rate significantly increased. On the contrary, nZVI decreased soil respiration and microbial abundance, but the addition of QY-1 could relieve this phenomenon. The results highlighted the ability of HA + QY-1 to remediate Cr contaminated soil and improve soil stability.

de la Fuente J, Moros M. Nanoparticle-based biosensors for detection of extracellular vesicles in liquid biopsies

Selecting the appropriate nanoparticle, functionalization chemistry and sensing methodology can speed up the translation of liquid biopsies into the clinic.

A versatile biomolecular detection platform based on photo-induced enhanced Raman spectroscopy

Surface-enhanced Raman spectroscopy (SERS) as one of the effective tools for sensitive and selective detection of biomolecules has attracted tremendous attention. Here, we construct a versatile biomolecular detection platform based on photo-induced enhanced Raman spectroscopy (PIERS) effect for ultrasensitive detection of multiple analytes. In our PIERS sensor, we exploit the molecular recognition capacity of aptamers and the high affinity of aptamers with analyte to trigger TiO₂@AgNP substrates binding with Raman tag-labeled gold nanoparticles probes via analyte, thus forming sandwich complexes. Additionally, combining plasmonic nanoparticles with photo-activated substrates allows PIERS sensor to achieve increased sensitivity beyond the normal SERS effect upon ultraviolet irradiation. Accordingly, the PIERS can be implemented for analysis of multiple analytes by designing different analyte aptamers, and we further demonstrate that the constructed PIERS sensor can serve as a versatile detection platform for sensitively analyzing various biomolecules including small molecules (adenosine triphosphate (ATP), limit of detection (LOD) of 0.1 nM), a biomarker (thrombin, LOD of 50 pM), and a drug (cocaine, LOD of 5 nM). Therefore, this versatile biomolecular detection platform based on PIERS effect for ultrasensitive detection of multiple analytes holds great promise to be a practical tool.

Enhanced synergistic effects from multiple iron oxide nanoparticles encapsulated within nitrogen-doped carbon nanocages for simple and label-free visual detection of blood glucose

Hollow-structured carbon materials play a crucial role in research of biosensors, energy storage and nanomedicine as a kind of material with advantages like high surface area, tunable pore volume, excellent mechanical properties, and good biocompatibility. Herein, we developed a simple, facile and controllable method for synthesis of Fe₃O₄ nanoparticles encapsulated in hollow carbon nanocages (FNHCs) with SiO₂ nanospheres as a sacrificial template. Owing to the unique structure of multiple Fe₃O₄ nanoparticles cores integrated with N-doped carbon nanocages, the as-synthesized FNHCs exhibited greatly enhanced peroxidase mimicking activity with extremely high signal-to-noise ratio of ∼91 fold. Also, it was found that the FNHCs possessed a higher peroxidase-like activity than that of other similar-structured Fe₃O₄ architectures (e.g. Fe₃O₄@C NPs). The resulting steady-state kinetic curve demonstrated the enzymatic activity of FNHCs with classic Michaelis-Menton kinetics following a ping-pong mechanism. On the basis of the superior enzymatic activity, the FNHCs performed as a high-efficiency peroxidase mimic, realizing facile, label-free, highly sensitive/selective colorimetric detection of H₂O₂ and glucose. Furthermore, the colorimetric sensor successfully determined glucose in patients' serum samples with high accuracy and precision, suggesting great potential for real applications.

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.

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

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

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

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

Cancer-Specific MicroRNA Analysis with a Nonenzymatic Nucleic Acid Circuit

Sensitive detection of gastric cancer-related biomarkers in human serum provides a promising means for early cancer diagnosis. Herein, we report the design of a nucleic acid circuit for gastric cancer-related microRNA-27a (miRNA-27a) detection based on dual toehold-mediated circular strand displacement amplification (CSDA). In the presence of miRNA-27a, the hybridization between miRNA-27a and probe DNA on magnetic beads through toehold 1 leads to the release of fluorescent DNA and the exposure of a new toehold 2 on linker DNA. After hybridization with catalytic DNA, CSDA is initiated and target miRNA-27a is released to participate in the next cyclic reaction; therefore, a greatly enhanced fluorescence signal is produced. The efficient magnetic separation makes the sensitive detection of miRNA-27a be accomplished within 45 min. With the efficient CSDA, the detection limit of the system (0.8 pM) is ∼100 folds lower than that of the system based on strand displacement without CSDA (79.3 pM). Furthermore, the system also showed good stability and sensitivity to discriminate single-base mismatch, which allows the detection of miRNA-27a in human serum samples. This study provides a novel platform and approach for the rapid quantitative determination of miRNA, which has great potential in clinical diagnosis and disease treatment.

An Aptamer-Based Near-Infrared Fluorescence Nanoprobe for Detecting and Imaging of Phospholamban Micropeptide in Cardiomyocytes

A growing body of evidence indicates that micropeptides encoded by long noncoding RNAs (lncRNAs) act independently or as regulators of larger proteins in fundamental biological processes, especially in the maintenance of cellular homeostasis. However, due to their small size and low intracellular expression, visual monitoring of micropeptides in living cells is still a challenge. In this work, we have designed and synthesized an aptamer-based near-infrared fluorescence nanoprobe for fluorescence imaging of phospholamban (PLN), which is an intracellular micropeptide that affects calcium homeostasis, and is closely associated with human heart failure in the clinic. The nanoprobe could respond specifically to PLN with excellent selectivity, high sensitivity, good nuclease stability, and biocompatibility, and it was successfully applied for imaging of changes in PLN levels in cardiomyocytes and in frozen sections of heart tissues. Further combined with clinical myocardial biopsy, we believe that the developed nanoprobe should be of great significance in later molecular pathology study of heart failure, which may help with diagnosis of early heart failure in the future. More importantly, for the first time nanoprobes were applied to visually monitor the changes of micropeptides in living cells and in frozen tissue sections, and the design concept of the aptamer-based nanoprobe can be extended to fluorescence detection of other micropeptides.

Antifouling (Bio)materials for Electrochemical (Bio)sensing

(Bio)fouling processes arising from nonspecific adsorption of biological materials (mainly proteins but also cells and oligonucleotides), reaction products of neurotransmitters oxidation, and precipitation/polymerization of phenolic compounds, have detrimental effects on reliable electrochemical (bio)sensing of relevant analytes and markers either directly or after prolonged incubation in rich-proteins samples or at extreme pH values. Therefore, the design of antifouling (bio)sensing interfaces capable to minimize these undesired processes is a substantial outstanding challenge in electrochemical biosensing. For this purpose, efficient antifouling strategies involving the use of carbon materials, metallic nanoparticles, catalytic redox couples, nanoporous electrodes, electrochemical activation, and (bio)materials have been proposed so far. In this article, biomaterial-based strategies involving polymers, hydrogels, peptides, and thiolated self-assembled monolayers are reviewed and critically discussed. The reported strategies have been shown to be successful to overcome (bio)fouling in a diverse range of relevant practical applications. We highlight recent examples for the reliable sensing of particularly fouling analytes and direct/continuous operation in complex biofluids or harsh environments. Opportunities, unmet challenges, and future prospects in this field are also pointed out.

Engineering Nanozymes Using DNA for Catalytic Regulation

DNA treatment of metal nanoparticles provides a potent tool for tuning their native properties and constructing advanced materials. However, there have been limited studies on interactions between DNA and nanomaterial-based artificial enzymes (nanozymes) to influence their intrinsic peroxidase-like properties. Here, we present the utilization of DNA as a capping ligand to engineer various bio-nanointerfaces for high-precise and adjustable regulation of catalytic behaviors of nanozymes toward the oxidation of substrates. The treatment of stiff double-stranded DNA only induced a negligible enhancement of the catalytic activity of nanozymes, and both coil-like single-stranded DNA and hairpin DNA-capped nanoparticles produced a medium signal increase. Interestingly, hybridization chain reaction (HCR) product-treated nanoparticles showed the highest peroxidase-like activities among four DNA structures. Furthermore, significant parameters that influence HCR process and the modulation of catalysis, such as the concentration of the hairpin DNA, the ionic strength, and the amount of nanozyme, were also systematically investigated. On the basis of HCR amplification and iron oxide (Fe₃O₄) nanoparticles, we develop a simple, fast, label-free, and sensitive colorimetric strategy for sensing of a Yersinia pestis-relevant DNA sequence with a detection limit as low as 100 pM as well as single nucleotide polymorphism discrimination. These results highlight DNA engineering as a facile strategy to regulate the catalytic activities of nanozymes and understand the interactions between metallic nanoparticles and nucleic acids for biosensing applications.

Synthesis of an ethyleneimine/tetrahedral DNA nanostructure complex and its potential application as a multi-functional delivery vehicle

Nowadays, DNA nanostructures are extensively researched for their biocompatibility, editable functionality, and structural stability. Tetrahedral DNA nanostructures (TDNs), widely known for their membrane permeability, are regarded as potential candidates for drug delivery. However, the stability and membrane permeability of TDNs call for further enhancement if in vivo usage is ascribed. To overcome the drawbacks of TDNs, ethylene imine (PEI, 25 kDa, branched)-a classic cationic polymer in the field of gene delivery-was applied. Via a facile one-pot synthesis method, a PEI/TDNs complex was formed. Subsequently, a DNase protection assay, a cytotoxicity assay, endocytosis-related experiments, and lysosome staining were performed to examine the potential of PEI/TDNs as a delivery vehicle. The combination of PEI and TDNs not only overcame the drawbacks of each substance but also retained their individual merits. Traditionally, drug-delivery vehicles that enable enhanced cell entry and lysosome escape are often compromised by their toxicity and poor multifunctionality. We believe this novel PEI/TDNs complex with enhanced systemic stability, biocompatibility, cell-entry ability, and lysosome-escape ability and unsurpassed editable functionality could be a powerful tool as a multi-functional delivery vehicle in targeted drug delivery, in vivo imaging, and other related fields.

Poly-adenine-mediated spherical nucleic acids for strand displacement-based DNA/RNA detection

DNA-gold nanoparticles (AuNPs) conjugate is one of the most versatile bionanomaterials for biomedical and clinical diagnosis. However, to finely tune the hybridization ability and precisely control the orientation and conformation of surface-tethered oligonucleotides on AuNPs remains a hurdle. In this work, we developed a poly adenine-mediated spherical nucleic acid (polyA-mediated SNA) strategy by assembling di-block DNA probes on gold nanoparticles (AuNPs) to spatially control interdistance and hybridization ability of oligonucleotides on AuNPs. By modulating length of poly A bound on the SNA with different degrees of constructing, we presented significant improved biosensing performance including high hybridization efficiency, and expanded dynamic range of analytes with more sensitive detection limit. Furthermore, this polyA design could facilitate the programmable detection for DNA in serum environment and simultaneous multicolor detection of three different microRNAs associated with pancreatic carcinoma. The demonstration of the link between modulation of SNA assembly strategy and biodetection capability will increase the development of high performance diagnostic tools for translational biomedicine.

Graphene-based nanomaterials in biosystems

Graphene-based nanomaterials have emerged as a novel type of materials with exceptional physicochemical properties and numerous applications in various areas. In this review, we summarize recent advances in studying interactions between graphene and biosystems. We first provide a brief introduction on graphene and its derivatives, and then discuss on the toxicology and biocompatibility of graphene, including the extracellular interactions between graphene and biomacromolecules, cellular studies of graphene, and in vivo toxicological effects. Next, we focus on various graphene-based practical applications in antibacterial materials, wound addressing, drug delivery, and water purification. We finally present perspectives on challenges and future developments in these exciting fields.

Programming biosensing sensitivity by controlling the dimension of nanostructured electrode

Development of new nanostructured materials has shown high impact for improving the performance of chemical and biological sensors. In this work, we show that by controlling the dimensions of the gold flower microelectrode (GFME), it is possible to regulate detection sensitivity of a sensor for rapid analysis of chemical species. A ~13-fold increase in sensitivity was achieved by enlarging the dimension of GFMEs from 70 to 330 μm, whereas the response dynamics are dimension-independent, with the signal attaining saturation ~20 s. Due to the intrinsic nanostructure on the microelectrode surface, our GFME exhibits excellent anti-interference property when applied to detect dopamine (DA) in the presence of 10-fold excess of ascorbic acid (AA). The regulable sensitivity, fast response dynamics, and excellent anti-interference property will make GFME an ideal sensing platform for biomedical applications. Graphical abstract ᅟ.

Framework-Nucleic-Acid-Enabled Biosensor Development

Nucleic acids have been actively exploited to develop various exquisite nanostructures due to their unparalleled programmability. Especially, framework nucleic acids (FNAs) with tailorable functionality and precise addressability hold great promise for biomedical applications. In this review, we summarize recent progress of FNA-enabled biosensing in homogeneous solutions, on heterogeneous surfaces, and inside cells. We describe the strategies to translate the structural order and rigidity of FNAs to interfacial engineering with high controllability, and approaches to realize multiplexing for highly parallel in vitro detection. We also envision the marriage of the currently available FNA tool sets with other emerging technologies to develop a new generation of biosensors for precision diagnosis and bioimaging.

Poly-adenine-mediated fluorescent spherical nucleic acid probes for live-cell imaging of endogenous tumor-related mRNA

Identification of tumor-related mRNA in living cells hold great promise for early cancer diagnosis and pathological research. Herein, we present poly-adenine (polyA)-mediated fluorescent spherical nucleic acid (FSNA) probes for intracellular mRNA detection with regulable sensitivities by programmably adjusting the loading density of DNA on gold nano-interface. Gold nanoparticles (AuNPs) functionalized with polyA-tailed recognition sequences were hybridized to fluorescent "reporter" strands to fabricate fluorescence-quenched FSNA probes. While exposed to target gene, the "reporter" strands were released from FSNA through strand displacement and fluorescence was recovered. With polyA20 tail as the attaching block, the detection limit of FSNA probes was calculated to be 0.31 nM, which is ~55 fold lower than that of thiolated probes without surface density regulation. Quantitative intracellular mRNA detection and imaging could be achieved with polyA-mediated FSNA probes within 2 hours, indicating their application potential in rapid and sensitive intracellular target imaging.

Systematic Study in Mammalian Cells Showing No Adverse Response to Tetrahedral DNA Nanostructure

The advent of DNA technology has demonstrated great potential in a wide range of applications, especially in the field of biology and biomedicine. However, current understanding of the toxicological effects and cellular responses of DNA nanostructures remains to be improved. Here, we chose tetrahedral DNA nanostructures (TDNs), a type of nanocarriers for delivering molecular drugs, as a model for systematic live-cell analysis of the biocompatibility of TDNs to normal bronchial epithelial cells, carcinoma cells, and macrophage. We found that the interaction behaviors of TDNs in different cell lines were very different, whereas after internalization, most of the TDNs in diverse cell lines were positioned to lysosomes. By a systematic assessment of cell responses after TDN exposure to various cells, we demonstrate that internalized TDNs have good innate biocompatibility. Interestingly, we found that TDN-bearing cells would not affect the cell cycle progression and accompany cell division and that TDNs were separated equally into two daughter cells. This study improves our understanding of the interaction of DNA nanostructures with living systems and their biocompatibility, which will be helpful for further designing DNA nanostructures for biomedical applications.

MoS2 Nanoprobe for MicroRNA Quantification Based on Duplex-Specific Nuclease Signal Amplification

MicroRNAs (miRNAs) play significant regulatory roles in physiologic and pathologic processes and are considered as important biomarkers for disease diagnostics and therapeutics. Simple, fast, sensitive, and selective detection of miRNAs, however, is challenged by their short length, low abundance, susceptibility to degradation, and homogenous sequence. Here, we report a novel design of nanoprobes for highly sensitive and selective detection of miRNAs based on MoS₂-loaded molecular beacons (MBs) and duplex-specific nuclease (DSN)-mediated signal amplification (DSNMSA). We show that MoS₂ nanosheets not only exhibit high affinity toward MBs but also act as an efficient quencher for absorbed MBs. The strong fluorescence-quenching ability of MoS₂ in combination with cyclic DSNMSA contributes to the superior sensitivity of our method, with a limit of detection 4 orders of magnitude lower than that of traditional hybridization methods. Moreover, the nanoprobes also show high selectivity for discriminating homogenous miRNA sequences with one-base differences because of the discrimination ability of MBs and DSN. Furthermore, we demonstrate that the MoS₂-loaded MB nanoprobes can be utilized for multiplexed detection of miRNAs. Given its high sensitivity and specificity, as well as the multiplexed function; this novel method as an effective tool shows a great promise for simultaneous quantitative analysis of multiple miRNAs in biomedical research and clinical diagnosis.

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.

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.

Logic Catalytic Interconversion of G-Molecular Hydrogel

By incorporating hemin into G-quadruplex (G₄) during cation-templated self-assembly between guanosine and KB(OH)₄, we have constructed an artificial enzyme hydrogel (AEH)-based system for the highly sensitive and selective detection of Pb²⁺. The sensing strategy is based on a Pb²⁺-induced decrease in AEH activity. Because of the higher efficiency of Pb²⁺ for stabilizing G₄ compared with K⁺, the Pb²⁺ ions substitute K⁺ and trigger hemin release from G₄, thus giving rise to a conformational interconversion accompanied by the loss of enzyme activity. The Pb²⁺-induced catalytic interconversion endows the AEH-based system with high sensitivity and selectivity for detecting Pb²⁺. As a result, the AEH-based system shows an excellent response for Pb²⁺ in the range from 1 pM to 50 nM with a limit of detection of ∼0.32 pM, which is much lower than that of the previously reported G₄-DNAzyme. We also demonstrate that this AEH-based system exhibits high selectivity toward Pb²⁺ over other metal ions. Furthermore, two two-input INHIBIT logic gates have been constructed via switching of the catalytic interconversion induced by K⁺ and Pb²⁺ or K⁺ and pH. Given its versatility, this AEH-based system provides a novel platform for sensing and biomolecular computation.

Inhibition of Epithelial-Mesenchymal Transition and Tissue Regeneration by Waterborne Titanium Dioxide Nanoparticles

Titanium dioxide nanoparticles (TiO₂NPs) are among the most widely manufactured nanomaterials with broad applications in food industry, cosmetics, and medicine. Although the toxicity of TiO₂NPs at high doses has been extensively explored, the potential health risks of TiO₂NPs exposure at nontoxic concentrations remain poorly understood. Epithelial-mesenchymal transition (EMT) plays pivotal roles in a diversity of physiological and pathological processes, including tissue regeneration and cancer metastasis. In this study, we find that the cellular uptake of TiO₂NPs inhibits EMT-mediated cell remodeling and cell migration without exhibiting cytotoxicity. Further investigation reveals that TiO₂NPs suppress the process of EMT through the blockade of transforming growth factor-β (TGFβ) signaling. Particularly, TiO₂NPs interact with the TGFβ receptor TβRI/II complex, induce its lysosomal degradation, and thereby downregulate expression of TGFβ target genes. Moreover, we show that waterborne TiO₂NPs do not elicit toxicity in healthy tissues but hamper EMT-mediated wound healing in two animal models. Long-term exposure of TiO₂NPs in environmental water and drinking water impede the regeneration of amputated fin in zebrafish and the recovery of intestinal mucosal damage in colitic mice. Our results reveal the previously unknown effects of TiO₂NPs during tissue remodeling and repair, which have significant implications in their risk assessment and management.

Epitope Binning Assay Using an Electron Transfer-Modulated Aptamer Sensor

Surface plasmon resonance and quartz crystal microbalance are workhorses of protein-DNA interaction research for over 20 years, providing ways to quantitatively determine the protein-DNA binding. However, the cost, necessary technical expertise, and severe nonspecific adsorption poses barriers to their use. Convenient and effective techniques for the measurement of protein-DNA binding affinity and the epitope binning between DNA and proteins for developing highly sensitive detection platform remain challenging. Here, we develop a binding-induced alteration in electron transfer kinetics of the redox reporter labeled (methylene blue) on DNA aptamer to measure the binding affinity between prostate-specific antigen (PSA) and aptamer. We demonstrate that the binding of PSA to aptamer decreases the electron transfer rate of methylene blue for ∼45%. Further, we identify the best pairwise selection of aptamers for developing sandwich assay by sorting from 10 pairwise modes with the PSA detection limit of 500 ng/mL. Our study provides promising ways to analyze the binding affinity between ligand and receptor and to sort pairwise between aptamers or antibodies for the development of highly sensitive sandwich immunoassays.