DNAzyme-Immobilizing Microgel Magnetic Beads Enable Rapid, Specific, Culture-Free, and Wash-Free Electrochemical Quantification of Bacteria in Untreated Urine

Advances in novel biosensors in biomedical applications

Biosensors, devices capable of detecting biomolecules or bioactive substances, have recently become one of the important tools in the fields of bioanalysis and medical diagnostics. A biosensor is an analytical system composed of biosensitive elements and signal-processing elements used to detect various biological and chemical substances. Biomimetic elements are key to biosensor technology and are the components in a sensor that are responsible for identifying the target analyte. The construction methods and working principles of biosensors based on synthetic biomimetic elements, such as DNAzyme, molecular imprinted polymers and aptamers, and their updated applications in biomedical analysis are summarised. Finally, the technical bottlenecks and future development prospects for biomedical analysis are summarised and discussed.

A Comparison of DNA-DNA Hybridization Kinetics in Complex Media on Planar and Nanostructured Electrodes

A comprehensive investigation into how nanostructures alter real-time DNA hybridization kinetics in both buffer and complex media and under a wide range of probe and target concentrations is currently lacking. In response, we use a real-time, wash-free, and in situ assay to study DNA hybridization kinetics by performing continuous electrochemical measurements in different media. We investigated the differences in hybridization kinetics under three regimes of probe density (low, medium, and high) and over three orders of magnitude of target concentrations (0.01-1 μM). Additionally, we compared the performance of planar and nanostructured electrodes in buffer, blood, urine, and saliva. Our experiments indicate that adding nanostructures to the transducer surface is only effective under a specific probe/target concentration regime. Additionally, we found that direct electrochemical readout is possible in the examined physiological media, with measurements in blood showing the highest and saliva showing the lowest signal magnitudes compared to buffer.

Electrochemical biosensors for clinical detection of bacterial pathogens: advances, applications, and challenges

Bacterial pathogens are responsible for a variety of human diseases, necessitating their prompt detection for effective diagnosis and treatment of infectious diseases. Over recent years, electrochemical methods have gained significant attention owing to their exceptional sensitivity and rapidity. This review outlines the current landscape of electrochemical biosensors employed in clinical diagnostics for the detection of bacterial pathogens. We categorize these biosensors into four types: amperometry, potentiometry, electrochemical impedance spectroscopy, and conductometry, targeting various bacterial components, including toxins, virulence factors, metabolic activity, and events related to bacterial adhesion and invasion. We discuss the merits and challenges associated with electrochemical methods, underscoring their rapid response, high sensitivity, and specificity, while acknowledging the necessity for skilled operators and potential interference from biological and environmental factors. Furthermore, we examine future prospects and potential applications of electrochemical biosensors in clinical diagnostics. While electrochemical biosensors offer a promising avenue for detecting bacterial pathogens, further research in optimizing the robustness and surmounting the challenges hindering their seamless integration into clinical practice is imperative.

Advances in DNA-based electrochemical biosensors for the detection of foodborne pathogenic bacteria

The detection of foodborne pathogenic bacteria is critical in preventing foodborne diseases. DNA-based electrochemical biosensors, with the merits of high sensitivity and short detection time, provide an effective detecting method for foodborne pathogens, attracting significant interest for the past few years. This review mainly describes the important research progress of DNA-based electrochemical biosensors for the detection of foodborne pathogenic bacteria through four perspectives: representative foodborne pathogens detection using electrochemical approaches, DNA immobilization strategies of aptamers, DNA-based signal amplification strategies used in electrochemical DNA sensors, and functional DNA used in electrochemical DNA sensors. Finally, perspectives and challenges are presented in this field. This review will contribute to DNA-based electrochemical biosensor in enhancing the nucleic acid signal amplification.

In-vitro Clinical Diagnostics using RNA-Cleaving DNAzymes

Over the last three decades, significant advancements have been made in the development of biosensors and bioassays that use RNA-cleaving DNAzymes (RCDs) as molecular recognition elements. While early examples of RCDs were primarily responsive to metal ions, the past decade has seen numerous RCDs reported for more clinically relevant targets such as bacteria, cancer cells, small metabolites, and protein biomarkers. Over the past 5 years several RCD-based biosensors have also been evaluated using either spiked biological matrixes or patient samples, including blood, serum, saliva, nasal mucus, sputum, urine, and faeces, which is a critical step toward regulatory approval and commercialization of such sensors. In this review, an overview of the methods used to generate RCDs and the properties of key RCDs that have been utilized for in vitro testing is first provided. Examples of RCD-based assays and sensors that have been used to test either spiked biological samples or patient samples are then presented, highlighting assay performance in different biological matrixes. A summary of current prospects and challenges for development of in vitro diagnostic tests incorporating RCDs and an overview of future directions of the field is also provided.

Microfluidic systems for infectious disease diagnostics

Microorganisms, encompassing both uni- and multicellular entities, exhibit remarkable diversity as omnipresent life forms in nature. They play a pivotal role by supplying essential components for sustaining biological processes across diverse ecosystems, including higher host organisms. The complex interactions within the human gut microbiota are crucial for metabolic functions, immune responses, and biochemical signalling, particularly through the gut-brain axis. Viruses also play important roles in biological processes, for example by increasing genetic diversity through horizontal gene transfer when replicating inside living cells. On the other hand, infection of the human body by microbiological agents may lead to severe physiological disorders and diseases. Infectious diseases pose a significant burden on global healthcare systems, characterized by substantial variations in the epidemiological landscape. Fast spreading antibiotic resistance or uncontrolled outbreaks of communicable diseases are major challenges at present. Furthermore, delivering field-proven point-of-care diagnostic tools to the most severely affected populations in low-resource settings is particularly important and challenging. New paradigms and technological approaches enabling rapid and informed disease management need to be implemented. In this respect, infectious disease diagnostics taking advantage of microfluidic systems combined with integrated biosensor-based pathogen detection offers a host of innovative and promising solutions. In this review, we aim to outline recent activities and progress in the development of microfluidic diagnostic tools. Our literature research mainly covers the last 5 years. We will follow a classification scheme based on the human body systems primarily involved at the clinical level or on specific pathogen transmission modes. Important diseases, such as tuberculosis and malaria, will be addressed more extensively.

Liquid Metal Nanocores Initiated Construction of Smart DNA-Polymer Microgels with Programmable and Regulable Functions and Near-Infrared Light-Driven Locomotion

Due to their sequence-directed functions and excellent biocompatibility, smart DNA microgels have attracted considerable research interest, and the combination of DNA microgels with functional nanostructures can further expand their applications in biosensing and biomedicine. Gallium-based liquid metals (LMs) exhibiting both fluidic and metallic properties hold great promise for the development of smart soft materials; in particular, LM particles upon sonication can mediate radical-initiated polymerization reactions, thus allowing the combination of LMs and polymeric matrix to construct "soft-soft" materials. Herein, by forming active surfaces under sonication, LM nanoparticles (LM NPs) initiated localized radical polymerization reactions allow the combination of functional DNA units and different polymeric backbones to yield multifunctional core/shell microgels. The localized polymerization reaction allows fine control of the microgel compositions, and smart DNA microgels with tunable catalytic activities can be constructed. Moreover, due to the excellent photothermal effect of LM NPs, the resulting temperature gradient between microgels and surrounding solution upon NIR light irradiation can drive the oriented locomotion of the microgels, and remote control of the activity of these smart microgels can be achieved. These microgels may hold promise for various applications, such as the development of in vivo and in vitro biosensing and drug delivery systems.

Theoretical Study of Microgel Functional Groups' Mobility

Polymer microgels, micrometer-sized cross-linked polymer particles, are considered to be a promising type of advanced materials for a wide range of applications. To enhance the microgels' applicability, it is essential to incorporate various functional groups into a microparticle polymer network. Yet, the availability of functional groups for the interaction with surroundings depends strongly on the properties of the polymer network and has a great impact on further effective usage. In this theoretical study, we address this question and, with the help of coarse-grained molecular dynamics computer simulations, assess the segmental mobility and accessibility of functional groups bound to polymer network depending on microgel architecture and solvent quality. Additionally, we evaluate the minimum number of functional groups needed to facilitate the hopping mechanism between the functional groups (i.e., charge transfer). As an example of practical implementation of the obtained results, we estimate the optimal network topology for redox-active microgels to provide the maximum charge capacity for the dispersion electrolyte in redox-flow batteries.

Apta FastZ: An Algorithm for the Rapid Identification of Aptamers with Defined Binding Affinities

Real-time biomolecular monitoring requires biosensors based on affinity reagents, such as aptamers, with moderate to low affinities for the best binding dynamics and signal gain. We recently reported Pro-SELEX, an approach that utilizes parallelized SELEX and high-content bioinformatics for the selection of aptamers with predefined binding affinities. The Pro-SELEX pipeline relies on an algorithm, termed AptaZ, that can predict the binding affinities of selected aptamers. The original AptaZ algorithm is computationally complex and slows the overall throughput of Pro-SELEX. Here, we present Apta FastZ, a rapid equivalent of AptaZ. The Apta FastZ algorithm considers the spare nature of the sequences from SELEX and is coded to avoid unnecessary comparison between sequences. As a result, Apta FastZ achieved a 10 to 40-fold faster computing speed compared to the original AptaZ algorithm while maintaining identical outcomes, allowing the bioinformatics to be completed within 1-10 h for large-scale data sets. We further validated the affinity of myeloperoxidase aptamers predicted by Apta FastZ by experiments and observed a high level of linear correlation between predicted scores and measured affinities. Taken together, the implementation of Apta FastZ could greatly accelerate the current Pro-SELEX workflow, allowing customized aptamers to be discovered within 3 days using preselected DNA libraries.

A Fluorogenic DNAzyme for A Thermally Stable Protein Biomarker from Fusobacterium nucleatum, a Human Bacterial Pathogen

Fusobacterium nucleatum has been correlated to many poor human conditions including oral infections, adverse pregnancies and cancer, and thus molecular tools capable of detecting this human pathogen can be used to develop diagnostic tests for them. Using a new selection method targeting thermally stable proteins without a counter-selection step, we derived an fluorogenic RNA-cleaving DNAzyme, named RFD-FN1, that can be activated by a thermally stable protein target that is unique to F. nucleatum subspecies. High thermal stability of protein targets is a very desirable attribute for DNAzyme-based biosensing directly with biological samples because nucleases found inherently in these samples can be heat-inactivated. We further demonstrate that RFD-FN1 can function as a fluorescent sensor in both human saliva and human stool samples. The discovery of RFD-FN1 paired with a highly thermal stable protein target presents opportunities for developing simpler diagnostic tests for this important pathogen.

Electrochemical point-of-care devices for the diagnosis of sepsis

Sepsis is a life-threatening dysfunction of organ systems caused by a dysregulated immune system because of an infectious process. It remains one of the leading causes of hospital mortality and of hospital readmissions in the United States. Mortality from sepsis increases with each hour of delayed treatment, therefore, diagnostic devices that can reduce the time from the onset of a patient's infection to the delivery of appropriate therapy are urgently needed. Likewise, tools that are capable of high-frequency testing of clinically relevant biomarkers are required to study disease progression. Electrochemical biosensors offer important advantages such as high sensitivity, fast response, miniaturization, and low cost that can be adapted to clinical needs. In this review paper, we discuss the current state, limitations, and future directions of electrochemical-based point-of-care detection platforms that contribute to the diagnosis and monitoring of sepsis.

Induced ultrasensitive electrochemical biosensor for target MDA-MB-231 cell cytoplasmic protein detection based on RNA-cleavage DNAzyme catalytic reaction

Herein, we implemented RNA-cleaving DNAzymes specific for the endogenous protein of breast cancer cells (MDA-MB -231) and programmed for electrochemical detection. Thionine-modified gold nanoparticles and modified magnetic nanoparticles are attached to the two ends of the DNAzyme molecule. The prepared probe is pulled to the surface of the electrode with the help of a magnetic field, and the signal caused by the electrochemical activity of thionine is observed on the surface of the electrode. The presence of a covalent gold nanoparticle-thionine hybrid as a highly electroactive/enhanced electrochemical label ensures a strong detection signal. After addition of the enzyme activator cofactor (MDA-MB -231 cytoplasmic cell protein), it reacts with the catalytic core of the enzyme sequence in the DNAzyme molecule and triggers the cleavage reaction in the substrate sequence of the DNAzyme molecule. During this process, the gold nanoparticle-thionine labels are detached from the probe and released into the solution. Inductive removal of gold nanoparticles leads to a decrease in the current related to the reduction of thionine on the electrode surface. The results show that this biosensor can detect this protein marker in the linear range of (1.0E-06 to 1.0E+01) pg/ml, with a detection limit (1.0129E-07 pg/ml), using differential pulse voltammetry as a measuring technique. As well as, electrochemical impedance spectroscopy (EIS).

Liquid NanoBiosensors Enable One-Pot Electrochemical Detection of Bacteria in Complex Matrices

There is a need for point-of-care bacterial sensing and identification technologies that are rapid and simple to operate. Technologies that do not rely on growth cultures, nucleic acid amplification, step-wise reagent addition, and complex sample processing are the key for meeting this need. Herein, multiple materials technologies are integrated for overcoming the obstacles in creating rapid and one-pot bacterial sensing platforms. Liquid-infused nanoelectrodes are developed for reducing nonspecific binding on the transducer surface; bacterium-specific RNA-cleaving DNAzymes are used for bacterial identification; and redox DNA barcodes embedded into DNAzymes are used for binding-induced electrochemical signal transduction. The resultant single-step and one-pot assay demonstrates a limit-of-detection of 10² CFU mL^-1 , with high specificity in identifying Escherichia coli amongst other Gram positive and negative bacteria including Klebsiella pneumoniae, Staphylococcus aureus, and Bacillus subtilis. Additionally, this assay is evaluated for analyzing 31 clinically obtained urine samples, demonstrating a clinical sensitivity of 100% and specify of 100%. When challenging this assay with nine clinical blood cultures, E. coli-positive and E. coli-negative samples can be distinguished with a probability of p < 0.001.

Electrochemical DNAzyme-based biosensors for disease diagnosis

DNAzyme-based electrochemical biosensors provide exceptional analytical sensitivity and high target recognition specificity for disease diagnosis. This review provides a critical perspective on the fundamental and applied impact of incorporating DNAzymes in the field of electrochemical biosensing. Specifically, we highlight recent advances in creating DNAzyme-based electrochemical biosensors for diagnosing infectious diseases, cancer and regulatory diseases. We also develop an understanding of challenges around translating the research in the field of DNAzyme-based electrochemical biosensors from labs to clinics, followed by a discussion on different strategies that can be applied to enhance the performance of the currently existing technologies to create truly point-of-care electrochemical DNAzyme biosensors.

Aptasensor for the Detection of Moraxella catarrhalis Adhesin UspA2

Innovative point-of-care (PoC) diagnostic platforms are desirable to surpass the deficiencies of conventional laboratory diagnostic methods for bacterial infections and to tackle the growing antimicrobial resistance crisis. In this study, a workflow was implemented, comprising the identification of new aptamers with high affinity for the ubiquitous surface protein A2 (UspA2) of the bacterial pathogen Moraxella catarrhalis and the development of an electrochemical biosensor functionalized with the best-performing aptamer as a bioreceptor to detect UspA2. After cell-systematic evolution of ligands by exponential enrichment (cell-SELEX) was performed, next-generation sequencing was used to sequence the final aptamer pool. The most frequent aptamer sequences were further evaluated using bioinformatic tools. The two most promising aptamer candidates, Apt1 and Apt1_RC (Apt1 reverse complement), had K_d values of 214.4 and 3.4 nM, respectively. Finally, a simple and label-free electrochemical biosensor was functionalized with Apt1_RC. The aptasensor surface modifications were confirmed by impedance spectroscopy and cyclic voltammetry. The ability to detect UspA2 was evaluated by square wave voltammetry, exhibiting a linear detection range of 4.0 × 10⁴-7.0 × 10⁷ CFU mL^-1, a square correlation coefficient superior to 0.99 and a limit of detection of 4.0 × 10⁴ CFU mL^-1 at pH 5.0. The workflow described has the potential to be part of a sensitive PoC diagnostic platform to detect and quantify M. catarrhalis from biological samples.

Versatility of the Preparation Method for Macroporous Cryogel Particles Utilizing the Inverse Leidenfrost Effect

We have investigated the versatility of a two-step preparation method, without a detergent, that combines both the inverse Leidenfrost effect and the cryogelation technique by using the macroporous particles of different kinds of monomers (four vinyl monomers) or a natural polymer (agarose). First, the precursor of polymers was dropped into liquid nitrogen to prepare the spherical frozen droplet by the inverse Leidenfrost effect. Second, the frozen droplets were cryo-polymerized at the frozen temperature; then, cryogel particles were prepared after thawing. Subsequently, the basic characteristics of the macroporous polymer particles obtained above were compared, focusing on the appearances, porous morphologies, and mechanical properties. It was found that the similar polymer particles could be obtained by the two-step preparation method, while there was a slight difference in their characteristics, depending on the type of monomers. Especially for the mechanical properties, the cryogel particles of the hydrophilic polymer exhibited a shape memory function with sponge-like elasticity, whereas the hydrophobic polymer particles were observed to be cracked after compression (i.e., no shape memory function). This work provides a versatile method of adopting various kinds of monomers and natural polymers for the preparation of macroporous particles. Hence, the method possibly has a potential to prepare and design "tailor-made" macroporous polymer particles for the application purpose.

Advances in the Translation of Electrochemical Hydrogel-Based Sensors

Novel biomaterials for bio- and chemical sensing applications have gained considerable traction in the diagnostic community with rising trends of using biocompatible and lowly cytotoxic material. Hydrogel-based electrochemical sensors have become a promising candidate for their swellable, nano-/microporous, and aqueous 3D structures capable of immobilizing catalytic enzymes, electroactive species, whole cells, and complex tissue models, while maintaining tunable mechanical properties in wearable and implantable applications. With advances in highly controllable fabrication and processability of these novel biomaterials, the possibility of bio-nanocomposite hydrogel-based electrochemical sensing presents a paradigm shift in the development of biocompatible, "smart," and sensitive health monitoring point-of-care devices. Here, recent advances in electrochemical hydrogels for the detection of biomarkers in vitro, in situ, and in vivo are briefly reviewed to demonstrate their applicability in ideal conditions, in complex cellular environments, and in live animal models, respectively, to provide a comprehensive assessment of whether these biomaterials are ready for point-of-care translation and biointegration. Sensors based on conductive and nonconductive polymers are presented, with highlights of nano-/microstructured electrodes that provide enhanced sensitivity and selectivity in biocompatible matrices. An outlook on current challenges that shall be addressed for the realization of truly continuous real-time sensing platforms is also presented.

Overview on the Design of Magnetically Assisted Electrochemical Biosensors

Electrochemical biosensors generally require the immobilization of recognition elements or capture probes on the electrode surface. This may limit their practical applications due to the complex operation procedure and low repeatability and stability. Magnetically assisted biosensors show remarkable advantages in separation and pre-concentration of targets from complex biological samples. More importantly, magnetically assisted sensing systems show high throughput since the magnetic materials can be produced and preserved on a large scale. In this work, we summarized the design of electrochemical biosensors involving magnetic materials as the platforms for recognition reaction and target conversion. The recognition reactions usually include antigen-antibody, DNA hybridization, and aptamer-target interactions. By conjugating an electroactive probe to biomolecules attached to magnetic materials, the complexes can be accumulated near to an electrode surface with the aid of external magnet field, producing an easily measurable redox current. The redox current can be further enhanced by enzymes, nanomaterials, DNA assemblies, and thermal-cycle or isothermal amplification. In magnetically assisted assays, the magnetic substrates are removed by a magnet after the target conversion, and the signal can be monitored through stimuli-response release of signal reporters, enzymatic production of electroactive species, or target-induced generation of messenger DNA.

Plasmon-Mediated Peroxidase-like Activity on an Asymmetric Nanotube Architecture for Rapid Visual Detection of Bacteria

Rapid and sensitive detection of bacteria from a complex real media remains a challenge. Herein, we report a visual bacterial sensing assay with excellent specificity, anti-interference ability, and sensitivity based on a surface plasmon resonance (SPR)-enhanced peroxidase (POD) mimetic. The POD mimetic based on Pt nanoparticles (NPs) asymmetrically decorated on Au/TiO₂ magnetic nanotubes (Au/Pt/MTNTs) is designed by combining the intrinsic photocatalytic activity of TiO₂ and the limited transport depth of light. It is revealed that the localized surface plasmon resonance (LSPR) effect of the asymmetric nanotubes is more effective in facilitating the generation of hot electrons, which are subsequently transferred to Pt and MTNTs, thus greatly promoting the catalytic performance. Using Staphylococcus aureus (S. aureus) as a model of Gram-positive bacteria, the dependence of the colorimetric reaction on the active sites of the POD mimetic is used for the sensing of target bacteria. Owing to the specific recognition between S. aureus and peptide, the fluorescein isothiocyanate (FITC) labeled peptide probes are captured by S. aureus and removed from the Au/Pt/MTNTs, leading to the recovery of POD-like activity and fluorescence emission of S. aureus. Particularly, benefiting from the Au-SPR effect and the magnetic feature of the Au/Pt/MTNTs, the recovery of catalytic activity induced an improved colorimetric assay with a wider linear response for S. aureus qualification and a detection limit of four cells, as well as satisfactory selectivity and feasibility for application in real samples. The plasmon-enhanced POD activity would provide a simple-yet-effective approach to achieve a colorimetric bioassay with high efficiency and sensitivity. This asymmetric design can also be utilized to engineer nanozymes in colorimetric assays for the specific detection of biotoxins, biomarkers, and cancer cells.

Electrochemical Aptasensor for the Detection of the Key Virulence Factor YadA of Yersinia enterocolitica

New point-of-care (POC) diagnosis of bacterial infections are imperative to overcome the deficiencies of conventional methods, such as culture and molecular methods. In this study, we identified new aptamers that bind to the virulence factor Yersinia adhesin A (YadA) of Yersinia enterocolitica using cell-systematic evolution of ligands by exponential enrichment (cell-SELEX). Escherichia coli expressing YadA on the cell surface was used as a target cell. After eight cycles of selection, the final aptamer pool was sequenced by high throughput sequencing using the Illumina Novaseq platform. The sequencing data, analyzed using the Geneious software, was aligned, filtered and demultiplexed to obtain the key nucleotides possibly involved in the target binding. The most promising aptamer candidate, Apt1, bound specifically to YadA with a dissociation constant (Kd) of 11 nM. Apt1 was used to develop a simple electrochemical biosensor with a two-step, label-free design towards the detection of YadA. The sensor surface modifications and its ability to bind successfully and stably to YadA were confirmed by cyclic voltammetry, impedance spectroscopy and square wave voltammetry. The biosensor enabled the detection of YadA in a linear range between 7.0 × 104 and 7.0 × 107 CFU mL−1 and showed a square correlation coefficient >0.99. The standard deviation and the limit of detection was ~2.5% and 7.0 × 104 CFU mL−1, respectively. Overall, the results suggest that this novel biosensor incorporating Apt1 can potentially be used as a sensitive POC detection system to aid the diagnosis of Y. enterocolitica infections. Furthermore, this simple yet innovative approach could be replicated to select aptamers for other (bacterial) targets and to develop the corresponding biosensors for their detection.