Polyclonal aptamer libraries as binding entities on a graphene FET based biosensor for the discrimination of apo- and holo-retinol binding protein 4

Specific gFET-Based Aptasensors for Monitoring of Microbiome Quality: Quantification of the Enteric Health-Relevant Bacterium Roseburia Intestinalis

Roseburia intestinalis, enriched in the gut, is closely associated with obesity, intestinal inflammation, and other diseases. A novel detection method for R. intestinalis to replace the commonly used 16S rRNA sequencing technique is aim to developed, thus enabling real-time and low-cost monitoring of gut microbiota. The optimal solution is to utilize rGO-FET (reduced graphene oxide field-effect transistor) functionalized with aptamers. Due to the high sensitivity of graphene sensors to electronic changes in the system, it is anticipated to achieve detection sensitivity that traditional fluorescence detection techniques cannot attain. The previous work reported a nucleic acid aptamer library, Ri 7_2, capable of quantitatively tracking R. intestinalis in complex systems. However, due to the complexity of the aptamer library itself, large-scale industrial synthesis is challenging, significantly limiting its further commercial application potential. Therefore, in this study, through Next-Generation Sequencing analysis, four representative single aptamers from the aptamer library is strategically selected, named A-Rose 1, A-Rose 2, A-Rose 3, and A-Rose 4, and confirmed their excellent performance similar to the aptamer library Ri 7_2. Furthermore, aptamer-modified rGO-FET demonstrated universality in detecting R. intestinalis in a series of biochemical analyses, providing a novel and powerful diagnostic tool for the clinical diagnosis of R. intestinalis.

Enhancing chemical signal transformation in lateral flow assays using aptamer-architectured plasmonic nanozymes and para-phenylenediamine

The widespread adoption and commercialization of lateral flow assays (LFAs) for clinical diagnosis have been hindered by limitations in sensitivity, specificity, and the absence of quantitative data. To address these challenges, we developed aptamer-architectured gold nanoparticles as nanozymes that catalytically convert para-phenylenediamine (PPD) into Bandrowski's base (BB), thereby amplifying signal strength and sensitivity. The physiochemical properties of the nanozymes were characterized and their specific binding efficiency was demonstrated using experimental studies. The nanozymes and PPD-based LFA test strips were evaluated for the detection of the COVID-19 spike protein in both test and clinical samples. Notably, we achieved a significant visual detection limit of 168 pg mL-1, with a signal quality enhancement of over 20-fold within 15-minute timeframe. Moreover, we rigorously tested 25 clinical samples to assess the transformative potential of the product, demonstrating a semi-quantitative analysis efficiency exceeding 90%. This performance outstripped commercially available LFA kits (87.5%). Notably, the colorimetric system exhibited an R2 value of 0.9989, a critical factor for clinical testing and industry integration. The incorporation of nanozymes and PPD in LFAs offers a cost-effective solution with significantly improved sensitivity, enabling the detection of ultra-low concentrations (picograms) of spike protein. By addressing key challenges in LFA-based diagnostics, the current technique underscores the potential of this transformative biomedical sensor for industry integration. It also highlights its suitability for commercialization, positioning it as a universal platform for diagnostic applications.

Bridging basic science and applied diagnostics: Comprehensive viral diagnostics enabled by graphene-based electronic biosensor technology advancements

This study presents a graphene field-effect transistor (gFET) biosensor with dual detection capabilities for SARS-CoV-2: one RNA detection assay to confirm viral positivity and the other for nucleocapsid (N-)protein detection as a proxy for infectiousness of the patient. This technology can be rapidly adapted to emerging infectious diseases, making an essential tool to contain future pandemics. To detect viral RNA, the highly conserved E-gene of the virus was targeted, allowing for the determination of SARS-CoV-2 presence or absence using nasopharyngeal swab samples. For N-protein detection, specific antibodies were used. Tested on 213 clinical nasopharyngeal samples, the gFET biosensor showed good correlation with RT-PCR cycle threshold values, proving its high sensitivity in detecting SARS-CoV-2 RNA. Specificity was confirmed using 21 pre-pandemic samples positive for other respiratory viruses. The gFET biosensor had a limit of detection (LOD) for N-protein of 0.9 pM, establishing a foundation for the development of a sensitive tool for monitoring active viral infection. Results of gFET based N-protein detection corresponded to the results of virus culture in all 16 available clinical samples and thus it also proved its capability to serve as a proxy for infectivity. Overall, these findings support the potential of the gFET biosensor as a point-of-care device for rapid diagnosis of SARS-CoV-2 infection and indirect assessment of infectiousness in patients, providing additional information for clinical and public health decision-making.

A Blautia producta specific gFET-based aptasensor for quantitative monitoring of microbiome quality

The use of health-relevant bacteria originating from human microbiomes for the control or therapy of diseases, including neurodegenerative disorders or diabetes, is currently gaining increasing importance in medicine. Directed and successful engineering of microbiomes via probiotic supplementation requires subtle, precise as well as, more importantly, easy, fast and convenient monitoring of its success, e.g., in patients' gut. Based on a previously described polyclonal SELEX aptamer library evolved against the human gut bacterium Blautia producta, we finally isolated three individual aptamers that proved their performance concerning affinity, specificity and robustness in reliably labeling the target bacterium and in combination with "contaminating" control bacteria. Using biofunctionalization molecules on gFETs, we could specifically quantify 101-106 cells per mL, retrace their number in mixtures and determine aptamer Kd-values around 2 nM. These measurements were possible even in the context of a real human stool sample. Our results qualify gFETs in combination with BL2, BL7 and BL8 aptamers as a promising foundation for the construction of respective sensing devices, which will open new avenues towards developing an intended monitoring technique for probiotic therapy and microbiome engineering approaches.

Electrolyte-gated amorphous IGZO transistors with extended gates for prostate-specific antigen detection

The prostate-specific antigen (PSA) test is considered an important way for preoperative diagnosis and accurate screening of prostate cancer. Current antigen detection methods, including radioimmunoassay, enzyme-linked immunosorbent assay and microfluidic electrochemical detection, feature expensive equipment, long testing time and poor stability. Here, we propose a portable biosensor composed of electrolyte-gated amorphous indium gallium zinc oxide (a-IGZO) transistors with an extended gate, which can achieve real-time, instant PSA detection at a low operating voltage (<2 V) owing to the liquid-free ionic conductive elastomer (ICE) serving as the gate dielectric. The electric double layer (EDL) capacitance in ICE enhances the accumulation of carriers in the IGZO channel, leading to strong gate modulation, which enables the IGZO transistor to have a small subthreshold swing (<0.5 V dec-1) and a high on-state current (∼4 × 10-4 A). The separate, biodegradable, and pluggable sensing pad, serving as an extended gate connected to the IGZO transistor, prevents contamination and depletion arising from direct contact with biomolecular buffers, enabling the IGZO transistor to maintain superior electronic performance for at least six months. The threshold voltage and channel current of the transistor exhibit excellent linear response to PSA molecule concentrations across five orders of magnitude ranging from 1 fg mL-1 to 10 pg mL-1, with a detection limit of 400 ag mL-1 and a detection time of ∼5.1 s. The fabricated biosensors offer a point-of-care system for antigen detection, attesting the feasibility of the electrolyte-gated transistors in clinical screening, healthcare diagnostics and biological management.

IMPATIENT-qPCR: monitoring SELEX success during in vitro aptamer evolution

SELEX (Systematic Evolution of Ligands by Exponential enrichment) processes aim on the evolution of high-affinity aptamers as binding entities in diagnostics and biosensing. Aptamers can represent game-changers as constituents of diagnostic assays for the management of instantly occurring infectious diseases or other health threats. Without in-process quality control measures SELEX suffers from low overall success rates. We present a quantitative PCR method for fast and easy quantification of aptamers bound to their targets. Simultaneous determination of melting temperatures (Tm) of each SELEX round delivers information on the evolutionary success via the correlation of increasing GC content and Tm alone with a round-wise increase of aptamer affinity to the respective target. Based on nine successful and published previous SELEX processes, in which the evolution/selection of aptamer affinity/specificity was demonstrated, we here show the functionality of the IMPATIENT-qPCR for polyclonal aptamer libraries and resulting individual aptamers. Based on the ease of this new evolution quality control, we hope to introduce it as a valuable tool to accelerate SELEX processes in general. IMPATIENT-qPCR SELEX success monitoring. Selection and evolution of high-affinity aptamers using SELEX technology with direct aptamer evolution monitoring using melting curve shifting analyses to higher Tm by quantitative PCR with fluorescence dye SYBR Green I. KEY POINTS: • Fast and easy analysis. • Universal applicability shown for a series of real successful projects.

Enriched Aptamer Libraries in Fluorescence-Based Assays for Rikenella microfusus-Specific Gut Microbiome Analyses

Rikenella microfusus is an essential intestinal probiotic with great potential. The latest research shows that imbalance in the intestinal flora are related to the occurrence of various diseases, such as intestinal diseases, immune diseases, and metabolic diseases. Rikenella may be a target or biomarker for some diseases, providing a new possibility for preventing and treating these diseases by monitoring and optimizing the abundance of Rikenella in the intestine. However, the current monitoring methods have disadvantages, such as long detection times, complicated operations, and high costs, which seriously limit the possibility of clinical application of microbiome-based treatment options. Therefore, the intention of this study was to evolve an enriched aptamer library to be used for specific labeling of R. microfusus, allowing rapid and low-cost detection methods and, ultimately the construction of aptamer-based biosensors. In this study, we used Rikenella as the target bacterium for an in vitro whole Cell-SELEX (Systematic Evolution of Ligands by EXponential Enrichment) to evolve and enrich specific DNA oligonucleotide aptamers. Five other prominent anaerobic gut bacteria were included in this process for counterselection and served as control cells. The aptamer library R.m-R13 was evolved with high specificity and strong affinity (Kd = 9.597 nM after 13 rounds of selection). With this enriched aptamer library, R. microfusus could efficiently be discriminated from the control bacteria in complex mixtures using different analysis techniques, including fluorescence microscopy or fluorometric suspension assays, and even in human stool samples. These preliminary results open new avenues toward the development of aptamer-based microbiome bio-sensing applications for fast and reliable monitoring of R. microfusus.

Extended-Gate Field-Effect Transistor Consisted of a CD9 Aptamer and MXene for Exosome Detection in Human Serum

Cancer progresses silently to the terminal stage of the impossible operable condition. There are many limitations in the treatment options of cancer, but diagnosis in an early stage can improve survival rates and low recurrence. Exosomes are the biomolecules released from cancer cells and are promising candidates for clinical diagnosis. Among them, the cluster of differentiation 9 (CD9) protein is an important exosomal biomarker that can be used for exosome determination. Therefore, here, a CD9 aptamer was first synthesized and applied to an extended-gate field-effect transistor (EGFET)-type biosensor containing a disposable sensing membrane to suggest the possibility of detecting exosomes in a clinical environment. Systematically evaluating ligands using the exponential enrichment (SELEX) technique was performed to select nucleic acid sequences that can specifically target the CD9 protein. Exosomes were detected according to the electrical signal changes on a membrane, which is an extended gate using an Au microelectrode. The fabricated biosensor showed a limit of detection (LOD) of 10.64 pM for CD9 proteins, and the detection range was determined from 10 pM to 1 μM in the buffer. In the case of the clinical test, the LOD and detection ranges of exosomes in human serum samples were 6.41 × 102 exosomes/mL and 1 × 103 to 1 × 107 exosomes/mL, respectively, showing highly reliable results with low error rates. These findings suggest that the proposed aptasensor can be a powerful tool for a simple and early diagnosis of exosomes.

Aptamer-functionalized field-effect transistor biosensors for disease diagnosis and environmental monitoring

Nano-biosensors that are composed of recognition molecules and nanomaterials have been extensively utilized in disease diagnosis, health management, and environmental monitoring. As a type of nano-biosensors, molecular specificity field-effect transistor (FET) biosensors with signal amplification capability exhibit prominent advantages including fast response speed, ease of miniaturization, and integration, promising their high sensitivity for molecules detection and identification. With intrinsic characteristics of high stability and structural tunability, aptamer has become one of the most commonly applied biological recognition units in the FET sensing fields. This review summarizes the recent progress of FET biosensors based on aptamer functionalized nanomaterials in medical diagnosis and environmental monitoring. The structure, sensing principles, preparation methods, and functionalization strategies of aptamer modified FET biosensors were comprehensively summarized. The relationship between structure and sensing performance of FET biosensors was reviewed. Furthermore, the challenges and future perspectives of FET biosensors were also discussed, so as to provide support for the future development of efficient healthcare management and environmental monitoring devices.

Aptamers as Novel Binding Molecules on an Antimicrobial Peptide-Armored Composite Hydrogel Wound Dressing for Specific Removal and Efficient Eradication of Pseudomonas aeruginosa

Here we present for the first time a potential wound dressing material implementing aptamers as binding entities to remove pathogenic cells from newly contaminated surfaces of wound matrix-mimicking collagen gels. The model pathogen in this study was the Gram-negative opportunistic bacterium Pseudomonas aeruginosa, which represents a considerable health threat in hospital environments as a cause of severe infections of burn or post-surgery wounds. A two-layered hydrogel composite material was constructed based on an established eight-membered focused anti-P. aeruginosa polyclonal aptamer library, which was chemically crosslinked to the material surface to form a trapping zone for efficient binding of the pathogen. A drug-loaded zone of the composite released the C14R antimicrobial peptide to deliver it directly to the bound pathogenic cells. We demonstrate that this material combining aptamer-mediated affinity and peptide-dependent pathogen eradication can quantitatively remove bacterial cells from the "wound" surface, and we show that the surface-trapped bacteria are completely killed. The drug delivery function of the composite thus represents an extra safeguarding property and thus probably one of the most important additional advances of a next-generation or smart wound dressing ensuring the complete removal and/or eradication of the pathogen of a freshly infected wound.

Applications of Graphene in Five Senses, Nervous System, and Artificial Muscles

Graphene remains of great interest in biomedical applications because of biocompatibility. Diseases relating to human senses interfere with life satisfaction and happiness. Therefore, the restoration by artificial organs or sensory devices may bring a bright future by the recovery of senses in patients. In this review, we update the most recent progress in graphene based sensors for mimicking human senses such as artificial retina for image sensors, artificial eardrums, gas sensors, chemical sensors, and tactile sensors. The brain-like processors are discussed based on conventional transistors as well as memristor related neuromorphic computing. The brain-machine interface is introduced for providing a single pathway. Besides, the artificial muscles based on graphene are summarized in the means of actuators in order to react to the physical world. Future opportunities remain for elevating the performances of human-like sensors and their clinical applications.

A Polyclonal Selex Aptamer Library Directly Allows Specific Labelling of the Human Gut Bacterium Blautia producta without Isolating Individual Aptamers

Recent studies have demonstrated that changes in the abundance of the intestinal bacterium Blautia producta, a potential probiotic, are closely associated with the development of various diseases such as obesity, diabetes, some neurodegenerative diseases, and certain cancers. However, there is still a lack of an effective method to detect the abundance of B. producta in the gut rapidly. Especially, DNA aptamers are now widely used as biometric components for medical testing due to their unique characteristics, including high chemical stability, low production cost, ease of chemical modification, low immunogenicity, and fast reproducibility. We successfully obtained a high-affinity nucleic acid aptamer library (B.p-R14) after 14 SELEX rounds, which efficiently discriminates B. producta in different analysis techniques including fluorometric suspension assays or fluorescence microscopy from other major gut bacteria in complex mixtures and even in human stool samples. These preliminary findings will be the basis towards aptamer-based biosensing applications for the fast and reliable monitoring of B. producta in the human gut microbiome.

A Polyclonal SELEX Aptamer Library Allows Differentiation of Candida albicans, C. auris and C. parapsilosis Cells from Human Dermal Fibroblasts

Easy and reliable identification of pathogenic species such as yeasts, emerging as problematic microbes originating from the genus Candida, is a task in the management and treatment of infections, especially in hospitals and other healthcare environments. Aptamers are seizing an already indispensable role in different sensing applications as binding entities with almost arbitrarily tunable specificities and optimizable affinities. Here, we describe a polyclonal SELEX library that not only can specifically recognize and fluorescently label Candida cells, but is also capable to differentiate C. albicans, C. auris and C. parapsilosis cells in flow-cytometry, fluorometric microtiter plate assays and fluorescence microscopy from human cells, exemplified here by human dermal fibroblasts. This offers the opportunity to develop diagnostic tools based on this library. Moreover, these specific and robust affinity molecules could also serve in the future as potent binding entities on biomaterials and as constituents of technical devices and will thus open avenues for the development of cost-effective and easily accessible next generations of electronic biosensors in clinical diagnostics and novel materials for the specific removal of pathogenic cells from human bio-samples.

A Polyclonal Aptamer Library for the Specific Binding of the Gut Bacterium Roseburia intestinalis in Mixtures with Other Gut Microbiome Bacteria and Human Stool Samples

Roseburia intestinalis has received attention as a potential probiotic bacterium. Recent studies have demonstrated that changes in its intestinal abundance can cause various diseases, such as obesity, enteritis and atherosclerosis. Probiotic administration or fecal transplantation alter the structure of the intestinal flora, offering possibilities for the prevention and treatment of these diseases. However, current monitoring methods, such as 16S rRNA sequencing, are complex and costly and require specialized personnel to perform the tests, making it difficult to continuously monitor patients during treatment. Hence, the rapid and cost-effective quantification of intestinal bacteria has become an urgent problem to be solved. Aptamers are of emerging interest because their stability, low immunogenicity and ease of modification are attractive properties for a variety of applications. We report a FluCell-SELEX polyclonal aptamer library specific for R. intestinalis isolated after seven evolution rounds, that can bind and label this organism for fluorescence microscopy and binding assays. Moreover, R. intestinalis can be distinguished from other major intestinal bacteria in complex defined mixtures and in human stool samples. We believe that this preliminary evidence opens new avenues towards aptamer-based electronic biosensors as new powerful and inexpensive diagnostic tools for the relative quantitative monitoring of R. intestinalis in gut microbiomes.