Aptamer based nanobiosensors: Promising healthcare devices

A perspective on the potential use of aptamer-based field-effect transistor sensors as biosensors for ovarian cancer biomarkers CA125 and HE4

Ovarian cancer (OC) is one of the most fatal gynaecological malignancies, primarily because of its typically asymptomatic early stages, which complicates early detection. Therefore, developing sensitive and appropriate biomarkers for efficient diagnosis of OC is urgently needed. Aptamers, short sequences of single-stranded DNA or RNA molecules, have become crucial in tumor diagnosis because of their high affinity for specific molecules produced by tumors. This ability allows aptamers to accurately detect OC, thus providing better survival rates and a reduced disease burden. Biosensors that combine recognition molecules and nanomaterials are essential in various fields, including disease diagnosis and health management. Molecular-specific field-effect transistor (FET) biosensors are particularly promising due to their rapid response times, ease of miniaturization, and high sensitivity in detecting OC. Aptamers, which are known for their stability and structural tunability, are increasingly being used as biological recognition units in FET biosensors, offering selective and high-affinity binding to target molecules that are ideal for medical diagnostics. This review explores the recent advancements in biosensors for OC detection, including FET biosensors with aptamer-functionalized nanomaterials for CA125 and HE4. Furthermore, this review provides an overview of the structure and sensing principles of these advanced biosensors, preparation methods and functionalization strategies that enhance their performance. Additionally, notable progress and potential of biosensors, including aptamer-functionalized FET biosensors for OC diagnosis have been summarized, emphasising their role and clinical validation in advancing medical diagnostics and improving patient outcomes through enhanced detection capabilities.

The use of aptamers as therapeutic inhibitors and biosensors of TNF-alpha

Tumor necrosis factor-alpha (TNF-α) is a pivotal cytokine in the pathogenesis of numerous inflammatory and autoimmune diseases. Precise and sensitive detection of TNF-α is essential for both clinical applications and research endeavors. In the realm of cytokine detection, particularly TNF-α, the development of highly sensitive and specific biosensors has become a focal point. The biosensing landscape encompasses a variety of biorecognition elements, each with its unique set of characteristics. TNF inhibitors come with a significant price tag and, notably, do not yield positive responses in all patients. Despite the availability of numerous FDA-approved biologic agents (e.g., infliximab, adalimumab, certolizumab pegol, etc.) and monoclonal antibodies (e.g., adalimumab) targeting TNF-α, aptamers tailored for blocking TNF-α activities have yet to receive approval. Aptamers have rapidly gained recognition as readily available, versatile, and highly effective molecular tools for both therapeutic and diagnostic purposes in the context of TNF-alpha. In this manuscript, we explore the potential of short single-stranded DNA or RNA sequences known as aptamers as biorecognition elements in biosensors designed for the detection of TNF-α. We delve into the progress made in the development of aptamer-based TNF-α inhibitors and shed light on successful studies in this burgeoning field.

AI-optimized electrochemical aptasensors for stable, reproducible detection of neurodegenerative diseases, cancer, and coronavirus

AI-optimized electrochemical aptasensors are transforming diagnostic testing by offering high sensitivity, selectivity, and rapid response times. Leveraging data-driven AI techniques, these sensors provide a non-invasive, cost-effective alternative to traditional methods, with applications in detecting molecular biomarkers for neurodegenerative diseases, cancer, and coronavirus. The performance metrics outlined in the comparative table illustrate the significant advancements enabled by AI integration. Sensitivity increases from 60 to 75 % in ordinary aptasensors to 85-95 %, while specificity improves from 70-80 % to 90-98 %. This enhanced performance allows for ultra-low detection limits, such as 10 fM for carcinoembryonic antigen (CEA) and 20 fM for mucin-1 (MUC1) using Electrochemical Impedance Spectroscopy (EIS), and 1 pM for prostate-specific antigen (PSA) with Differential Pulse Voltammetry (DPV). Similarly, Square Wave Voltammetry (SWV) and potentiometric sensors have detected alpha-fetoprotein (AFP) at 5 fM and epithelial cell adhesion molecule (EpCAM) at 100 fM, respectively. AI integration also enhances reproducibility, reduces false positives and negatives (from 15-20 % to 5-10 %), and significantly decreases response times (from 10-15 s to 2-3 s). These advancements improve data processing speeds (from 10 to 20 min per sample to 2-5 min) and calibration accuracy (<2 % margin of error compared to 5-10 %), while expanding application scope to multi-target biomarker detection. This review highlights how these advancements position AI-optimized electrochemical aptasensors as powerful tools for personalized treatment, point-of-care testing, and continuous health monitoring. Despite a higher cost ($500-$1,500/unit), their enhanced portability and diagnostic performance promise to revolutionize healthcare, environmental monitoring, and food safety, ultimately improving public health outcomes.

Targeting PCSK9 as a key player in lipid metabolism: exploiting the therapeutic and biosensing potential of aptamers

The degradation of low-density lipoprotein receptor (LDLR) is induced by proprotein convertase subtilisin/kexin type 9 (PCSK9), resulting in elevated plasma concentrations of LDL cholesterol. Therefore, inhibiting the interactions between PCSK9 and LDLR is a desirable therapeutic goal for managing hypercholesterolemia. Aptamers, which are RNA or single-stranded DNA sequences, can recognize their targets based on their secondary structure. Aptamers exhibit high selectivity and affinity for binding to target molecules. The systematic evolution of ligands by exponential enrichment (SELEX), a combination of biological approaches, is used to screen most aptamers in vitro. Due to their unique advantages, aptamers have garnered significant interest since their discovery and have found extensive applications in various fields. Aptamers have been increasingly utilized in the development of biosensors for sensitive detection of pathogens, analytes, toxins, drug residues, and malignant cells. Furthermore, similar to monoclonal antibodies, aptamers can serve as therapeutic tools. Unlike certain protein therapeutics, aptamers do not elicit antibody responses, and their modified sugars at the 2'-positions generally prevent toll-like receptor-mediated innate immune responses. The focus of this review is on aptamer-based targeting of PCSK9 and the application of aptamers both as biosensors and therapeutic agents.

ssDNA-Modified Gold Nanoparticles as a Tool to Detect miRNA Biomarkers in Osteoarthritis

Recently, miRNAs have been established as promising, specific biomarkers for the diagnosis of many diseases, including osteoarthritis. Herein, we report a ssDNA-based detection method for miRNAs implicated in osteoarthritis, specifically, miR-93 and miR-223. In this study, gold nanoparticles (AuNPs) were modified with oligonucleotide ssDNA to detect miRNAs circulating in the blood in healthy subjects and patients suffering from osteoarthritis. The detection method was based on the colorimetric and spectrophotometric assessment of biofunctionalized AuNPs upon interaction with the target and their subsequent aggregation. Results showed that these methods could be used to detect easily and rapidly miR-93 but not miR-223 in osteoarthritic patients, and they could potentially be used as a diagnostic tool for blood biomarkers. Visual-based detection as well as spectroscopic methods are simple, rapid, and label-free, due to which they can be used as a diagnostic tool.

Neuro-nanotechnology: diagnostic and therapeutic nano-based strategies in applied neuroscience

Artificial, de-novo manufactured materials (with controlled nano-sized characteristics) have been progressively used by neuroscientists during the last several decades. The introduction of novel implantable bioelectronics interfaces that are better suited to their biological targets is one example of an innovation that has emerged as a result of advanced nanostructures and implantable bioelectronics interfaces, which has increased the potential of prostheses and neural interfaces. The unique physical-chemical properties of nanoparticles have also facilitated the development of novel imaging instruments for advanced laboratory systems, as well as intelligently manufactured scaffolds and microelectrodes and other technologies designed to increase our understanding of neural tissue processes. The incorporation of nanotechnology into physiology and cell biology enables the tailoring of molecular interactions. This involves unique interactions with neurons and glial cells in neuroscience. Technology solutions intended to effectively interact with neuronal cells, improved molecular-based diagnostic techniques, biomaterials and hybridized compounds utilized for neural regeneration, neuroprotection, and targeted delivery of medicines as well as small chemicals across the blood-brain barrier are all purposes of the present article.

Aptamer-based biosensors for Pseudomonas aeruginosa detection

Pseudomonas aeruginosa possesses innate antibiotic resistance mechanisms, and carbapenem-resistant Pseudomonas aeruginosa has been considered the number one priority in the 2017 WHO list of antimicrobial-resistant crucial hazards. Early detection of Pseudomonas aeruginosa can circumvent treatment challenges. Various techniques have been developed for the detection of P. aeruginosa detection. Biosensors have recently attracted unprecedented attention in the field of point-of-care diagnostics due to their easy operation, rapid, low cost, high sensitivity, and selectivity. Biosensors can convert the specific interaction between bioreceptors (antibodies, aptamers) and pathogens into optical, electrical, and other signal outputs. Aptamers are novel and promising alternatives to antibodies as biorecognition elements mainly synthesized by systematic evolution of ligands by exponential enrichment and have predictable secondary structures. They have comparable affinity and specificity for binding to their target to antibody recognition. Since 2015, there have been about 2000 journal articles published in the field of aptamer biosensors, of which 30 articles were on the detection of P. aeruginosa. Here, we have focused on outlining the recent progress in the field of aptamer-based biosensors for P. aeruginosa detection based on optical, electrochemical, and piezoelectric signal transduction methods.

Aptamers for SARS-CoV-2: Isolation, Characterization, and Diagnostic and Therapeutic Developments

The SARS-CoV-2 virus and COVID-19 pandemic continue to demand effective diagnostic and therapeutic solutions. Finding these solutions requires highly functional molecular recognition elements. Nucleic acid aptamers represent a possible solution. Characterized by their high affinity and specificity, aptamers can be rapidly identified from random-sequence nucleic acid libraries. Over the past two years, many labs around the world have rushed to create diverse aptamers that target two important structural proteins of SARS-CoV-2: the spike (S) protein and nucleocapsid (N) protein. These have led to the identification of many aptamers that show real promise for the development of diagnostic tests and therapeutic agents for SARS-CoV-2. Herein we review all these developments, with a special focus on the development of diverse aptasensors for detecting SARS-CoV-2. These include electrochemical and optical sensors, lateral flow devices, and aptamer-linked immobilized sorbent assays.

Nucleic acid paranemic structures: a promising building block for functional nanomaterials in biomedical and bionanotechnological applications

Over the past few decades, DNA has been recognized as a powerful self-assembling material capable of crafting supramolecular nanoarchitectures with quasi-angstrom precision, which promises various applications in the fields of materials science, nanoengineering, and biomedical science. Notable structural features include biocompatibility, biodegradability, high digital encodability by Watson-Crick base pairing, nanoscale dimension, and surface addressability. Bottom-up fabrication of complex DNA nanostructures relies on the design of fundamental DNA motifs, including parallel (PX) and antiparallel (AX) crossovers. However, paranemic or PX motifs have not been thoroughly explored for the construction of DNA-based nanostructures compared to AX motifs. In this review, we summarize the developments of PX-based DNA nanostructures, highlight the advantages as well as challenges of PX-based assemblies, and give an overview of the structural and chemical features that lend their utilization in a variety of applications. The works presented cover PX-based DNA nanostructures in biological systems, dynamic systems, and biomedical contexts. The possible future advances of PX structures and applications are also summarized, discussed, and postulated.

State of the Art of Chemosensors in a Biomedical Context

Healthcare is undergoing large transformations, and it is imperative to leverage new technologies to support the advent of personalized medicine and disease prevention. It is now well accepted that the levels of certain biological molecules found in blood and other bodily fluids, as well as in exhaled breath, are an indication of the onset of many human diseases and reflect the health status of the person. Blood, urine, sweat, or saliva biomarkers can therefore serve in early diagnosis of diseases such as cancer, but also in monitoring disease progression, detecting metabolic disfunctions, and predicting response to a given therapy. For most point-of-care sensors, the requirement that patients themselves can use and apply them is crucial not only regarding the diagnostic part, but also at the sample collection level. This has stimulated the development of such diagnostic approaches for the non-invasive analysis of disease-relevant analytes. Considering these timely efforts, this review article focuses on novel, sensitive, and selective sensing systems for the detection of different endogenous target biomarkers in bodily fluids as well as in exhaled breath, which are associated with human diseases.

Effect of DNA Aptamer Concentration on the Conductivity of a Water-Gated Al:ZnO Thin-Film Transistor-Based Biosensor

Field-effect transistor-based biosensors (bio-FETs) are promising candidates for the rapid high-sensitivity and high-selectivity sensing of various analytes in healthcare, clinical diagnostics, and the food industry. However, bio-FETs still have several unresolved problems that hinder their technological transfer, such as electrical stability. Therefore, it is important to develop reliable, efficient devices and establish facile electrochemical characterization methods. In this work, we have fabricated a flexible biosensor based on an Al:ZnO thin-film transistor (TFT) gated through an aqueous electrolyte on a polyimide substrate. In addition, we demonstrated techniques for establishing the operating range of such devices. The Al:ZnO-based devices with a channel length/width ratio of 12.35 and a channel thickness of 50 nm were produced at room temperature via magnetron sputtering. These Al:ZnO-based devices exhibited high field-effect mobility (μ = 6.85 cm2/Vs) and threshold voltage (Vth = 654 mV), thus showing promise for application on temperature-sensitive substrates. X-ray photoelectron spectroscopy was used to verify the chemical composition of the deposited films, while the morphological aspects of the films were assessed using scanning electron and atomic force microscopies. The gate-channel electric capacitance of 40 nF/cm2 was determined using electrochemical impedance spectroscopy, while the electrochemical window of the gate-channel system was determined as 1.8 V (from -0.6 V to +1.2 V) using cyclic voltammetry. A deionized water solution of 10 mer (CCC AAG GTC C) DNA aptamer (molar weight -2972.9 g/mol) in a concentration ranging from 1-1000 pM/μL was used as an analyte. An increase in aptamer concentration caused a proportional decrease in the TFT channel conductivity. The techniques demonstrated in this work can be applied to optimize the operating parameters of various semiconductor materials in order to create a universal detection platform for biosensing applications, such as multi-element FET sensor arrays based on various composition nanostructured films, which use advanced neural network signal processing.

Graphene Based Nanohybrid Aptasensors in Environmental Monitoring: Concepts, Design and Future Outlook

In view of ever-increasing environmental pollution, there is an immediate requirement to promote cheap, multiplexed, sensitive and fast biosensing systems to monitor these pollutants or contaminants. Aptamers have shown numerous advantages in being used as molecular recognition elements in various biosensing devices. Graphene and graphene-based materials/nanohybrids combined with several detection methods exhibit great potential owing to their exceptional optical, electronic and physicochemical properties which can be employed extensively to monitor environmental contaminants. For environmental monitoring applications, aptamers have been successfully combined with graphene-based nanohybrids to produce a wide range of innovative methodologies. Aptamers are immobilized at the surface of graphene based nanohybrids via covalent and non-covalent strategies. This review highlights the design, working principle, recent developmental advances and applications of graphene based nanohybrid aptasensors (GNH-Apts) (since January 2014 to September 2021) with a special emphasis on two major signal-transduction methods, i.e., optical and electrochemical for the monitoring of pesticides, heavy metals, bacteria, antibiotics, and organic compounds from different environmental samples (e.g., water, soil and related). Lastly, the challenges confronted by scientists and the possible future outlook have also been addressed. It is expected that high-performance graphene-based nanohybrid aptasensors would find broad applications in the field of environmental monitoring.

Aptamer-based biosensing through the mapping of encoding upconversion nanoparticles for sensitive CEA detection

An aptamer-based assay through the mapping and enumeration of encoding UCNPs for digital detection of CEA is reported.

Potential applications of aptamers in veterinary science

Aptamers are small nucleic acids that fold in a three-dimensional conformation allowing them to bind specifically to a target. This target can be an organic molecule, free or carried in cells or tissues, or inorganic components, such as metal ions. Analogous to monoclonal antibodies, aptamers however have certain advantages over the latter: e.g., high specificity for their target, no to low immunogenicity and easy in vitro selection. Since their discovery more than 30 years ago, aptamers have led to various applications, although mainly restricted to basic research. This work reviews the applications of aptamers in veterinary science to date. First, we present aptamers, how they are selected and their properties, then we give examples of applications in food and environmental safety, as well as in diagnosis and medical treatment in the field of veterinary medicine. Because examples of applications in veterinary medicine are scarce, we explore the potential avenues for future applications based on discoveries made in human medicine. Aptamers may offer new possibilities for veterinarians to diagnose certain diseases—particularly infectious diseases—more rapidly or “at the patient’s bedside”. All the examples highlight the growing interest in aptamers and the premises of a potential market. Aptamers may benefit animals as well as their owners, breeders and even public health in a “One Health” approach.

Novel Detection of Nasty Bugs, Prevention Is Better than Cure

Hospital-acquired infections (HAIs) are a growing concern around the world. They contribute to increasing mortality and morbidity rates and are an economic threat. All hospital patients have the potential to contract an HAI, but those with weakened or inferior immune systems are at highest risk. Most hospital patients will contract at least one HAI, but many will contract multiple ones. Bacteria are the most common cause of HAIs and contribute to 80-90% of all HAIs, with Staphylococcus aureus, Clostridium difficile, Escherichia coli, Acinetobacter baumannii, Pseudomonas aeruginosa and Klebsiella pneumoniae accounting for the majority. Each of these bacteria are highly resistant to antibiotics and can produce a protective film, known as a biofilm, to further prevent their eradication. It has been shown that by detecting and eradicating bacteria in the environment, infection rates can be reduced. The current methods for detecting bacteria are time consuming, non-specific, and prone to false negatives or false positives. Aptamer-based biosensors have demonstrated specific, time-efficient and simple detection, highlighting the likelihood that they could be used in a similar way to detect HAI-causing bacteria.

Biosensors for the Detection of Bacterial and Viral Clinical Pathogens

Biosensors are measurement devices that can sense several biomolecules, and are widely used for the detection of relevant clinical pathogens such as bacteria and viruses, showing outstanding results. Because of the latent existing risk of facing another pandemic like the one we are living through due to COVID-19, researchers are constantly looking forward to developing new technologies for diagnosis and treatment of infections caused by different bacteria and viruses. Regarding that, nanotechnology has improved biosensors' design and performance through the development of materials and nanoparticles that enhance their affinity, selectivity, and efficacy in detecting these pathogens, such as employing nanoparticles, graphene quantum dots, and electrospun nanofibers. Therefore, this work aims to present a comprehensive review that exposes how biosensors work in terms of bacterial and viral detection, and the nanotechnological features that are contributing to achieving a faster yet still efficient COVID-19 diagnosis at the point-of-care.

Predicting Future Prospects of Aptamers in Field-Effect Transistor Biosensors

Aptamers, in sensing technology, are famous for their role as receptors in versatile applications due to their high specificity and selectivity to a wide range of targets including proteins, small molecules, oligonucleotides, metal ions, viruses, and cells. The outburst of field-effect transistors provides a label-free detection and ultra-sensitive technique with significantly improved results in terms of detection of substances. However, their combination in this field is challenged by several factors. Recent advances in the discovery of aptamers and studies of Field-Effect Transistor (FET) aptasensors overcome these limitations and potentially expand the dominance of aptamers in the biosensor market.

A DNA Aptamer Targeting Galectin-1 as a Novel Immunotherapeutic Strategy for Lung Cancer

Galectin-1 (Gal-1) is a pleiotropic homodimeric β-galactoside-binding protein with a single carbohydrate recognition domain. It has been implicated in several biological processes that are important during tumor progression. Several lines of evidence have indicated that Gal-1 is involved in cancer immune escape and induces T cell apoptosis. These observations all emphasized Gal-1 as a novel target for cancer immunotherapy. Here, we developed a novel Gal-1-targeting DNA aptamer (AP-74 M-545) and demonstrated its antitumor effect by restoring immune function. AP-74 M-545 binds to Gal-1 with high affinity. AP-74 M-545 targets tumors in murine tumor models but suppresses tumor growth only in immunocompetent C57BL/6 mice, not in immunocompromised non-obese diabetic (NOD)/severe combined immunodeficiency (SCID) mice. Immunohistochemistry revealed increased CD4⁺ and CD8⁺ T cells in AP-74 M-545-treated tumor tissues. AP-74 M-545 suppresses T cell apoptosis by blocking the binding of Gal-1 to CD45, the main receptor and apoptosis mediator of Gal-1 on T cells. Collectively, our data suggest that the Gal-1 aptamer suppresses tumor growth by blocking the interaction between Gal-1 and CD45 to rescue T cells from apoptosis and restores T cell-mediated immunity. These results indicate that AP-74 M-545 may be a potential strategy for cancer immunotherapy.

Lysin cell-binding domain-functionalized magnetic beads for detection of Staphylococcus aureus via inhibition of fluorescence of Amplex Red/hydrogen peroxide assay by intracellular catalase

Accurate and rapid identification of Staphylococcus aureus (S. aureus) is of great significance for controlling the food poisoning and infectious diseases caused by S. aureus. In this study, a novel strategy that combines lysin cell-binding domain (CBD)-based magnetic separation with fluorescence detection was developed for the specific and sensitive quantification of S. aureus in authentic samples. The S. aureus cells were separated from the sample matrix by lysin CBD-functionalized magnetic beads. Following lysis by lysostaphin, intracellular catalase was released from S. aureus cells and detected by a fluorometric system composed of horseradish peroxidase (HRP), hydrogen peroxide (H₂O₂), and Amplex Red. S. aureus was quantified via the inhibitory effect of the released intracellular catalase on the fluorometric system since the catalase could decompose the H₂O₂. Optimized conditions afforded a calibration curve for S. aureus ranging from 1.0 × 10² to 1.0 × 10⁷ CFU mL^-1. The detection limit was as low as 78 CFU mL^-1 in phosphate-buffered saline (PBS), and the total detection process could be completed in less than 50 min. Other bacteria associated with common food-borne and nosocomial infections negligibly interfered with S. aureus detection, except for Staphylococcus epidermidis, which may have slightly interfered. Moreover, the potential of this proposed method for practical applications has been demonstrated by detection assays of sterilized milk and human serum. Graphical abstract.

Microfluidic Chip for Multiplex Detection of Trace Chemical Contaminants Based on Magnetic Encoded Aptamer Probes and Multibranched DNA Nanostructures as Signal Tags

The development of multiplex assays to simultaneously monitor multiclass chemical contaminants that commonly coexist in foods, such as heavy metal ions, antibiotics, and estrogen residues, is gaining attention. Here, a microfluidic chip (MC)-based multianalysis method coupled with magnetic encoded aptamer probes was used for simultaneous detection of kanamycin, 17β-estradiol, and lead ion (Pb²⁺). Using this innovative strategy, the magnetic bead (MB)-based encoded probes labeled with aptamer hybrid chains were first used to selectively capture multiple targets, followed by generating single-stranded primers. The primers triggered a multibranched hybridization chain reaction (mHCR). Finally, three kinds of complementary strands (C-DNAs) with different lengths were hybridized with the arms of the mHCR products to form three types of multibranched DNA nanostructures. The decrement signals of C-DNAs were employed for qualification of targets. As the signal tags corresponded to different targets, the DNA nanostructures realized "one target for the decrease of massive C-DNAs" to improve sensitivity. The use of MB-based encoded probes could achieve magnetic separation to eliminate interference in the complex. The detection limits of this method were 1.76 × 10^-4 nM (kanamycin), 1.18 × 10^-4 nM (17β-estradiol), and 1.29 × 10^-4 nM (lead ion). Furthermore, the MC platform is reusable and can be used for more than 4000 samples. The assay combining the MC with MB-based encoded probes with multibranched DNA signal tags offers a universal, reusable, and high-throughput detection platform for screening multiclass chemical contaminants in food samples with complex matrices.

Current Trends in the Biosensors for Biological Warfare Agents Assay

Biosensors are analytical devices combining a physical sensor with a part of biological origin providing sensitivity and selectivity toward analyte. Biological warfare agents are infectious microorganisms or toxins with the capability to harm or kill humans. They can be produced and spread by a military or misused by a terrorist group. For example, Bacillus anthracis, Francisella tularensis, Brucella sp., Yersinia pestis, staphylococcal enterotoxin B, botulinum toxin and orthopoxviruses are typical biological warfare agents. Biosensors for biological warfare agents serve as simple but reliable analytical tools for the both field and laboratory assay. There are examples of commercially available biosensors, but research and development of new types continue and their application in praxis can be expected in the future. This review summarizes the facts and role of biosensors in the biological warfare agents' assay, and shows current commercially available devices and trends in research of the news. Survey of actual literature is provided.