Recent advancements in aptamers as promising nanotool for therapeutic and diagnostic applications

Aptamers are single-strand oligonucleotide molecules having certain structural interactions which allow them to bind to specific targets. Modified nucleotides are added during or after a selection procedure like Systematic Evolution of Ligands by Exponential Enrichment i.e., SELEX to enhance the characteristics and functionality of aptamers. Aptamers are extensible molecular tools with several uses such as in drug administration, biosensing, bioimaging, drug therapies and diagnostics. The ability to detect is improved by using aptamer-based sensors in conjunction with biological molecules among other sensing techniques. Chemical modification, and strong resistance to denaturation, aptamers are appropriate biological recognizing agents for developing sensitive and repeatable aptasensors. This review discusses the most current developments in the aptamers, SELEX method, applications of aptamers as innovative diagnostic, therapeutic & theragnostic tool along with major limitations & prospective directions in the future.

Synergistic applications of quantum dots and magnetic nanomaterials in pathogen detection: a comprehensive review

The rapid and accurate detection of pathogens is crucial for effective disease prevention and management in healthcare, food safety, and environmental monitoring. While conventional pathogen detection methods like culture-based techniques and PCR are sensitive and selective, they are often time-consuming, require skilled operators, and are not suitable for point-of-care or on-site testing. To address these limitations, innovative sensor technologies have emerged that leverage the unique properties of nanomaterials. Quantum dots (QDs) and magnetic nanomaterials are two classes of nanomaterials that have shown particular promise for pathogen sensing. This review comprehensively examines the synergistic applications of QDs and magnetic nanomaterials for detecting bacteria, viruses, phages, and parasites.

A review of biomolecules conjugated lanthanide up-conversion nanoparticles-based fluorescence probes in food safety and quality monitoring applications

Upconversion nanoparticles (UCNPs) are known to possess unique characteristics, which allow them to overcome a number of issues that plague traditional fluorescence probes. UCNPs have been employed in a variety of applications, but it is arguably in the realm of optical sensors where they have shown the most promise. Biomolecule conjugated UCNPs-based fluorescence probes have been developed to detect and quantify a wide range of analytes, from metal ions to biomolecules, with great specificity and sensitivity. In this review, we have given much emphasis on the recent trends and progress in the preparation strategies of bioconjugated UCNPs and their potential application as fluorescence sensors in the trace level detection of food industry-based toxicants and adulterants. The paper discusses the preparation and functionalisation strategies of commonly used biomolecules over the surface of UCNPs. The use of different sensing strategies namely heterogenous and homogenous assays, underlying fluorescence mechanisms in the detection process of food adulterants are summarized in detail. This review might set a precedent for future multidisciplinary research including the development of novel biomolecules conjugated UCNPs for potential applications in food science and technology.

Nanomaterial interfaces designed with different biorecognition elements for biosensing of key foodborne pathogens

Foodborne diseases caused by pathogen bacteria are a serious problem toward the safety of human life in a worldwide. Conventional methods for pathogen bacteria detection have several handicaps, including trained personnel requirement, low sensitivity, laborious enrichment steps, low selectivity, and long-term experiments. There is a need for precise and rapid identification and detection of foodborne pathogens. Biosensors are a remarkable alternative for the detection of foodborne bacteria compared to conventional methods. In recent years, there are different strategies for the designing of specific and sensitive biosensors. Researchers activated to develop enhanced biosensors with different transducer and recognition elements. Thus, the aim of this study was to provide a topical and detailed review on aptamer, nanofiber, and metal organic framework-based biosensors for the detection of food pathogens. First, the conventional methods, type of biosensors, common transducer, and recognition element were systematically explained. Then, novel signal amplification materials and nanomaterials were introduced. Last, current shortcomings were emphasized, and future alternatives were discussed.

Ultrasensitive detection of Staphylococcus aureus using a non-fluorescent cDNA-grafted dark BBQ®-650 chromophore integrated hydrophilic upconversion nanoparticles/aptamer system

A highly structured fluorometric bioassay has been proposed for screening Staphylococcus aureus (S. aureus). The study exploits (i) the spectral attributes of the hexagonal NaYF₄:Yb,Er upconversion nanoparticle (UCNP)-coated 3-aminopropyl)triethoxysilane; (ii) the intrinsic non-fluorescent quenching features of the highly stable dark blackberry (BBQ®-650) receptor; (iii) the aptamer (Apt-) biorecognition and binding affinity, and (iv) the complementary DNA hybridizer-linkage efficacy. The principle relied on the excited state energy transfer between the donor Apt-labeled NH₂-UCNPs at the 3' end, and cDNA-grafted BBQ®-650 at the 5' end, as the effective receptors. The donor moieties in proximity (< 10.0 nm) trigger hybridization with the cDNA-grafted dark BBQ®-650, as the receptors of energy from the ²F_5/2 level of Yb³⁺ ions to initiate the Förster resonance energy transfer pathway. This was confirmed by the decline in the excited-state lifetimes from 223.52 μs (τ₁) to 179.26 μs (τ₂). The existence of the target S. aureus in the bioassay attracts the Apt- resulting in the detachment of the acceptor, and disintegration of the complex configuration via conformation reversal. The re-activated fluorescence monitored at λex/em = 980/652 nm, as a function of the logarithmic concentration of S. aureus (42 to 4.2 × 10⁸ CFU mL^-1), yielded an ultra-low detection response of 2.0 CFU mL^-1. The bioassay screening of S. aureus in real samples revealed satisfactory recoveries (92.44-107.82%) and validation results (p > 0.05). Hence, the comprehensive Apt-labeled NH₂-UCNPs-cDNA-grafted dark BBQ®-650 bioassay offered fast and precise S. aureus screening in food and environmental settings.

Aptamers Enhance Oncolytic Viruses' Antitumor Efficacy

Oncolytic viruses are highly promising for cancer treatment because they target and lyse tumor cells. These genetically engineered vectors introduce therapeutic or immunostimulatory genes into the tumor. However, viral therapy is not always safe and effective. Several problems are related to oncolytic viruses' targeted delivery to the tumor and immune system neutralization in the bloodstream. Cryoprotection and preventing viral particles from aggregating during storage are other critical issues. Aptamers, short RNA, or DNA oligonucleotides may help to crawl through this bottleneck. They are not immunogenic, are easily synthesized, can be chemically modified, and are not very demanding in storage conditions. It is possible to select an aptamer that specifically binds to any target cell, oncolytic virus, or molecule using the SELEX technology. This review comprehensively highlights the most important research and methodological approaches related to oncolytic viruses and nucleic acid aptamers. Here, we also analyze possible future research directions for combining these two methodologies to improve the effectiveness of cancer virotherapy.

Engineered upconversion nanocarriers for synergistic breast cancer imaging and therapy: Current state of art

Breast cancer is the most common type of cancer in women and is the second leading cause of cancer-related deaths worldwide. Early diagnosis and effective therapeutic interventions are critical determinants that can improve survival and quality of life in breast cancer patients. Nanotheranostics are emerging interventions that offer the dual benefit of in vivo diagnosis and therapeutics through a single nano-sized carrier. Rare earth metal-doped upconversion nanoparticles (UCNPs) with their ability to convert near-infrared light to visible light or UV light in vivo settings have gained special attraction due to their unique luminescence and tumor-targeting properties. In this review, we have discussed applications of UCNPs in drug and gene delivery, photothermal therapy (PTT), photodynamic therapy (PDT) and tumor targeting in breast cancer. Further, present challenges and future opportunities for UCNPs in breast cancer treatment have also been mentioned.

Advanced techniques for performing photodynamic therapy in deep-seated tissues

Photodynamic therapy (PDT) is a promising localized cancer treatment modality. It has been used successfully to treat a range of dermatological conditions with comparable efficacy to conventional treatments. However, some drawbacks limit the clinical utility of PDT in treating deep-seated tumors. Notably, the penetration limitation of UV and visible light, commonly applied to activate photosensitizers, makes PDT incompetent in treating deep-seated tumors. Development in light delivery technologies, especially fiber optics, led to improved clinical strategies for accessing deep tissues for irradiation. However, PDT efficacy issues remained partly due to light penetration limitations. In this review, we first summarized the current PDT applications for deep-seated tumor treatment. Then, the most recent progress in advanced techniques to overcome the light penetration limitation in PDT, including using functional nanomaterials that can either self-illuminate or be activated by near-infrared (NIR) light and X-rays as transducers, and implantable light delivery devices were discussed. Finally, current challenges and future opportunities of these technologies were discussed, which we hope may inspire the development of more effective techniques to enhance PDT efficacy against deep-seated tumors.

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.

Aptamer-Based High-Throughput Screening Model for Efficient Selection and Evaluation of Natural Ingredients against SGIV Infection

Singapore grouper iridovirus (SGIV) causes high economic losses in mariculture. Effective drugs for managing SGIV infection are urgently required. Medicinal plant resources are rich in China. Medicinal plants have a long history and significant curative effects in the treatment of many diseases. Reverse-transcription quantitative real-time PCR is the most commonly used method for detecting virus infection and assessing antiviral efficacy with high accuracy. However, their applications are limited due to high reagent costs and complex time-consuming operations. Aptamers have been applied in some biosensors to achieve the accurate detection of pathogens or diseases through signal amplification. This study aimed to establish an aptamer-based high-throughput screening (AHTS) model for the efficient selection and evaluation of medicinal plants components against SGIV infection. Q2-AHTS is an expeditious, rapid method for selecting medicinal plant drugs against SGIV, which was characterized as being dram, high-speed, sensitive, and accurate. AHTS strategy reduced work intensity and experimental costs and shortened the whole screening cycle for effective ingredients. AHTS should be suitable for the rapid selection of effective components against other viruses, thus further promoting the development of high-throughput screening technology.

Advances in aptamer-based nuclear imaging

Aptamers are short oligonucleotides that bind to specific target molecules. They have been extensively explored in biomedical applications, including biosensing, medical imaging, and disease treatment. Their adjustable affinity for specific biomarkers stimulates more translational efforts, such as nuclear imaging of tumors in preclinical and clinical settings. In this review, we present recent advances of aptamer-based nuclear imaging and compare aptamer tracers with other biogenic probes in forms of peptides, nanobodies, monoclonal antibodies, and antibody fragments. Fundamental properties of aptamer-based radiotracers are highlighted and potential directions to improve aptamer's imaging performance are discussed. Despite many translational obstacles to overcome, we envision aptamers to be a versatile tool for cancer nuclear imaging in the near future.

Temperature and pH-Dependent Behaviors of mAb Drugs: A Case Study for Trastuzumab

The distortions in the high-order structure of therapeutic monoclonal antibodies (mAbs) under different environmental conditions acutely affect mAb stability, resulting in altered safety, efficacy, and shelf-life profiles. The overall stability of mAbs depends on many factors, and it requires complementary techniques for an in-depth analysis. The stability of mAbs can be characterized by differential centrifugal sedimentation (DCS), differential scanning calorimetry (DSC), differential scanning fluorimetry (DSF), and size exclusion chromatography (SEC) techniques. In this report, temperature-ramped dynamic light scattering (DLS), and circular dichroism (CD) spectroscopy were employed as complementary tools to show how temperature and pH affect the aggregation of a model mAb, trastuzumab, in solution. The results showed that the aggregation onset temperature of trastuzumab defined by DLS was 75 °C, which decreases the amount of β-sheets and causes a slight increase in helix structures. Moreover, the melting temperature of trastuzumab was determined to be between 80–83 °C by temperature-ramped CD spectrophotometry, which is in line with the Tm of trastuzumab’s Fab region tested with DSC. Thus, unfolding and aggregation of trastuzumab start simultaneously at 75 °C, and unfolding triggers the aggregation. The temperature-ramped CD and DLS methods are robust tools to determine the thermal behavior of biosimilars in various solution conditions. Their complementary usage provides solid scientific background for regulatory applications and a better understanding of mAb instability and its relationship with structural changes.

Upconversion Nanoprobes Based on a Horseradish Peroxidase-Regulated Dual-Mode Strategy for the Ultrasensitive Detection of Staphylococcus aureus in Meat

Staphylococcus aureus (S. aureus) is one of the foodborne pathogens that can cause infectious diseases and food poisoning. Herein, colorimetric and fluorescent dual-mode nanoprobes were developed for ultrasensitive detection of S. aureus to immediately respond to public health emergencies, reduce false positives, and improve measurement accuracy and persuasiveness. The nanoprobe consists of aptamer-labeled magnetic nanoparticles (apt-MNPs) as the capture signal probe and horseradish peroxidase and complementary DNA-functionalized upconversion nanoparticles (HRP-UCNPs-cDNA) as the chromogenic signal probe. In the absence of S. aureus, the probe forms an immune complex through base complementation with an observable signal. When S. aureus is introduced to this system, it preferentially binds to the apt-MNPs, releasing HRP-UCNPs-cDNA from the apt-MNPs and restoring the chromogenic probe signal. Under optimum conditions, an ultrasensitive assay of S. aureus was obtained, with limits of detection of 22 CFU mL^-1 for fluorescence and 20 CFU mL^-1 for colorimetry in a linear range of 56-5.6 × 10⁶ CFU mL^-1. Additionally, the standard plate counting method confirmed the reliability and accuracy of the established nanoprobe with an insignificant difference. Hence, the developed dual-mode platform has extensive application prospects for speedy and specific determination of S. aureus in meat.

Lanthanide ion (Ln3+ )-based upconversion sensor for quantification of food contaminants: A review

The food safety issue has gradually become the focus of attention in modern society. The presence of food contaminants poses a threat to human health and there are a number of interesting researches on the detection of food contaminants. Upconversion nanoparticles (UCNPs) are superior to other fluorescence materials, considering the benefits of large anti-Stokes shifts, high chemical stability, non-autofluorescence, good light penetration ability, and low toxicity. These properties render UCNPs promising candidates as luminescent labels in biodetection, which provides opportunities as a sensitive, accurate, and rapid detection method. This paper intended to review the research progress of food contaminants detection by UCNPs-based sensors. We have proposed the key criteria for UCNPs in the detection of food contaminants. Additionally, it highlighted the construction process of the UCNPs-based sensors, which includes the synthesis and modification of UCNPs, selection of the recognition elements, and consideration of the detection principle. Moreover, six kinds of food contaminants detected by UCNPs technology in the past 5 years have been summarized and discussed fairly. Last but not least, it is outlined that UCNPs have great potential to be applied in food safety detection and threw new insight into the challenges ahead.

Biosensing based on upconversion nanoparticles for food quality and safety applications

Food safety and quality regulations inevitably call for sensitive and accurate analytical methods to detect harmful contaminants in food and to ensure safe food for the consumer. Both novel and well-established biorecognition elements, together with different transduction schemes, enable the simple and rapid analysis of various food contaminants. Upconversion nanoparticles (UCNPs) are inorganic nanocrystals that convert near-infrared light into shorter wavelength emission. This unique photophysical feature, along with narrow emission bandwidths and large anti-Stokes shift, render UCNPs excellent optical labels for biosensing because they can be detected without optical background interferences from the sample matrix. In this review, we show how this exciting technique has evolved into biosensing platforms for food quality and safety monitoring and highlight recent applications in the field.

Recent Advances in Aptamer-Based Biosensors for Detection of Pseudomonas aeruginosa

Increasing concerns about nosocomial infection, food and environmental safety have prompted the development of rapid, accurate, specific and ultrasensitive methods for the early detection of critical pathogens. Pseudomonas aeruginosa is one of the most common pathogens that cause infection. It is ubiquitous in nature, being found in water, soil, and food, and poses a great threat to public health. The conventional detection technologies are either time consuming or readily produce false positive/negative results, which makes them unsuitable for early diagnosis and spot detection of P. aeruginosa. To circumvent these drawbacks, many efforts have been made to develop biosensors using aptamers as bio-recognition elements. Various aptamer-based biosensors for clinical diagnostics, food, and environmental monitoring of P. aeruginosa have been developed in recent years. In this review, we focus on the latest advances in aptamer-based biosensors for detection of P. aeruginosa. Representative biosensors are outlined according to their sensing mechanisms, which include optical, electrochemical and other signal transduction methods. Possible future trends in aptamer biosensors for pathogen detection are also outlined.

Biosensors for rapid detection of Salmonella in food: A review

Salmonella is one of the main causes of foodborne infectious diseases, posing a serious threat to public health. It can enter the food supply chain at various stages of production, processing, distribution, and marketing. High prevalence of Salmonella necessitates efficient and effective approaches for its identification, detection, and monitoring at an early stage. Because conventional methods based on plate counting and real-time polymerase chain reaction are time-consuming and laborious, novel rapid detection methods are urgently needed for in-field and on-line applications. Biosensors provide many advantages over conventional laboratory assays in terms of sensitivity, specificity, and accuracy, and show superiority in rapid response and potential portability. They are now recognized as promising alternative tools and one of the most on-site applicable and end user-accessible methods for rapid detection. In recent years, we have witnessed a flourishing of studies in the development of robust and elaborate biosensors for detection of Salmonella in food. This review aims to provide a comprehensive overview on Salmonella biosensors by highlighting different signal-transducing mechanisms (optical, electrochemical, piezoelectric, etc.) and critically analyzing its recent trends, particularly in combination with nanomaterials, microfluidics, portable instruments, and smartphones. Furthermore, current challenges are emphasized and future perspectives are discussed.

Current Perspectives on Aptamers as Diagnostic Tools and Therapeutic Agents

Aptamers are synthetic single-stranded DNA or RNA sequences selected from combinatorial oligonucleotide libraries through the well-known in vitro selection and iteration process, SELEX. The last three decades have witnessed a sudden boom in aptamer research, owing to their unique characteristics, like high specificity and binding affinity, low immunogenicity and toxicity, and ease in synthesis with negligible batch-to-batch variation. Aptamers can specifically bind to the targets ranging from small molecules to complex structures, making them suitable for a myriad of diagnostic and therapeutic applications. In analytical scenarios, aptamers are used as molecular probes instead of antibodies. They have the potential in the detection of biomarkers, microorganisms, viral agents, environmental pollutants, or pathogens. For therapeutic purposes, aptamers can be further engineered with chemical stabilization and modification techniques, thus expanding their serum half-life and shelf life. A vast number of antagonistic aptamers or aptamer-based conjugates have been discovered so far through the in vitro selection procedure. However, the aptamers face several challenges for its successful clinical translation, and only particular aptamers have reached the marketplace so far. Aptamer research is still in a growing stage, and a deeper understanding of nucleic acid chemistry, target interaction, tissue distribution, and pharmacokinetics is required. In this review, we discussed aptamers in the current diagnostics and theranostics applications, while addressing the challenges associated with them. The report also sheds light on the implementation of aptamer conjugates for diagnostic purposes and, finally, the therapeutic aptamers under clinical investigation, challenges therein, and their future directions.

Plasmonic Selection of ssDNA Aptamers against Fibroblast Growth Factor Receptor

In this work, we describe the selection of ssDNA aptamers targeting fibroblast growth factor receptor binding protein 3 K650E, which has roles in cell division, growth, and differentiation through the kinase cascade. The selection process was based on the label-free, real-time monitoring of binding interactions by surface plasmon resonance, allowing for convenient manipulation of the selection rounds. Next generation sequencing data provided four major motif families from which nine individual sequences were selected based on their abundance levels. Electrophoretic mobility shift assays revealed binding of the selected aptamers to the target protein without significant interference from fibroblast growth factor receptor binding protein 2, indicating the selectivity of the aptamers. The dissociation constant at equilibrium for the best aptamer candidate, SU-3, was found to be (28.2 ± 19.6) × 10^-9 M (n = 5) using a single-cycle kinetic analysis method. Advantages of the experimental setup and potential applications of the selected aptamers are discussed.

Aptamer and nanomaterial based FRET biosensors: a review on recent advances (2014-2019)

Fluorescence resonance energy transfer, one of the most powerful phenomena for elucidating molecular interactions, has been extensively utilized as a biosensing tool to provide accurate information at the nanoscale. Numerous aptamer- and nanomaterial-based FRET bioassays has been developed for detection of a large variety of molecules. Affinity probes are widely used in biosensors, in which aptamers have emerged as advantageous biorecognition elements, due to their chemical and structural stability. Similarly, optically active nanomaterials offer significant advantages over conventional organic dyes, such as superior photophysical properties, large surface-to-volume ratios, photostability, and longer shelf life. In this report (with 175 references), the use of aptamer-modified nanomaterials as FRET couples is reviewed: quantum dots, upconverting nanoparticles, graphene, reduced graphene oxide, gold nanoparticles, molybdenum disulfide, graphene quantum dots, carbon dots, and metal-organic frameworks. Tabulated summaries provide the reader with useful information on the current state of research in the field. Graphical abstract Schematic representation of a fluorescence resonance energy transfer-based aptamer nanoprobe in the absence and presence of a given target molecule (analyte). Structures are not drawn to their original scales.