Light-activated oxidative capacity of isoquinoline alkaloids for universal, homogeneous, reliable, colorimetric assays with DNA aptamers.

Aptamers are good affinity receptors for bio-assays, while colorimetric method is suitable for point-of-care sensing via direct visualization. But previously aptamers often need complex re-engineering for colorimetric measurement at the cost of affinity and performance. Here isoquinoline alkaloids are found to own unique light-activated oxidative capacity, which can be specifically triggered by unmodified aptamers. This feature is universal for two alkaloids to efficiently oxidize four chromogenic substrates with obvious color changes. Based on a dye-displacement process, we have developed a novel light-activated aptamer system for the colorimetric assay of estradiol. It shows a good sensitivity with a detection limit of 326 nM, and this homogeneous assay is reliable to avoid artifacts in previous heterogeneous scheme. Besides, it is proven to be a universal design to assay other two targets. Significantly, they do not employ any aptamers re-engineering but only simply use their parental aptamers. Therefore, this light-activated oxidative capacity of isoquinoline alkaloid can serve as an ideal tool for colorimetric assay of various targets based on aptamer's specific recognition.

Structure-based insights into fluorogenic RNA aptamers.

Fluorogenic RNA aptamers are in vitro-selected RNA molecules capable of binding to specific fluorophores, significantly increasing their intrinsic fluorescence. Over the past decade, the color palette of fluorescent RNA aptamers has greatly expanded. The emergence and development of these fluorogenic RNA aptamers has introduced a powerful approach for visualizing RNA localization and transport with high spatiotemporal resolution in live cells. To date, a variety of tertiary structures of fluorogenic RNA aptamers have been determined using X-ray crystallography or NMR spectroscopy. Many of these fluorogenic RNA aptamers feature base quadruples or base triples in their fluorophore-binding sites. This review summarizes the structure-based investigations of fluorogenic RNA aptamers, with a focus on their overall folds, ligand-binding pockets and fluorescence activation mechanisms. Additionally, the exploration of how structures guide rational optimization to enhance RNA visualization techniques is discussed.

Process, advances, and perspectives of graphene oxide-SELEX for the development of aptamer molecular probes: A comprehensive review.

BACKGROUND: Aptamers are screened via the systematic evolution of ligands by exponential enrichment (SELEX) and are widely used in molecular diagnostics and targeted therapies. The development of efficient and convenient SELEX technology has facilitated rapid access to high-performance aptamers, thereby advancing the aptamer industry. Graphene oxide (GO) serves as an immobilization matrix for libraries in GO-SELEX, making it suitable for screening aptamers against diverse targets. RESULTS: This review summarizes the detailed steps involved in GO-SELEX, including monitoring methods, various sublibrary acquisition methods, and practical applications from its inception to the present day. In addition, the potential of GO-SELEX in the development of broad-spectrum aptamers is explored, and its current limitations for future development are emphasized. This review effectively promotes the application of the GO-SELEX technique by providing valuable insights and assisting researchers interested in conducting related studies. SIGNIFICANCE AND NOVELTY: To date, no review on the topic of GO-SELEX has been published, making it challenging for researchers to initiate studies in this area. We believe that this review will broaden the SELEX options available to researchers, ensuring that they can meet the growing demand for molecular probes in the scientific domain.

Enhanced SELEX Platforms for Aptamer Selection with Improved Characteristics: A Review.

This review delves into the advancements in molecular recognition through enhanced SELEX (Systematic Evolution of Ligands by Exponential Enrichment) platforms and post-aptamer modifications. Aptamers, with their superior specificity and affinity compared to antibodies, are central to this discussion. Despite the advantages of the SELEX process-encompassing stages like ssDNA library preparation, incubation, separation, and PCR amplification-it faces challenges, such as nuclease susceptibility. To address these issues and propel aptamer technology forward, we examine next-generation SELEX platforms, including microfluidic-based SELEX, capillary electrophoresis SELEX, cell-based aptamer selection, counter-SELEX, in vivo SELEX, and high-throughput sequencing SELEX, highlighting their respective merits and innovations. Furthermore, this article underscores the significance of post-aptamer modifications, particularly chemical strategies that enhance aptamer stability, reduce renal filtration, and expand their target range, thereby broadening their utility in diagnostics, therapeutics, and nanotechnology. By synthesizing these advanced SELEX platforms and modifications, this review illuminates the dynamic progress in aptamer research and outlines the ongoing efforts to surmount existing challenges and enhance their clinical applicability, charting a path for future breakthroughs in this evolving field.

Screening biotoxin aptamer and their application of optical aptasensor in food stuff: a review.

Biotoxins are ranges of toxic substances produced by animals, plants, and microorganisms, which could contaminate foods during their production, processing, transportation, or storage, thus leading to foodborne illness, even food terrorism. Therefore, proposing simple, rapid, and effective detection methods for ensuring food free from biotoxin contamination shows a highly realistic demand. Aptamers are single-stranded oligonucleotides obtained from the systematic evolution of ligands by performing exponential enrichment (SELEX). They can specifically bind to wide ranges of targets with high affinity; thus, they have become important recognizing units in safety monitoring in food control and anti-terrorism. In this paper, we reviewed the technical points and difficulties of typical aptamer screening processes for biotoxins. For promoting the understanding of food control in the food supply chain, the latest progresses in rapid optical detection of biotoxins based on aptamers were summarized. In the end, we outlined some challenges and prospects in this field. We hope this paper could stimulate widespread interest in developing advanced sensing systems for ensuring food safety.

Monoclonal antibodies and aptamers: The future therapeutics for Alzheimer's disease.

Alzheimer's disease (AD) is considered the most common and prevalent form of dementia of adult-onset with characteristic progressive impairment in cognition and memory. The cure for AD has not been found yet and the treatments available until recently were only symptomatic. Regardless of multidisciplinary approaches and efforts made by pharmaceutical companies, it was only in the past two years that new drugs were approved for the treatment of the disease. Amyloid beta (Aß) immunotherapy is at the core of this therapy, which is one of the most innovative approaches looking to change the course of AD. This technology is based on synthetic peptides or monoclonal antibodies (mAb) to reduce Aß levels in the brain and slow down the advance of neurodegeneration. Hence, this article reviews the state of the art about AD neuropathogenesis, the traditional pharmacologic treatment, as well as the modern active and passive immunization describing approved drugs, and drug prototypes currently under investigation in different clinical trials. In addition, future perspectives on immunotherapeutic strategies for AD and the rise of the aptamer technology as a non-immunogenic alternative to curb the disease progression are discussed.

Aptamer-Functionalized Magnetic Ti3C2 Based Nanoplatform for Simultaneous Enrichment and Detection of Exosomes.

Exosomes are nanovesicles secreted by cells, which play a crucial role in various pathological processes. Exosomes have shown great promise as tumor biomarkers because of the abundant secretion during tumor formation. The development of a convenient, efficient, and cost-effective method for simultaneously enriching and detecting exosomes is of utmost importance for both basic research and clinical applications. In this study, an aptamer-functionalized magnetic Ti3C2 composite material (Fe3O4@Ti3C2@PEI@DSP@aptamer@FAM-ssDNA) is prepared for the simultaneous enrichment and detection of exosomes. CD63 aptamers are utilized to recognize and capture the exosomes, followed by magnetic separation. The exosomes are then released by cleaving the disulfide bonds of DSP. Compared to traditional methods, Fe3O4@Ti3C2@PEI@DSP@aptamer@FAM-ssDNA exhibited superior efficiency in enriching exosomes while preserving their structural and functional integrity. Detection of exosome concentration is achieved through the fluorescence quenching of Ti3C2 and the competitive binding between the exosomes and a fluorescently labeled probe. This method exhibited a low detection limit of 4.21 × 104 particles mL-1, a number that is comparable to the state-of-the-art method in the detection of exosomes. The present study demonstrates a method of simultaneous enrichment and detection of exosomes with a high sensitivity, accuracy, specificity, and cost-effectiveness providing significant potential for clinical research and diagnosis.

Unbiased plasma profiling using pre-selected RNA aptamer pools predicts mortality in COVID-19 and identifies protein risk factors.

The impact of the COVID-19 pandemic demands effective prognostic tools for precise risk evaluation and timely intervention. This study utilized the APTASHAPE technology to profile plasma proteins in COVID-19 patient samples. Employing a highly diverse 2'-fluoro-protected RNA aptamer pool enriched toward proteins in the plasma samples from COVID-19 patients, we performed a single round of parallel selection on the derivation cohort and identified 93 discriminatory aptamers capable of distinguishing COVID-19 and healthy plasma samples. A subset of these aptamers was then used to predict 30-day mortality with high sensitivity and specificity in a validation cohort of 165 patients. We predicted 30-day mortality with areas under the curve (AUCs) of 0.91 in females and 0.68 in males. Affinity purification coupled with mass spectrometry analysis of the aptamer-targeted proteins identified potential biomarkers associated with disease severity, including complement system components. The study demonstrates the APTASHAPE technology as an unbiased approach that not only aids in predicting disease outcomes but also offers insights into gender-specific differences, shedding light on the nuanced aspects of COVID-19 pathophysiology. In conclusion, the findings highlight the promise of APTASHAPE as a valuable tool for estimating risk factors in COVID-19 patients and enabling stratification for personalized treatment management.

A comprehensive review of the application of Zr-based metal-organic frameworks for electrochemical sensors and biosensors.

A family of inorganic-organic hybrid crystalline materials made up of organic ligands and metal cations or clusters is known as metal-organic frameworks (MOFs). Because of their unique stability, intriguing characteristics, and structural diversity, zirconium-based MOFs (Zr-MOFs) are regarded as one of the most interesting families of MOF materials for real-world applications. Zr-MOFs that have the ligands, metal nodes, and guest molecules enclosed show distinct electrochemical reactions. They can successfully and sensitively identify a wide range of substances, which is important for both environmental preservation and human health. The rational design and synthesis of Zr-MOF electrochemical sensors and biosensors, as well as their applications in the detection of drugs, biomarkers, pesticides, food additives, hydrogen peroxide, and other materials, are the main topics of this comprehensive review. We also touch on the current issues and potential future paths for Zr-MOF electrochemical sensor research.

From biogenesis to aptasensors: advancements in analysis for tumor-derived extracellular vesicles research.

Extracellular vesicles (EVs) are enclosed by a nanoscale phospholipid bilayer membrane and typically range in size from 30 to 200 nm. They contain a high concentration of specific proteins, nucleic acids, and lipids, reflecting but not identical to the composition of the parent cell. The inherent characteristics and variety of EVs give them extensive and unique advantages in the field of cancer identification and treatment. Recently, EVs have been recognized as potential tumor markers for the detection of cancer. Aptamers, which are molecules of single-stranded DNA or RNA, demonstrate remarkable specificity and affinity for their targets by adopting distinct tertiary structures. Aptamers offer various advantages over their protein counterparts, such as reduced immunogenicity, the ability for convenient large-scale synthesis, and straightforward chemical modification. In this review, we summarized EVs biogenesis, sample collection, isolation, storage and characterization, and finally provided a comprehensive survey of analysis techniques for EVs detection that are based on aptamers.

Topical application of a CCL22-binding aptamer suppresses contact allergy.

Allergic contact dermatitis is a prevalent occupational disease with limited therapeutic options. The chemokine CCL22, a ligand of the chemokine receptor CCR4, directs the migration of immune cells. Here, it is shown that genetic deficiency of CCL22 effectively ameliorated allergic reactions in contact hypersensitivity (CHS), a commonly used mouse model of allergic contact dermatitis. For the pharmacological inhibition of CCL22, DNA aptamers specific for murine CCL22 were generated by the systematic evolution of ligands by exponential enrichment (SELEX). Nine CCL22-binding aptamers were initially selected and functionally tested in vitro. The 29-nt DNA aptamer AJ102.29m profoundly inhibited CCL22-dependent T cell migration and did not elicit undesired Toll-like receptor-dependent immune activation. AJ102.29m efficiently ameliorated CHS in vivo after systemic application. Moreover, CHS-associated allergic symptoms were also reduced following topical application of the aptamer on the skin. Microscopic analysis of skin treated with AJ102.29m ex vivo demonstrated that the aptamer could penetrate into the epidermis and dermis. The finding that epicutaneous application of the aptamer AJ102.29m in a cream was as effective in suppressing the allergic reaction as intraperitoneal injection paves the way for therapeutic use of aptamers beyond the current routes of systemic administration.

START: A Versatile Platform for Bacterial Ligand Sensing with Programmable Performances.

Recognition of signaling molecules for coordinated regulation of target genes is a fundamental process for biological systems. Cells often rely on transcription factors to accomplish these intricate tasks, yet the subtle conformational changes of protein structures, coupled with the complexity of intertwined protein interaction networks, pose challenges for repurposing these for bioengineering applications. This study introduces a novel platform for ligand-responsive gene regulation, termed START (Synthetic Trans-Acting Riboswitch with Triggering RNA). Inspired by the bacterial ligand sensing system, riboswitch, and the synthetic gene regulator, toehold switch, the START platform enables the implementation of synthetic biosensors for various ligands. Rational sequence design with targeted domain optimization yields high-performance STARTs with a dynamic range up to 67.29-fold and a tunable ligand sensitivity, providing a simple and intuitive strategy for sensor engineering. The START platform also exhibits modularity and composability to allow flexible genetic circuit construction, enabling seamless implementation of OR, AND, and NOT Boolean logic gates for multiple ligand inputs. The START design principle is capable of broadening the suite of synthetic biosensors for diverse chemical and protein ligands, providing a novel riboregulator chassis for synthetic biology and bioengineering applications.

Empowering Exosomes with Aptamers for Precision Theranostics.

As information messengers for cell-to-cell communication, exosomes, typically small membrane vesicles (30-150 nm), play an imperative role in the physiological and pathological processes of living systems. Accumulating studies have demonstrated that exosomes are potential biological candidates for theranostics, including liquid biopsy-based diagnosis and drug delivery. However, their clinical applications are hindered by several issues, especially their unspecific detection and insufficient targeting ability. How to upgrade the accuracy of exosome-based theranostics is being widely explored. Aptamers, benefitting from their admirable characteristics, are used as excellent molecular recognition elements to empower exosomes for precision theranostics. With high affinity against targets and easy site-specific modification, aptamers can be incorporated with platforms for the specific detection of exosomes, thus providing opportunities for advancing disease diagnostics. Furthermore, aptamers can be tailored and functionalized on exosomes to enable targeted therapeutics. Herein, this review emphasizes the empowering of exosomes by aptamers for precision theranostics. A brief introduction of exosomes and aptamers is provided, followed by a discussion of recent progress in aptamer-based exosome detection for disease diagnosis, and the emerging applications of aptamer-functionalized exosomes for targeted therapeutics. Finally, current challenges and opportunities in this research field are presented.

Multiplexed and Quantitative Imaging of Live-Cell Membrane Proteins by a Precise and Controllable DNA-Encoded Amplification Reaction.

Amplifying DNA conjugated affinity ligands can improve the sensitivity and multiplicity of cell imaging and play a crucial role in comprehensively deciphering cellular heterogeneity and dynamic changes during development and disease. However, the development of one-step, controllable, and quantitative DNA amplification methods for multiplexed imaging of live-cell membrane proteins is challenging. Here, we introduce the template adhesion reaction (TAR) method for assembling amplifiable DNA sequences with different affinity ligands, such as aptamers or antibodies, for amplified and multiplexed imaging of live-cell membrane proteins with high quantitative fidelity. The precisely controllable TAR enables proportional amplification of membrane protein targets with variable abundances by modulating the concentration ratios of hairpin templates and primers, thus allowing sensitive visualization of multiple membrane proteins with enhanced signal-to-noise ratios (SNRs) without disturbing their original ratios. Using TAR, we achieved signal-enhanced imaging of six proteins on the same live-cell within 1-2 h. TAR represents an innovative and programmable molecular toolkit for multiplexed profiling of membrane proteins in live-cells.

Aptamers: ushering in new hopes in targeted glioblastoma therapy.

Glioblastoma, a formidable brain cancer, has remained a therapeutic challenge due to its aggressive nature and resistance to conventional treatments. Recent data indicate that aptamers, short synthetic DNA or RNA molecules can be used in anti-cancer therapy due to their better tumour penetration, specific binding affinity, longer retention in tumour sites and their ability to cross the blood-brain barrier. With the ability to modify these oligonucleotides through the selection process, and using rational design to modify them, post-SELEX aptamers offer several advantages in glioblastoma treatment, including precise targeting of cancer cells while sparing healthy tissue. This review discusses the pivotal role of aptamers in glioblastoma therapy and diagnosis, emphasising their potential to enhance treatment efficacy and also highlights recent advancements in aptamer-based therapies which can transform the landscape of glioblastoma treatment, offering renewed hope to patients and clinicians alike.

Single-Molecule RNA Imaging in Live Cells with an Avidity-Based Fluorescent Light-Up Aptamer biRhoBAST.

Observing individual RNA molecules provides valuable insights into their regulation, interactions with other cellular components, organization, and functions. Although fluorescent light-up aptamers (FLAPs) have recently shown promise for RNA imaging, their wider applications have been mostly hindered by poor brightness and photostability. We recently developed an avidity-based FLAP known as biRhoBAST that allows for single-molecule RNA imaging in live or fixed cells and tracking individual mRNA molecules in living cells due to its excellent photostability and high brightness. Here, we present step-by-step detailed protocols starting from cloning biRhoBAST repeats into the target RNA sequence, to imaging dynamics of single mRNA molecules. Additionally, we address the validation of single-molecule imaging experiments through single-molecule fluorescence in situ hybridization (smFISH) and colocalization studies.

Nanobiosensors based on on-site detection approaches for rapid pesticide sensing in the agricultural arena: A systematic review of the current status and perspectives.

The extensive use of chemical pesticides has significantly boosted agricultural food crop yields. Nevertheless, their excessive and unregulated application has resulted in food contamination and pollution in environmental, aquatic, and agricultural ecosystems. Consequently, the on-site monitoring of pesticide residues in agricultural practices is paramount to safeguard global food and conservational safety. Traditional pesticide detection methods are cumbersome and ill-suited for on-site pesticide finding. The systematic review provides an in-depth analysis of the current status and perspectives of nanobiosensors (NBS) for pesticide detection in the agricultural arena. Furthermore, the study encompasses the fundamental principles of NBS, the various transduction mechanisms employed, and their incorporation into on-site detection platforms. Conversely, the assortment of transduction mechanisms, including optical, electrochemical, and piezoelectric tactics, is deliberated in detail, emphasizing its advantages and limitations in pesticide perception. Incorporating NBS into on-site detection platforms confirms a vital feature of their pertinence. The evaluation reflects the integration of NBS into lab-on-a-chip systems, handheld devices, and wireless sensor networks, permitting real-time monitoring and data-driven decision-making in agronomic settings. The potential for robotics and automation in pesticide detection is also scrutinized, highlighting their role in improving competence and accuracy. Finally, this systematic review provides a complete understanding of the current landscape of NBS for on-site pesticide sensing. Consequently, we anticipate that this review offers valuable insights that could form the foundation for creating innovative NBS applicable in various fields such as materials science, nanoscience, food technology and environmental science.

Biosensors for Detection of Hepatitis B Virus: Review.

Hepatitis B is still one of the most important infectious diseases among humans, which is considered a serious threat to their lives. Early diagnosis of this disease can be an effective measure in stopping the chain of transmission and treatment of the disease. In this review study, an attempt has been made to explain the use of biosensors as a fast, high-efficiency, and low-cost method in diagnosis. The biosensors prepared for hepatitis detection included DNA-based, aptamers-based, protein-based, enzyme-based, antibody-based, and polymers-based biosensors, each of which had different advantages. The results of this review showed that almost all introduced biosensors had an acceptable performance. However, we suggest that aptamers are desirable for biosensing applications because they can change their structure to properly bind to their target, are cost-effective to prepare, and are highly sensitive.

Novel approaches for bacterial toxin neutralization; current advances and future perspectives.

This review outlines diverse strategies for neutralizing bacterial toxins which are a significant threat to human health. Effective toxin neutralization is crucial in preventing and treating bacterial infections, especially those caused by antibiotic-resistant strains. Promising approaches include using monoclonal antibodies that target toxins and combining them with agents that directly target bacteria. Aptamers, synthetic molecules that bind to specific targets, provide a rapid and tailored method for inhibiting toxin activity and detecting pathogens. Cell membrane-coated nanoparticles mimic host cells and effectively neutralize toxins by diverting them and stimulating immune responses. These advancements have the potential to combat bacterial infections and alleviate the associated public health burden.

Therapeutic Applications of Aptamers.

Affinity reagents, or target-binding molecules, are quite versatile and are major workhorses in molecular biology and medicine. Antibodies are the most famous and frequently used type and they have been used for a wide range of applications, including laboratory techniques, diagnostics, and therapeutics. However, antibodies are not the only available affinity reagents and they do have significant drawbacks, including laborious and costly production. Aptamers are one potential alternative that have a variety of unique advantages. They are single stranded DNA or RNA molecules that can be selected for binding to many targets including proteins, carbohydrates, and small molecules-for which antibodies typically have low affinity. There are also a variety of cost-effective methods for producing and modifying nucleic acids in vitro without cells, whereas antibodies typically require cells or even whole animals. While there are also significant drawbacks to using aptamers in therapeutic applications, including low in vivo stability, aptamers have had success in clinical trials for treating a variety of diseases and two aptamer-based drugs have gained FDA approval. Aptamer development is still ongoing, which could lead to additional applications of aptamer therapeutics, including antitoxins, and combinatorial approaches with nanoparticles and other nucleic acid therapeutics that could improve efficacy.