Updates on Aptamer Research

Nervous necrosis virus induced vacuolization is a Rab5- and actin-dependent process

Cytoplasmic vacuolization is commonly induced by bacteria and viruses, reflecting the complex interactions between pathogens and the host. However, their characteristics and formation remain unclear. Nervous necrosis virus (NNV) infects more than 100 global fish species, causing enormous economic losses. Vacuolization is a hallmark of NNV infection in host cells, but remains a mystery. In this study, we developed a simple aptamer labelling technique to identify red-spotted grouper NNV (RGNNV) particles in fixed and live cells to explore RGNNV-induced vacuolization. We observed that RGNNV-induced vacuolization was positively associated with the infection time and virus uptake. During infection, most RGNNV particles, as well as viral genes, colocalized with vacuoles, but not giant vacuoles > 3 μm in diameter. Although the capsid protein (CP) is the only structural protein of RGNNV, its overexpression did not induce vacuolization, suggesting that vacuole formation probably requires virus entry and replication. Given that small Rab proteins and the cytoskeleton are key factors in regulating cellular vesicles, we further investigated their roles in RGNNV-induced vacuolization. Using live cell imaging, Rab5, a marker of early endosomes, was continuously located in vacuoles bearing RGNNV during giant vacuole formation. Rab5 is required for vacuole formation and interacts with CP according to siRNA interference and Co-IP analysis. Furthermore, actin formed distinct rings around small vacuoles, while vacuoles were located near microtubules. Actin, but not microtubules, plays an important role in vacuole formation using chemical inhibitors. These results provide valuable insights into the pathogenesis and control of RGNNV infections.

Investigation of the Affinity of Aptamers for Bacteria by Surface Plasmon Resonance Imaging Using Nanosomes

The cell-SELEX method enables efficient selection of aptamers that bind whole bacterial cells. However, after selection, it is difficult to determine their binding affinities using common screening methods because of the large size of the bacteria. Here we propose a simple surface plasmon resonance imaging method (SPRi) for aptamer characterization using bacterial membrane vesicles, called nanosomes, instead of whole cells. Nanosomes were obtained from membrane fragments after mechanical cell disruption in order to preserve the external surface epitopes of the bacterium used for their production. The study was conducted on Bacillus cereus (B. cereus), a Gram-positive bacterium commonly found in soil, rice, vegetables, and dairy products. Four aptamers and one negative control were initially grafted onto a biochip. The binding of B. cereus cells and nanosomes to immobilized aptamers was then compared. The use of nanosomes instead of cells provided a 30-fold amplification of the SPRi signal, thus allowing the selection of aptamers with higher affinities. Aptamer SP15 was found to be the most sensitive and selective for B. cereus ATCC14579 nanosomes. It was then truncated into three new sequences (SP15M, SP15S1, and SP15S2) to reduce its size while preserving the binding site. Fitting the results of the SPRi signal for B. cereus nanosomes showed a similar trend for SP15 and SP15M, and a slightly higher apparent association rate constant kon for SP15S2, which is the truncation with a high probability of a G-quadruplex structure. These observations were confirmed on nanosomes from B. cereus ATCC14579 grown in milk and from the clinical strain B. cereus J066. The developed method was validated using fluorescence microscopy on whole B. cereus cells and the SP15M aptamer labeled with a rhodamine. This study showed that nanosomes can successfully mimic the bacterial membrane with great potential for facilitating the screening of specific ligands for bacteria.

Aptamer-Drug conjugates for a targeted and synergistic anticancer Response: Exploiting T30923-5-fluoro-2'-deoxyuridine (INT-FdU) derivatives

One of the most appealing approaches for cancer treatment is targeted therapy, which is based on the use of drugs able to target cancer cells without affecting normal ones. This strategy lets to overcome the major limitation of conventional chemotherapy, namely the lack of specificity of anticancer drugs, which often leads to severe side effects, decreasing the therapy effectiveness. Delivery of cell-killing substances to tumor cells is one-way targeted drug therapy can work. Generally, monoclonal antibodies are combined with chemotherapeutic drugs, allowing cellular uptake through the binding to their targets on the surface of cancer cells. Aptamer-drug conjugates represent a promising alternative solution to antibodies to minimize off-target effects, considering the remarkable selective binding capabilities of aptamers. In this study, to enhance the therapeutic efficacy of the antineoplastic agent 5-fluoro-2'-deoxyuridine (FdU) in various cancer cells, we focused on the development of a novel conjugate using the antiproliferative aptamer T30923 (INT) as a drug vehicle. Three derivatives composed of T30923 conjugated with a different number of FdU units were synthesized, and their structural and biological properties were thoroughly characterized, highlighting their potential for targeted and synergistic anticancer responses.

Aptamers and Nanobodies as New Bioprobes for SARS-CoV-2 Diagnostic and Therapeutic System Applications

The global challenges posed by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) pandemic have underscored the critical importance of innovative and efficient control systems for addressing future pandemics. The most effective way to control the pandemic is to rapidly suppress the spread of the virus through early detection using a rapid, accurate, and easy-to-use diagnostic platform. In biosensors that use bioprobes, the binding affinity of molecular recognition elements (MREs) is the primary factor determining the dynamic range of the sensing platform. Furthermore, the sensitivity relies mainly on bioprobe quality with sufficient functionality. This comprehensive review investigates aptamers and nanobodies recently developed as advanced MREs for SARS-CoV-2 diagnostic and therapeutic applications. These bioprobes might be integrated into organic bioelectronic materials and devices, with promising enhanced sensitivity and specificity. This review offers valuable insights into advancing biosensing technologies for infectious disease diagnosis and treatment using aptamers and nanobodies as new bioprobes.

Surface modification of lipid nanoparticles for gene therapy

Gene therapies have the potential to target and effectively treat a variety of diseases including cancer as well as genetic, neurological, and autoimmune disorders. Although we have made significant advances in identifying non-viral strategies to deliver genetic cargo, certain limitations remain. In general, gene delivery is challenging for several reasons including the instabilities of nucleic acids to enzymatic and chemical degradation and the presence of restrictive biological barriers such as cell, endosomal and nuclear membranes. The emergence of lipid nanoparticles (LNPs) helped overcome many of these challenges. Despite its success, further optimization is required for LNPs to yield efficient gene delivery to extrahepatic tissues, as LNPs favor accumulation in the liver after systemic administration. In this mini-review, we provide an overview of current preclinical approaches in that LNP surface modification was leveraged for cell and tissue targeting by conjugating aptamers, antibodies, and peptides among others. In addition to their cell uptake and efficiency-enhancing effects, we outline the (dis-)advantages of the different targeting moieties and commonly used conjugation strategies.

A dual action electrochemical molecularly imprinted aptasensor for ultra-trace detection of carbendazim

Carbendazim is often used in agriculture to prevent crop diseases, even though it has been associated with health concerns. To ensure the safety of food products and comply with environmental regulations, an ultrasensitive method for carbendazim determination must be developed. In this study, a new electrochemical molecularly imprinted polymer-aptasensor based on hemin-Al-metal organic framework@gold nanoparticles (H-Al-MOF@AuNPs) was developed for sensitive and selective carbendazim detection. Hemin linked to the surface of the Al-metal organic framework also possesses outstanding peroxidase-like qualities that can electrocatalyse the reduction of H2O2. Thus, H-Al-MOF functions as an in-situ probe. Additionally, AuNPs offer many binding sites to load carbendazim aptamers and create an imprinted polymer-aptasensing interface. Dopamine is the chemical functional monomer in the electropolymerised film, while carbendazim is the template molecule. Thus, compared to the molecularly imprinted polymer or aptasensor alone, the molecularly imprinted polymer-aptasensor showed greater selectivity due to the synergistic action of the polymer and carbendazim aptamer towards carbendazim. A decrease in peak current was observed by differential pulse voltammetry (DPV) and chronoamperometry (CA) as the concentration of carbendazim increased. This possibly resulted from carbendazim connecting to the carbendazim aptamer and simultaneously blocking the imprinted polymer cavities on the surface of the modified electrode, which reduced the transfer of electrons. Signals were observed for hemin DPV and H2O2 catalytic reduction CA. DPV and CA showed that the linear ranges for carbendazim were 0.3 fmol L-1-10 pmol L-1 and 0.7 fmol L-1-10 pmol L-1, respectively, with limits of detection of 80 and 300 amol L-1. Satisfactory recoveries were obtained with tap water, apple juice, and tomato juice samples, demonstrating that the proposed sensor has potential for food and environmental analysis.

Nucleic Acid Aptamer-Based Biosensors: A Review

Aptamers, short strands of either DNA, RNA, or peptides, known for their exceptional specificity and high binding affinity to target molecules, are providing significant advancements in the field of health. When seamlessly integrated into biosensor platforms, aptamers give rise to aptasensors, unlocking a new dimension in point-of-care diagnostics with rapid response times and remarkable versatility. As such, this review aims to present an overview of the distinct advantages conferred by aptamers over traditional antibodies as the molecular recognition element in biosensors. Additionally, it delves into the realm of specific aptamers made for the detection of biomarkers associated with infectious diseases, cancer, cardiovascular diseases, and metabolomic and neurological disorders. The review further elucidates the varying binding assays and transducer techniques that support the development of aptasensors. Ultimately, this review discusses the current state of point-of-care diagnostics facilitated by aptasensors and underscores the immense potential of these technologies in advancing the landscape of healthcare delivery.

Advantages of Material Biofunctionalization Using Nucleic Acid Aptamers in Tissue Engineering and Regenerative Medicine

Material engineering is a fundamental issue in the applications of materials in the medical field. One of the aspects of material engineering is incorporating recognition sites on the surface of biomaterials, which plays an essential role in increasing the efficiency of tissue engineering scaffolds in various aspects. The application of peptides and antibodies to establish the recognition and adhesion sites has limitations, such as fragility and instability under physical and chemical processes. Therefore, synthetic ligands such as nucleic acid aptamers have received much attention for easy synthesis, minimal immunogenicity, high specificity, and stability under processing. Due to the effective role of these ligands in increasing the efficiency of engineered constructs in this study, the advantages of nucleic acid aptamers in tissue engineering will be reviewed. Aptamer-functionalized biomaterials can attract endogenous stem cells to wounded areas and organize their actions to facilitate tissue regeneration. This approach harnesses the body's inherent regeneration potential to treat many diseases. Also, increased efficacy in controlled release, slow and targeted drug delivery are important issues in drug delivery for tissue engineering approaches which can be achieved by incorporating aptamers in drug delivery systems. Aptamer-functionalized scaffolds have very applications, such as diagnosis of cancer, hematological infections, narcotics, heavy metals, toxins, controlled release from the scaffolds, and in vivo cell tracing. Aptasensors, as a result of many advantages over other traditional assay methods, can replace older methods. Furthermore, their unique targeting mechanism also targets compounds with no particular receptors. Targeting cell homing, local and targeted drug delivery, cell adhesion efficacy, cytocompatibility and bioactivity of scaffolds, aptamer-based biosensor, and aptamer-functionalized scaffolds are the topics that will be examined in this review study.

Does COVID-19 Trigger the Risk for the Development of Parkinson's Disease? Therapeutic Potential of Vitamin C

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) causes coronavirus disease 2019 (COVID-19), which was proclaimed a pandemic by the World Health Organization (WHO) in March 2020. There is mounting evidence that older patients with multimorbidity are more susceptible to COVID-19 complications than are younger, healthy people. Having neuroinvasive potential, SARS-CoV-2 infection may increase susceptibility toward the development of Parkinson's disease (PD), a progressive neurodegenerative disorder with extensive motor deficits. PD is characterized by the aggregation of α-synuclein in the form of Lewy bodies and the loss of dopaminergic neurons in the dorsal striatum and substantia nigra pars compacta (SNpc) of the nigrostriatal pathway in the brain. Increasing reports suggest that SARS-CoV-2 infection is linked with the worsening of motor and non-motor symptoms with high rates of hospitalization and mortality in PD patients. Common pathological changes in both diseases involve oxidative stress, mitochondrial dysfunction, neuroinflammation, and neurodegeneration. COVID-19 exacerbates the damage ensuing from the dysregulation of those processes, furthering neurological complications, and increasing the severity of PD symptomatology. Phytochemicals have antioxidant, anti-inflammatory, and anti-apoptotic properties. Vitamin C supplementation is found to ameliorate the common pathological changes in both diseases to some extent. This review aims to present the available evidence on the association between COVID-19 and PD, and discusses the therapeutic potential of vitamin C for its better management.

Investigation of Performance Parameters of Spherical Gold Nanoparticles in Localized Surface Plasmon Resonance Biosensing

In this paper, we present numerical and experimental results on Localized Surface Plasmon Resonance (LSPR) refractive index (RI) sensitivity, Figure of Merit (FoM), and penetration depth (dp) dependence on spherical gold nanoparticles (AuNPs) size, and the effects of AuNP dimer interparticle distance (ds) studied numerically. These parameters were calculated and observed for d = 20, 40, 60, 80, and 100 nm diameter spherical AuNPs. Our investigation shows d = 60 nm AuNPs give the best FoM. The AuNP dimer interparticle distance can significantly influence the RI sensitivity. Therefore, the effect of distances between pairs of d = 20 nm and 60 nm AuNPs is shown. We discuss the importance of penetration depth information for AuNPs functionalized with aptamers for biosensing in the context of aptamer size.

Ionic liquids functionalized Fe3O4-based colorimetric biosensor for rapid determination of ochratoxin A

A stainless steel mesh (SSM) with the feature of flexibility was employed as the colorimetric biosensor substrate, and aptamer was bond onto the surface of the SSM. Through the cross-linking of ionic liquids (ILs), AuPt nanoparticles were deposited  onto the surface of Fe3O4 material to obtain a magnetic nanozyme with high peroxidase catalytic activity and rapid color change. Through the competing interaction of OTA and cDNA with aptamer, AuPt@IL@Fe3O4 signal probe was separated to catalyze the 3,3',5,5'-tetramethylbenzidine/hydrogen peroxide (TMB/H2O2) system to observe the color by bare eye and record the absorbance at 652 nm using a UV-spectrophotometer. Through the study of the catalytic properties on the basis of the Michaelis equation, AuPt@IL@Fe3O4 nanozyme presented a Vmax of 3.85 × 10-8 M s-1 and Km of 0.01 mM. Under the optimized conditions, the linear range of the colorimetric biosensor towards OTA was 5-100 ng mL-1, and the detection limit was 0.078 ng mL-1. This biosensor was applied to beer and corn samples with recoveries of 70.4-102.6% and 93.3-104.7%, respectively. Results showed that this sensor is a portable, rapid, economical, sensitive visual sensing platform towards mycotoxin in real samples.

The assessment of molecular dynamics results of three-dimensional RNA aptamer structure prediction

Aptamers are single-stranded DNA or RNA that bind to specific targets such as proteins, thus having similar characteristics to antibodies. It can be synthesized at a lower cost, with no batch-to-batch variations, and is easier to modify chemically than antibodies, thus potentially being used as therapeutic and biosensing agents. The current method for RNA aptamer identification in vitro uses the SELEX method, which is considered inefficient due to its complex process. Computational models of aptamers have been used to predict and study the molecular interaction of modified aptamers to improve affinity. In this study, we generated three-dimensional models of five RNA aptamers from their sequence using mFold, RNAComposer web server, and molecular dynamics simulation. The model structures were then evaluated and compared with the experimentally determined structures. This study showed that the combination of mFold, RNAComposer, and molecular dynamics simulation could generate 14-16, 28, or 29 nucleotides length of 3D RNA aptamer with similar geometry and topology to the experimentally determined structures. The non-canonical basepair structure of the aptamer loop was formed through the MD simulation, which also improved the three-dimensional RNA aptamers model. Clustering analysis was recommended to choose the more representative model.

In Situ Monitoring of Aptamer-Protein Binding on a ZnO Surface Using Spectroscopic Ellipsometry

The dissolution of zinc oxide is investigated using spectroscopic ellipsometry to investigate its suitability as a platform for biosensing applications. The results indicate that once the ZnO surface has been functionalised, it is suitably protected, and no significant dissolving of the ZnO occurs. The binding kinetics of the SARS-CoV-2 spike protein on aptamer-functionalised zinc oxide surfaces are subsequently investigated. Values are extracted for the refractive index and associated optical constants for both the aptamer layer used and the protein itself. It is shown that upon an initial exposure to the protein, a rapid fluctuation in the surface density is observed. After around 20 min, this effect stabilises, and a fixed increase in the surface density is observed, which itself increases as the concentration of the protein is increased. This technique and setup are demonstrated to have a limit-of-detection down to 1 nanomole (nM) and display a linear response to concentrations up to 100 nM.

Spatial Control of Receptor Dimerization Using Programmable DNA Nanobridge

Receptor dimerization is an essential mechanism for the activation of most receptor tyrosine kinases by ligands. Thus, regulating the nanoscale spatial distribution of cell surface receptors is significant for studying both intracellular signaling pathways and cellular behavior. However, there are currently very limited methods for exploring the effects of modulating the spatial distribution of receptors on their function by using simple tools. Herein, we developed an aptamer-based double-stranded DNA bridge acting as "DNA nanobridge", which regulates receptor dimerization by changing the number of bases. On this basis, we confirmed that the different nanoscale arrangements of the receptor can influence receptor function and its downstream signals. Among them, the effect gradually changed from helping to activate to inhibiting as the length of DNA nanobridge increased. Hence, it can not only effectively inhibit receptor function and thus affect cellular behavior but also serve as a fine-tuning tool to get the desired signal activity. Our strategy is promising to provide insight into the action of receptors in cell biology from the perspective of spatial distribution.

Staphylococcus aureus Detection in Milk Using a Thickness Shear Mode Acoustic Aptasensor with an Antifouling Probe Linker

Contamination of food by pathogens can pose a serious risk to health. Therefore, monitoring for the presence of pathogens is critical to identify and regulate microbiological contamination of food. In this work, an aptasensor based on a thickness shear mode acoustic method (TSM) with dissipation monitoring was developed to detect and quantify Staphylococcus aureus directly in whole UHT cow's milk. The frequency variation and dissipation data demonstrated the correct immobilization of the components. The analysis of viscoelastic properties suggests that DNA aptamers bind to the surface in a non-dense manner, which favors the binding with bacteria. The aptasensor demonstrated high sensitivity and was able to detect S. aureus in milk with a 33 CFU/mL limit of detection. Analysis was successful in milk due to the sensor's antifouling properties, which is based on 3-dithiothreitol propanoic acid (DTT_COOH) antifouling thiol linker. Compared to bare and modified (dithiothreitol (DTT), 11-mercaptoundecanoic acid (MUA), and 1-undecanethiol (UDT)) quartz crystals, the sensitivity of the sensor's antifouling in milk improved by about 82-96%. The excellent sensitivity and ability to detect and quantify S. aureus in whole UHT cow's milk demonstrates that the system is applicable for rapid and efficient analysis of milk safety.

Determination of chloramphenicol in food using nanomaterial-based electrochemical and optical sensors-A review

Chloramphenicol (CAP) is a widely used antibiotic for the treatment of sick animals owing to its potent action and low cost. However, the accumulation of CAP in the human body can cause irreversible aplastic anemia and hematopoietic toxicity. Accordingly, development of various analytical techniques for the rapid detection of CAP in animal products and the related processed foods is necessary. Among these analytical techniques, electrochemical and optical sensors offer many advantages for CAP detection, including high sensitivity, simple operation and fast analysis speed. In this review, we summarize recent application of carbon nanomaterials, metal nanoparticles, metal oxide nanoparticles and metal organic framework in the development of electrochemical and optical sensors for CAP detection (2010-2022). Based on the advantages and disadvantages of nanomaterials, electrochemical and optical sensors are summarized in this review. The preparation and synthesis of electrochemical and optical sensors and nanomaterials in the field of rapid detection are prospected.

Screening, characterization and specific binding mechanism of aptamers against human plasminogen Kringle 5

Plasminogen Kringle 5 is one of the most potent cytokines identified to inhibit the proliferation and migration of vascular endothelial cells. Herein, six aptamer candidates that specifically bind to Kringle 5 were generated by the systematic evolution of ligands by exponential enrichment (SELEX). After 10 rounds of screening against Kringle 5, a highly enriched ssDNA pool was sequenced and the representative aptamers were subjected to binding assays to evaluate their affinity and specificity. The preferred aptamer KG-4, which demonstrated a low dissociation constant (K_d) of ∼ 432 nM and excellent selectivity for Kringle 5. A conserved "motif" of eight bases located at the stem-loop intersection, common to the aptamer, was further confirmed as the recognition element for binding with Kringle 5. The bulge formed by the motif and depression on the lysine binding site of Kringle 5 were both located at the binding interface, and the "induced fit" between their structures played a central role in the recognition process. Kringle 5 interacts KG-4 primarily through enthalpy-driven van der Waals forces and hydrogen bond. The key nucleotides A34 and C35 at motif on KG-4 and the positively charged amino acids in the loop 1 and loop 4 regions on Kringle 5 play a major role in the interaction. Furthermore, KG-4 dose-dependently reduced the proliferation inhibition of vascular endothelial cells by Kringle 5 and had a blocking effect on the function of Kringle 5 in inhibiting migration and promoting apoptosis of vascular endothelial cells in vitro. This study put a new light on protein-aptamer binding mechanism and may provide insight into the treatment of ischemic diseases by target depletion of Kringle 5.

Aptamer-based Advances in Skin Cancer Research

Cancer diseases have been one of the biggest health threats for the last two decades. Approximately 9% of all diagnosed cancers are skin cancers, including melanoma and non-melanoma. In all cancer cases, early diagnosis is essential to achieve efficient treatment. New solutions and advanced techniques for rapid diagnosis are constantly being sought. Aptamers are single-stranded RNA or DNA synthetic sequences or peptides, which offer novel possibilities to this area of research by specifically binding selected molecules, the so-called cancer biomarkers. Nowadays, they are widely used as diagnostic probes in imaging and targeted therapy. In this review, we have summarized the recently made advances in diagnostics and treatment of skin cancers, which have been achieved by combining aptamers with basic or modern technologies.

Electrochemical Aptasensing for Lifestyle and Chronic Disease Management

Over the past decade, researchers have investigated electrochemical sensing for the purpose of fabricating wearable point-of-use platforms. These wearable platforms have the ability to non-invasively track biomarkers that are clinically relevant and provide a comprehensive evaluation of the user's health. Due to many significant operational advantages, aptamer-based sensing is gaining traction.Aptamer-based sensors have properties like long-term stability, resistance to denaturation, and high sensitivity. Using electrochemical sensing with aptamer-based biorecognition is advantageous because it provides significant benefits like lower detection limits, a wider range of operations, and, most importantly, the ability to detect using a label-free approach. This paper provides an outlook into the current state of electrochemical aptasensing. This review looks into the significance of the detection of biomarkers like glucose, cortisol etc., for the purpose of lifestyle and chronic disease monitoring. Moreover, this review will also provide a comprehensive evaluation of the current challenges and prospects in this field.

Aptamer-Based Tumor-Targeted Diagnosis and Drug Delivery

Early cancer identification is crucial for providing patients with safe and timely therapy. Highly dependable and adaptive technologies will be required to detect the presence of biological markers for cancer at very low levels in the early stages of tumor formation. These techniques have been shown to be beneficial in encouraging patients to develop early intervention plans, which could lead to an increase in the overall survival rate of cancer patients. Targeted drug delivery (TDD) using aptamer is promising due to its favorable properties. Aptamer is suitable for superior TDD system candidates due to its desirable properties including a high binding affinity and specificity, a low immunogenicity, and a chemical composition that can be simply changed.Due to these properties, aptamer-based TDD application has limited drug side effect along with organ damages. The development of aptasensor has been promising in TDD for cancer cell treatment. There are biomarkers and expressed molecules during cancer cell development; however, only few are addressed in aptamer detection study of those molecules. Its great potential of attachment of binding to specific target molecule made aptamer a reliable recognition element. Because of their unique physical, chemical, and biological features, aptamers have a lot of potential in cancer precision medicine.In this review, we summarized aptamer technology and its application in cancer. This includes advantages properties of aptamer technology over other molecules were thoroughly discussed. In addition, we have also elaborated the application of aptamer as a direct therapeutic function and as a targeted drug delivery molecule (aptasensor) in cancer cells with several examples in preclinical and clinical trials.

Anti-nucleolin Aptamer as a Boom in Rehabilitation of Breast Cancer

Breast cancer is the second leading cause of cancer-related deaths. It is important to target the complex pathways using a suitable targeted delivery system. Targeted delivery systems can effectively act on cancer cells and lead to the annihilation of tumor proliferation. They mainly employ targeting agents like aptamers linked to the formulation. Based on the expression of the receptors on the surface of the cancer cells, suitable aptamers can be developed. AS1411 is one such aptamer that has the ability to bind to the over-expressed nucleolin present in breast cancer cells. Nucleolin is a phosphoprotein that is involved in various aspects, like cell growth, differentiation and survival. Mostly they are found in the nucleolus, nucleus, cytoplasm and cell surface. The shuttling effect of the nucleolin between the nucleus and cytoplasm serves as a bonus for the AS1411 aptamer. Because of the shutting effect, the internalization of the drug compound or chemotherapeutic drug inside the cell can be achieved. In this article, we have discussed nucleolin, anti-nucleolin aptamer, namely, AS1411, and its application in exhibiting various anticancer activities, including apoptosis, anti-angiogenesis, anti-metastasis, stimulation of tumor suppressor (i.e., P53), and inhibition of tumor inducer. Further, the ways of internalization, namely macropinocytosis, are also discussed. Additionally, we have also discussed the superiority of the aptamer compared to the antibodies as well as the limitations of the aptamers. By considering all the above parameters, we hope this aptamer will be effective in the management and eradication of breast cancer cells.

Quartz Crystal Microbalance-Based Aptasensors for Medical Diagnosis

Aptamers are important materials for the specific determination of different disease-related biomarkers. Several methods have been enhanced to transform selected target molecule-specific aptamer bindings into measurable signals. A number of specific aptamer-based biosensors have been designed for potential applications in clinical diagnostics. Various methods in combination with a wide variety of nano-scale materials have been employed to develop aptamer-based biosensors to further increase sensitivity and detection limit for related target molecules. In this critical review, we highlight the advantages of aptamers as biorecognition elements in biosensors for target biomolecules. In recent years, it has been demonstrated that electrode material plays an important role in obtaining quick, label-free, simple, stable, and sensitive detection in biological analysis using piezoelectric devices. For this reason, we review the recent progress in growth of aptamer-based QCM biosensors for medical diagnoses, including virus, bacteria, cell, protein, and disease biomarker detection.

Luminescence Nanomaterials for Biosensing Applications

Due to their capabilities of immobilizing more bioreceptor parts with reduced volumes, nanomaterials have emerged as potential tools for increasing sensitivity to specific molecules. Furthermore, carbon nanotube, gold nanoparticles, polymer nanoparticles, semiconductor quantum dots, graphene, nano-diamonds and graphene are among the nanomaterials that are under investigation. Due to the fast development of such a field of research, review summarises the classification of biosensors using main receptors, and designing biosensors. Numerous studies have concentrated on the manipulation of Persistent luminescence nanoparticles (PLNPs) in biosensing, cell tracking, bioimaging, and cancer therapy due to the effective removal of the autofluorescence interferences from tissues and the ultra-long near-infrared afterglow emission. As luminescence has a unique optical property, it can be detected without constant external illumination, preventing autofluorescence and light dispersion through tissues. These successes sparked an increasing curiosity in creating novel PLNP kinds with desired superior properties and multiple purposes. In this review, we emphasize the most recent developments in biosensing, imaging, and image-guided therapy while summarizing the research on synthesis methods, bio applications, bio membrane modification and bio-safety of PLNPs. Finally, the remaining issues and difficulties are examined together with prospective future developments in the field of biomedical applications.

Future perspectives on aptamer for application in food authentication

Food fraudulence and food contamination are major concerns, particularly among consumers with specific dietary, cultural, lifestyle, and religious requirements. Current food authentication methods have several drawbacks and limitations, necessitating the development of a simpler, more sensitive, and rapid detection approach for food screening analysis, such as an aptamer-based biosensor system. Although the use of aptamer is growing in various fields, aptamer applications for food authentication are still lacking. In this review, we discuss the limitations of existing food authentication technologies and describe the applications of aptamer in food analyses. We also project several potential targets or marker molecules to be targeted in the SELEX process. Finally, this review highlights the drawbacks of current aptamer technologies and outlines the potential route of aptamer selection and applications for successful food authentication. This review provides an overview of the use of aptamer in food research and its potential application as a molecular reporter for rapid detection in food authentication process. Developing databases to store all biochemical profiles of food and applying machine learning algorithms against the biochemical profiles are urged to accelerate the identification of more reliable biomarker molecules as aptamer targets for food authentication.

Exploring the Utility of ssDNA Aptamers Directed against Snake Venom Toxins as New Therapeutics for Snakebite Envenoming

Snakebite is a neglected tropical disease that causes considerable death and disability in the tropical world. Although snakebite can cause a variety of pathologies in victims, haemotoxic effects are particularly common and are typically characterised by haemorrhage and/or venom-induced consumption coagulopathy. Antivenoms are the mainstay therapy for treating the toxic effects of snakebite, but despite saving thousands of lives annually, these therapies are associated with limited cross-snake species efficacy due to venom variation, which ultimately restricts their therapeutic utility to particular geographical regions. In this study, we sought to explore the potential of ssDNA aptamers as toxin-specific inhibitory alternatives to antibodies. As a proof of principle model, we selected snake venom serine protease toxins, which are responsible for contributing to venom-induced coagulopathy following snakebite envenoming, as our target. Using SELEX technology, we selected ssDNA aptamers against recombinantly expressed versions of the fibrinogenolytic SVSPs ancrod from the venom of C. rhodostoma and batroxobin from B. atrox. From the resulting pool of specific ssDNA aptamers directed against each target, we identified candidates that exhibited low nanomolar binding affinities to their targets. Downstream aptamer-linked immobilised sorbent assay, fibrinogenolysis, and coagulation profiling experiments demonstrated that the candidate aptamers were able to recognise native and recombinant SVSP toxins and inhibit the toxin- and venom-induced prolongation of plasma clotting times and the consumption of fibrinogen, with inhibitory potencies highly comparable to commercial polyvalent antivenoms. Our findings demonstrate that rationally selected toxin-specific aptamers can exhibit broad in vitro cross-reactivity against toxin isoforms found in different snake venoms and are capable of inhibiting toxins in pathologically relevant in vitro and ex vivo models of venom activity. These data highlight the potential utility of ssDNA aptamers as novel toxin-inhibiting therapeutics of value for tackling snakebite envenoming.

A sequential toggle cell-SELEX DNA aptamer for targeting Staphylococcus aureus, Streptococcus agalactiae, and Escherichia coli bacteria

BACKGROUND

Mastitis is an inflammation of the mammary glands caused by a microbial infection. The common bacteria causing this infection in dairy farms are Staphylococcus aureus, Streptococcus agalactiae, and Escherichia coli. The aptamer is a new biosensor platform for detecting pathogens; however, its use for simultaneous detection of S. aureus, S. agalactiae, and E. coli bacteria has not been reported. This study's objective is to isolate and characterize polyclonal DNA aptamer with broad reactivity to the mastitis bacteria S. aureus, S. agalactiae, and E. coli using a sequential toggle cell-SELEX.

METHODS AND RESULTS

The DNA aptamer pool from SELEX 15 was inserted into the pGEM-T easy plasmid. Furthermore, the transformant clones were selected by PCR colony, plasmid isolation, and sequencing. Six DNA aptamers, consisting of S15K3, S15K4, S15K6, S15K13, S15K15, and S15K20 with a constant region and the right size of 81 bp were derived from the sequencing analysis. The secondary structure of the DNA was predicted using Mfold software. The DNA was analyzed with binding characteristics, including binding capacity and affinity (Kd), using qPCR. The results indicated aptamer S15K15 has the highest binding ability into S. agalactiae, while S15K13 performed binding capacity most to E. coli EPEC 4, and S15K3 has the highest capacity of binding to S. aureus BPA-12.

CONCLUSION

Aptamer S15K3 has the best binding characteristics on all three bacterial targets.

A rapid fluorescent aptasensor for point-of-care detection of C-reactive protein

In this paper, we report on a novel fluorescent aptasensor based on aptamers modified by both nitrogen-doped graphene quantum dots (N-GQDs) and gold nanoparticles (AuNPs) for the detection of C-reactive protein (CRP). FRET effect is utilized in our aptasensor by the change of aptamers conformation when binding with the target. An obvious fluorescence quench of the N-GQDs can be observed when CRP appears in the assay due to electron transfer between the donor and accepter. A detection limit of 0.2 ng/mL can be achieved by our sensor in PBS buffer which is much lower than the physiological CRP level in human serum. Also, CRP levels in different patients' serum are tested with our assay. Since our aptasensor is rapid (detection time less than 40 min), one-step and very simple to operate, we believe it has great potential to apply for point-of-care testing (POCT).

A Novel Sandwich ELASA Based on Aptamer for Detection of Largemouth Bass Virus (LMBV)

Largemouth bass virus (LMBV) is a major viral pathogen in largemouth bass culture, usually causing high mortality and heavy economic losses. Accurate and early detection of LMBV is crucial for diagnosis and control of the diseases caused by LMBV. Previously, we selected the specific aptamers, LA38 and LA13, targeting LMBV by systematic evolution of ligands by exponential enrichment (SELEX). In this study, we further generated truncated LA38 and LA13 (named as LA38s and LA13s) with high specificity and affinities and developed an aptamer-based sandwich enzyme-linked apta-sorbent assay (ELASA) for LMBV diagnosis. The sandwich ELASA showed high specificity and sensitivity for the LMBV detection, without cross reaction with other viruses. The detection limit of the ELASA was as low as 1.25 × 10² LMBV-infected cells, and the incubation time of the lysate and biotin labeled aptamer was as short as 10 min. The ELASA could still detect LMBV infection in spleen lysates at dilutions of 1/25, with good consistency of qRT-PCR. For the fish samples collected from the field, the sensitivity of ELASA was 13.3% less than PCR, but the ELASA was much more convenient and less time consuming. The procedure of ELASA mainly requires washing and incubation, with completion in approximately 4 h. The sandwich ELASA offers a useful tool to rapidly detect LMBV rapidly, contributing to control and prevention of LMBV infection.

Modulation of Aptamer-Ligand-Binding by Complementary Oligonucleotides: A G-Quadruplex Anti-Ochratoxin A Aptamer Case Study

Short oligonucleotides are widely used for the construction of aptamer-based sensors and logical bioelements to modulate aptamer-ligand binding. However, relationships between the parameters (length, location of the complementary region) of oligonucleotides and their influence on aptamer-ligand interactions remain unclear. Here, we addressed this task by comparing the effects of short complementary oligonucleotides (ssDNAs) on the structure and ligand-binding ability of an aptamer and identifying ssDNAs' features that determine these effects. Within this, the interactions between the OTA-specific G-quadruplex aptamer 1.12.2 (5'-GATCGGGTGTGGGTGGCGTAAAGGGA GCATCGGACA-3') and 21 single-stranded DNA (ssDNA) oligonucleotides complementary to different regions of the aptamer were studied. Two sets of aptamer-ssDNA dissociation constants were obtained in the absence and in the presence of OTA by isothermal calorimetry and fluorescence anisotropy, respectively. In both sets, the binding constants depend on the number of hydrogen bonds formed in the aptamer-ssDNA complex. The ssDNAs' having more than 23 hydrogen bonds with the aptamer have a lower aptamer dissociation constant than for aptamer-OTA interactions. The ssDNAs' having less than 18 hydrogen bonds did not affect the aptamer-OTA affinity. The location of ssDNA's complementary site in the aptamer affeced the kinetics of the interaction and retention of OTA-binding in aptamer-ssDNA complexes. The location of the ssDNA site in the aptamer G-quadruplex led to its unfolding. In the presence of OTA, the unfolding process was longer and takes from 20 to 70 min. The refolding in the presence of OTA was possible and depends on the length and location of the ssDNA's complementary site. The location of the ssDNA site in the tail region led to its rapid displacement and wasn't affecting the G-qaudruplex's integrity. It makes the tail region more perspective for the development of ssDNA-based tools using this aptamer.

Fighting the Huntington's Disease with a G-Quadruplex-Forming Aptamer Specifically Binding to Mutant Huntingtin Protein: Biophysical Characterization, In Vitro and In Vivo Studies

A set of guanine-rich aptamers able to preferentially recognize full-length huntingtin with an expanded polyglutamine tract has been recently identified, showing high efficacy in modulating the functions of the mutated protein in a variety of cell experiments. We here report a detailed biophysical characterization of the best aptamer in the series, named MS3, proved to adopt a stable, parallel G-quadruplex structure and show high nuclease resistance in serum. Confocal microscopy experiments on HeLa and SH-SY5Y cells, as models of non-neuronal and neuronal cells, respectively, showed a rapid, dose-dependent uptake of fluorescein-labelled MS3, demonstrating its effective internalization, even in the absence of transfecting agents, with no general cytotoxicity. Then, using a well-established Drosophila melanogaster model for Huntington's disease, which expresses the mutated form of human huntingtin, a significant improvement in the motor neuronal function in flies fed with MS3 was observed, proving the in vivo efficacy of this aptamer.

Translation of aptamers toward clinical diagnosis and commercialization

The dominance of antibodies in diagnostics has gradually changed following the discovery of aptamers in the early 1990s. Aptamers offer inherent advantages over traditional antibodies, including higher specificity, higher affinity, smaller size, greater stability, ease of manufacture, and low immunogenicity, rendering them the best candidates for point-of-care testing (POCT). In the past 20 years, the research community and pharmaceutical companies have made great efforts to promote the development of aptamer technology. Macugen® (pegaptanib) was the first aptamer drug approved by the US Food and Drug Administration (FDA), and various aptamer-based diagnostics show great promise in preclinical research and clinical trials. In this review, we introduce recent literature, ongoing clinical trials, commercial reagents of aptamer-based diagnostics, discuss the FDA regulatory mechanisms, and highlight the prospects and challenges in translating these studies into viable clinical diagnostic tools.

Detection of E. coli Bacteria in Milk by an Acoustic Wave Aptasensor with an Anti-Fouling Coating

Milk is a significant foodstuff around the world, being produced and consumed in large quantities. The safe consumption of milk requires that the liquid has an acceptably low level of microbial contamination and has not been subjected to spoiling. Bacterial safety limits in milk vary by country but are typically in the thousands per mL of sample. To rapidly determine if samples contain an unsafe level of bacteria, an aptamer-based sensor specific to Escherichia coli bacteria was developed. The sensor is based on an ultra-high frequency electromagnetic piezoelectric acoustic sensor device (EMPAS), with the aptamer being covalently bound to the sensor surface by the anti-fouling linker, MEG-Cl. The sensor is capable of the selective measurement of E. coli in PBS and in cow’s milk samples down to limits of detection of 35 and 8 CFU/mL, respectively, which is well below the safe limits for commercial milk products. This sensing system shows great promise for the milk industry for the purpose of rapid verification of product safety.

Molecularly imprinted electrochemical aptasensor based on functionalized graphene and nitrogen-doped carbon quantum dots for trace cortisol assay

This paper proposes a novel electrochemical aptasensor that integrates molecular imprinting techniques for trace analysis of cortisol. This sensor is based on functionalized graphene and nitrogen-doped carbon quantum dots. The morphology and structure of the modified electrode were characterized by scanning electron microscopy and Raman spectroscopy. The functional monomer aptamer and the template molecule cortisol were adsorbed on the electrode by electrostatic adsorption to construct an imprinted sensing platform. Under the optimal conditions, such as the concentration of template molecule, the ratio of template to functional monomer, the elution and adsorption time, the sensor exhibits linearity and a low detection limit of 10^-12-10^-8 M and 3.3 × 10^-13 M, which is more sensitive than other reported cortisol analysis methods. In addition, this sensor can realize the determination of cortisol in salivary samples with high recovery values, showing great development potential in the field of life sciences.

The impact of protein corona on the biological behavior of targeting nanomedicines

For successful translation of targeting nanomedicines from bench to bedside, it is vital to address their most common drawbacks namely rapid clearance and off-target accumulation. These complications evidently originate from a phenomenon called "protein corona (PC) formation" around the surface of targeting nanoparticles (NPs) which happens once they encounter the bloodstream and interact with plasma proteins with high collision frequency. This phenomenon endows the targeting nanomedicines with a different biological behavior followed by an unexpected fate, which is usually very different from what we commonly observe in vitro. In addition to the inherent physiochemical properties of NPs, the targeting ligands could also remarkably dictate the amount and type of adsorbed PC. As very limited studies have focused their attention on this particular factor, the present review is tasked to discuss the best simulated environment and latest characterization techniques applied to PC analysis. The effect of PC on the biological behavior of targeting NPs engineered with different targeting moieties is further discussed. Ultimately, the recent progresses in manipulation of nano-bio interfaces to achieve the most favorite therapeutic outcome are highlighted.

A new method based on guanine rich aptamer structural change for carcinoembryonic antigen detection

Carcinoembryonic antigen (CEA) is one of the most widely used tumor marker around the world, it mainly used for gastrointestinal cancers, especially in colorectal malignancy. At present, the detection methods of CEA are mostly based on antigen-antibody binding, whereas these methods were limited by the high costs and long waiting times in massive population tumor screening. During the experiments, we interestingly found that the fluorescence signal would be dramatically altered when the secondary structure of fluorescent modified guanine-rich DNA changed. Then we explored the reasons and established a new method for CEA detection, this method brings a simple, fast and cheap sensing platform for detection of biomarkers. It has great potential in screening of tumors among the group and is expected to provide prospective effects for tumor treatment.

Novel and efficient method for loading aptamer-conjugated liposomes with arsenic trioxide for targeting cancer cells

Although the therapeutic effect of liposomal arsenic trioxide arsenic trioxide (ATO) in the treatment of solid tumours has been confirmed, its dose-limiting loading is a challenging issue. To solve the problems in the preparation of liposomal ATO, different loading strategies were evaluated and compared. In addition, liposomes decorated with anti-nucleolin aptamers were developed as a novel formulation for targeted delivery with high loading efficiency and sustained releasing property in order to treat solid tumours. The liposomes were prepared by a thin-film method exploiting the passive loading strategy of Co(II) hydrogen arsenite (CHA). The structural characteristics of the liposomes were also investigated by Fourier transform infra-red spectroscopy (FT-IR), dynamic light scattering (DLS), zeta potentiometry, field emission scanning electron microscopy (FESEM), and Energy Dispersive X-ray Diffraction (EDX) techniques. To evaluate the potential cytotoxicity of this liposomal drug vehicle in vitro, MTT assay was performed on HT-29 cancer cell line. The results showed that the synthesised liposomes loaded with CHA exhibited high entrapment efficiency (77%). MTT assays showed a significant difference between the percentage of viable cells when HT -29 cells were treated with free ATO and liposomal formulation which can be corresponded to the sustained release of the drug from the liposomes. The results of this study may lead to a promising strategy for the effective treatment of solid tumours.

Label-free bioassay with graphene oxide-based fluorescent aptasensors: A review

Bioassays using a fluorophore and DNA aptamer have been extensively developed due to the ultrasensitivity of fluorophores and recognition ability of DNA aptamers. Conventional fluorescent aptamer-based sensors (aptasensors) require chemical labeling between the fluorophore and aptamer and is technologically impracical for various sensing and assay applications. A simple "mix and go" strategy has been introduced that uses label-free technology as a platform for sensor development. The biosensors comprise a fluorophore, a ssDNA aptamer, and eco-friendly graphene oxide (GO). In the absence of the sensor target, GO quenches the fluorescence of the fluorophore and single-strand DNA aptamer complex. When the target is added, the DNA aptamer conformationally turns into a duplex, G-quadruplexe, or other secondary structure. This structure change leads to release of GO by the fluorophore-aptamer-target complex, generating dramatic fluorescence recovery and amplification. With this sensing method, the DNA aptamer does not need to be chemically labeled. Therefore, flexible fluorophore indicators and ssDNA aptamers can be used in this label-free aptasensing strategy. In this review, we discuss various unlabeled fluorophores, including synthetic small molecular fluorophores and genetically encoded fluorescent proteins, as indicators for generating GO-based fluorescent DNA aptasensors for label-free bioassay.

AS1411 Nucleolin-Specific Binding Aptamers Reduce Pathological Angiogenesis through Inhibition of Nucleolin Phosphorylation

Proliferative retinopathies produces an irreversible type of blindness affecting working age and pediatric population of industrialized countries. Despite the good results of anti-VEGF therapy, intraocular and systemic complications are often associated after its intravitreal use, hence novel therapeutic approaches are needed. The aim of the present study is to test the effect of the AS1411, an antiangiogenic nucleolin-binding aptamer, using in vivo, ex vivo and in vitro models of angiogenesis and propose a mechanistic insight. Our results showed that AS1411 significantly inhibited retinal neovascularization in the oxygen induced retinopathy (OIR) in vivo model, as well as inhibited branch formation in the rat aortic ex vivo assay, and, significantly reduced proliferation, cell migration and tube formation in the HUVEC in vitro model. Importantly, phosphorylated NCL protein was significantly abolished in HUVEC in the presence of AS1411 without affecting NFκB phosphorylation and -21 and 221-angiomiRs, suggesting that the antiangiogenic properties of this molecule are partially mediated by a down regulation in NCL phosphorylation. In sum, this new research further supports the NCL role in the molecular etiology of pathological angiogenesis and identifies AS1411 as a novel anti-angiogenic treatment.

Highly Sensitive Electrochemical Aptasensor for Detection of Glypican-3 Using Hemin-Reduced Graphene Oxide-Platinum Nanoparticles Coupled with Conductive Reduced Graphene Oxide-Gold Nanoparticles

An electrochemical aptasensor for quantitatively detecting glypican-3 (GPC3) was constructed by combining hemin-reduced graphene oxide-platinum (H-rGO-Pt) nanoparticles (NPs) with reduced graphene oxide-gold (rGO-Au) nanoparticles (NPs). Herein, the rGO-Au NPs deposited onto screen-printed electrodes resulted in signal amplification due to their large surface areas. Meanwhile, highly conductive H-rGO-Pt NPs acted as a sensing medium that improved electrical conductivity and as an indicator for monitoring peak current for determination. A GPC3 aptamer (GPC3apt) with a low equilibrium dissociation constant was used as a bio-recognition molecule. GPC3apt specifically captured GPC3 proteins and formed aptamer-GPC3 complexes, which impeded electron transfer and thus hampered the redox signal of hemin in H-rGO-Pt NPs. This developed electrochemical aptasensor showed a linear response to GPC3 (from 0.001 μg/mL to 10 μg/mL) and had a detection limit of 0.001 μg/mL. This work provides a low-cost and highly sensitive detection with and good recovery for GPC3 and holds great promise for the clinical diagnosis of hepatocellular carcinoma.

Design and clinical developments of aptamer-drug conjugates for targeted cancer therapy

BACKGROUND

Aptamer has been called "chemical antibody" which displays the specific affinity to target molecules compared to that of antibodies and possesses several therapeutic advantages over antibodies in terms of size, accessibility to synthesis, and modification. Based on the attractive properties, aptamers have been interested in many directions and now are emerged as new target-designed cancer drug.

MAIN BODY

Currently, new types of aptamers have been reported and attracted many scientists' interesting. Due to simplicity of chemical modification and ready-made molecular engineering, scientists have developed newly designed aptamers conjugated with a wide range of therapeutics, aptamer-drug conjugates; ApDCs, from chemotherapy to phototherapy, gene therapy, and vaccines. ApDCs display synergistic therapeutic effects in cancer treatment.

CONCLUSION

In this paper, we reviewed various kinds of ApDCs, i.e., ApDC nucleotide analogs, ApDC by drug intercalation, and ApDC by using chemical linker. Current data prove these ApDCs have sufficient potential to complete clinical development soon. Advanced technology of cancer drug delivery and combination treatment of cancers enables aptamer and conjugated drug (ApDCs) efficient means for targeted cancer treatment that reduces potential toxicity and increases therapeutic efficacy.

Nanoparticle-Guided Brain Drug Delivery: Expanding the Therapeutic Approach to Neurodegenerative Diseases

Neurodegenerative diseases (NDs) represent a heterogeneous group of aging-related disorders featured by progressive impairment of motor and/or cognitive functions, often accompanied by psychiatric disorders. NDs are denoted as 'protein misfolding' diseases or proteinopathies, and are classified according to their known genetic mechanisms and/or the main protein involved in disease onset and progression. Alzheimer's disease (AD), Parkinson's disease (PD) and Huntington's disease (HD) are included under this nosographic umbrella, sharing histopathologically salient features, including deposition of insoluble proteins, activation of glial cells, loss of neuronal cells and synaptic connectivity. To date, there are no effective cures or disease-modifying therapies for these NDs. Several compounds have not shown efficacy in clinical trials, since they generally fail to cross the blood-brain barrier (BBB), a tightly packed layer of endothelial cells that greatly limits the brain internalization of endogenous substances. By engineering materials of a size usually within 1-100 nm, nanotechnology offers an alternative approach for promising and innovative therapeutic solutions in NDs. Nanoparticles can cross the BBB and release active molecules at target sites in the brain, minimizing side effects. This review focuses on the state-of-the-art of nanoengineered delivery systems for brain targeting in the treatment of AD, PD and HD.

Improving aptamer performance with nucleic acid mimics: de novo and post-SELEX approaches

Aptamers are structural single-stranded oligonucleotides generated in vitro to bind to a specific target molecule. Aptamers' versatility can be enhanced with nucleic acid mimics (NAMs) during or after a selection process, also known as systematic evolution of ligands by exponential enrichment (SELEX). We address advantages and limitations of the technologies used to generate NAM aptamers, especially the applicability of existing engineered polymerases to replicate NAMs and methodologies to improve aptamers after SELEX. We also discuss the limitations of existing methods for sequencing NAM sequences and bioinformatic tools to predict NAM aptamer structures. As a conclusion, we suggest that NAM aptamers might successfully compete with molecular tools based on proteins such as antibodies for future application.

An aptamer highly specific to cellulose enables the analysis of the association of cellulose with matrix cell wall polymers in vitro and in muro

The current toolbox of cell wall-directed molecular probes has been pivotal for advancing basic and application-oriented plant carbohydrate research; however, it still exhibits limitations regarding target diversity and specificity. Scarcity of probes targeting intramolecular associations between cell wall polymers particularly hinders our understanding of the cell wall microstructure and affects the development of effective means for its efficient deconstruction for bioconversion. Here we report a detailed characterization of a cellulose-binding DNA aptamer CELAPT MINI using a combination of various in vitro biochemical, biophysical, and molecular biology techniques. Our results show evidence for its high specificity towards long non-substituted β-(1-4)-glucan chains in both crystalline and amorphous forms. Fluorescent conjugates of CELAPT MINI are applicable as in situ cellulose probes and are well suited for various microscopy techniques, including super-resolution imaging. Compatibility of fluorescent CELAPT MINI variants with immunodetection of cell wall matrix polymers enabled them simultaneously to resolve the fibrillar organization of complex cellulose-enriched pulp material and to quantify the level of cellulose masking by xyloglucan and xylan. Using enzymatically, chemically, or genetically modulated Brachypodium internode sections we showed the diversity in cell wall packing among various cell types and even cell wall microdomains. We showed that xylan is the most prominent, but not the only, cellulose-masking agent in Brachypodium internode tissues. These results collectively highlight the hitherto unexplored potential to expand the cell wall probing toolbox with highly specific and versatile in vitro generated polynucleotide probes.

Identification and Engineering of Aptamers for Theranostic Application in Human Health and Disorders

An aptamer is a short sequence of synthetic oligonucleotides which bind to their cognate target, specifically while maintaining similar or higher sensitivity compared to an antibody. The in-vitro selection of an aptamer, applying a conjoining approach of chemistry and molecular biology, is referred as Systematic Evolution of Ligands by Exponential enrichment (SELEX). These initial products of SELEX are further modified chemically in an attempt to make them stable in biofluid, avoiding nuclease digestion and renal clearance. While the modification is incorporated, enough care should be taken to maintain its sensitivity and specificity. These modifications and several improvisations have widened the window frame of aptamer applications that are currently not only restricted to in-vitro systems, but have also been used in molecular imaging for disease pathology and treatment. In the food industry, it has been used as sensor for detection of different diseases and fungal infections. In this review, we have discussed a brief history of its journey, along with applications where its role as a therapeutic plus diagnostic (theranostic) tool has been demonstrated. We have also highlighted the potential aptamer-mediated strategies for molecular targeting of COVID-19. Finally, the review focused on its future prospective in immunotherapy, as well as in identification of novel biomarkers in stem cells and also in single cell proteomics (scProteomics) to study intra or inter-tumor heterogeneity at the protein level. Small size, chemical synthesis, low batch variation, cost effectiveness, long shelf life and low immunogenicity provide advantages to the aptamer over the antibody. These physical and chemical properties of aptamers render them as a strong biomedical tool for theranostic purposes over the existing ones. The significance of aptamers in human health was the key finding of this review.

Charge-Transfer Interactions Stabilize G-Quadruplex-Forming Thrombin Binding Aptamers and Can Improve Their Anticoagulant Activity

In the search for optimized thrombin binding aptamers (TBAs), we herein describe the synthesis of a library of TBA analogues obtained by end-functionalization with the electron-rich 1,5-dialkoxy naphthalene (DAN) and the electron-deficient 1,8,4,5-naphthalenetetra-carboxylic diimide (NDI) moieties. Indeed, when these G-rich oligonucleotides were folded into the peculiar TBA G-quadruplex (G4) structure, effective donor-acceptor charge transfer interactions between the DAN and NDI residues attached to the extremities of the sequence were induced, providing pseudo-cyclic structures. Alternatively, insertion of NDI groups at both extremities produced TBA analogues stabilized by π-π stacking interactions. All the doubly-modified TBAs were characterized by different biophysical techniques and compared with the analogues carrying only the DAN or NDI residue and unmodified TBA. These modified TBAs exhibited higher nuclease resistance, and their G4 structures were markedly stabilized, as evidenced by increased Tm values compared to TBA. These favorable properties were also associated with improved anticoagulant activity for one DAN/NDI-modified TBA, and for one NDI/NDI-modified TBA. Our results indicated that TBA pseudo-cyclic structuring by ad hoc designed end-functionalization represents an efficient approach to improve the aptamer features, while pre-organizing and stabilizing the G4 structure but allowing sufficient flexibility to the aptamer folding, which is necessary for optimal thrombin recognition.