Aptamer chemistry

Triblock polyadenine-based electrochemical aptasensor for ultra-sensitive detection of carcinoembryonic antigen via exonuclease III-assisted target recycling and hybridization chain reaction

Carcinoembryonic antigen (CEA), a key colon biomarker, demands a precise detection method for cancer diagnosis and prognosis. This study introduces a novel electrochemical aptasensor using a triblock polyadenine probe for ultra-sensitive detection of CEA. The method leverages Exonuclease III (Exo III)-assisted target recycling and hybridization chain reaction. The triblock polyadenine probe self-assembles on the bare gold electrode through the strong affinity between adenine and gold electrode, blocking CEA diffusion and providing a large immobilization surface. CEA binding to hairpin probe 1 (HP1), followed by the hybridization between HP1 and hairpin probe 2 (HP2), triggers DNA cleavage by Exo III, amplifying the signal via a hybridization chain reaction and producing numerous dsDNA walkers that generates a dramatic electrochemical impedance signal. Under optimized conditions, the aptasensor achieved two ultra-low detection limits: 0.39 ag∙mL-1 within the concentration range of 5 ag∙mL-1 to 5 × 106 ag∙mL-1, and 1.5 ag∙mL-1 within the concentration range of 5 × 106 ag∙mL-1 to 1 × 1010 ag∙mL-1. Its performance in human serum samples meets the practical standards, offering a promising new tool for ultrasensitive tumor marker detection, potentially revolutionizing early cancer diagnosis.

Aptamer-based assembly systems for SARS-CoV-2 detection and therapeutics

Nucleic acid aptamers are oligonucleotide chains with molecular recognition properties. Compared with antibodies, aptamers show advantages given that they are readily produced via chemical synthesis and elicit minimal immunogenicity in biomedicine applications. Notably, aptamer-encoded nucleic acid assemblies further improve the binding affinity of aptamers with the targets due to their multivalent synergistic interactions. Specially, aptamers can be engineered with special topological arrangements in nucleic acid assemblies, which demonstrate spatial and valence matching towards antigens on viruses, thus showing potential in the detection and therapeutic applications of viruses. This review presents the recent progress on the aptamers explored for SARS-CoV-2 detection and infection treatment, wherein applications of aptamer-based assembly systems are introduced in detail. Screening methods and chemical modification strategies for aptamers are comprehensively summarized, and the types of aptamers employed against different target domains of SARS-CoV-2 are illustrated. The evolution of aptamer-based assembly systems for the detection and neutralization of SARS-CoV-2, as well as the construction principle and characteristics of aptamer-based DNA assemblies are demonstrated. The typically representative works are presented to demonstrate how to assemble aptamers rationally and elaborately for specific applications in SARS-CoV-2 diagnosis and neutralization. Finally, we provide deep insights into the current challenges and future perspectives towards aptamer-based nucleic acid assemblies for virus detection and neutralization in nanomedicine.

Qualifying P-glycoprotein in drug-resistant ovarian cancer cells: a dual-mode aptamer probe approach

Drug resistance presents a significant obstacle in treating human ovarian cancer. The development of effective methods for detecting drug-resistant cancer cells is pivotal for tailoring personalized therapies and prognostic assessments. In this investigation, we introduce a dual-mode detection technique employing a fluorogenic aptamer probe for the qualification of P-glycoprotein (P-gp) in drug-resistant ovarian cancer cells. The probe, initially in an "off" state due to the proximity of a quencher to the fluorophore, exhibits increased fluorescence intensity upon binding with the target. The fluorescence enhancement shows a linear correlation with both the concentration of P-gp and the presence of P-gp in drug-resistant ovarian cancer cells. This correlation is quantifiable, with detection limits of 1.56 nM and 110 cells per mL. In an alternate mode, the optimized fluorophores, attached to the aptamer, form larger complexes upon binding to the target protein, which diminishes the rotation speed, thereby augmenting fluorescence polarization. The alteration in fluorescence polarization enables the quantitative analysis of P-gp in the cells, ranging from 100 to 1500 cells per milliliter, with a detection limit of 40 cells per mL. Gene expression analyses, protein expression studies, and immunofluorescence imaging further validated the reliability of our aptamer-based probe for its specificity towards P-gp in drug-resistant cancer cells. Our findings underscore that the dual-mode detection approach promises to enhance the diagnosis and treatment of multidrug-resistant ovarian cancer.

In Vivo Evaluation of 68Ga-Labeled NOTA-EGFRvIII Aptamer in EGFRvIII-Positive Glioblastoma Xenografted Model

EGFRvIII is expressed only in tumor cells and strongly in glioblastoma and is considered a promising target in cancer diagnosis and therapy. Aptamers are synthetic single-stranded oligonucleotides that bind to biochemical target molecules with high binding affinity and specificity. This study examined the potential of the 68Ga-NOTA-EGFRvIII aptamer as a nuclear imaging probe for visualizing EGFRvIII-expressing glioblastoma by positron emission tomography (PET). EGFRvIII aptamer was selected using the SELEX technology, and flow cytometry and fluorescence microscopy verified the high binding affinity to EGFRvIII positive U87MG vIII 4.12 glioma cells but not to EGFRvIII negative U87MG cells. The EGFRvIII aptamer was conjugated with a chelator (1,4,7-triazanonane-1,4,7-triyl)triacetic acid (NOTA) for 68Ga-labeling. The 68Ga-NOTA-EGFRvIII aptamer was prepared using the preconcentration-based labeling method with a high radiolabeling yield at room temperature. Ex vivo biodistribution analyses confirmed the significantly higher tumor uptake of the 68Ga-NOTA-EGFRvIII aptamer in EGFRvIII-expressing xenograft tumors than that in EGFRvIII negative tumors, confirming the specific tumor uptake of the 68Ga-NOTA-EGFRvIII aptamer in vivo. PET imaging studies revealed a high retention rate of the 68Ga-NOTA-EGFRvIII aptamer in U87MG vIII 4.12 tumors but only low uptake levels in U87-MG tumors, suggesting that the 68Ga-NOTA-EGFRvIII aptamer may be used as a PET imaging agent for EGFRvIII-expressing glioblastoma.

Improving synthesis and binding affinities of nucleic acid aptamers and their therapeutics and diagnostic applications

Nucleic acid aptamers have captivated the attention of analytical and medicinal scientists globally due to their several advantages as recognition molecules over conventional antibodies because of their small size, simple and inexpensive synthesis, broad target range, and high stability in varied environmental conditions. These recognition molecules can be chemically modified to make them resistant to nuclease action in blood serum, reduce rapid renel clearance, improve the target affinity and selectivity, and make them amenable to chemically conjugate with a support system that facilitates their selective applications. This review focuses on the development of efficient aptamer candidates and their application in clinical diagnosis and therapeutic applications. Significant advances have been made in aptamer-based diagnosis of infectious and non-infectious diseases. Collaterally, the progress made in therapeutic applications of aptamers is encouraging, as evident from their use in diagnosing cancer, neurodegenerative diseases, microbial infection, and in imaging. This review also updates the progress on clinical trials of many aptamer-based products of commercial interests. The key development and critical issues on the subject have been summarized in the concluding remarks.

Aptamers: Promising Reagents in Biomedicine Application

Nucleic acid aptamers, often termed "chemical antibodies," are short, single-stranded DNA or RNA molecules, which are selected by SELEX. In addition to their high specificity and affinity comparable to traditional antibodies, aptamers have numerous unique advantages such as wider identification of targets, none or low batch-to-batch variations, versatile chemical modifications, rapid mass production, and lack of immunogenicity. These characteristics make aptamers a promising recognition probe for scientific research or even clinical application. Aptamer-functionalized nanomaterials are now emerged as a promising drug delivery system for various diseases with decreased side-effects and improved efficacy. In this review, the technological strategies for generating high-affinity and biostable aptamers are introduced. Moreover, the development of aptamers for their application in biomedicine including aptamer-based biosensors, aptamer-drug conjugates and aptamer functionalized nanomaterials is comprehensively summarized.

Fluorescent DNA-Silver nanoclusters in food safety detection: From synthesis to application

In recent years, the conventional preparation of silver nanoclusters (AgNCs) has attracted much attention due to their ultra-small size, tunable fluorescence, easy-to-engineer, as well as biocompatible material. Moreover, its great affinity towards cytosine bases on single-stranded DNA has led to the construction of biosensors, especially aptamers, for a broad variety of applications in food safety and environmental protection. In past years, numerous researchers paid attention to the construction of AgNCs aptasensor. Therefore, this review will be an effort to summarize the synthetic strategy along with the influences of factors on synthesis, categorize the sensing mechanism of aptamer-functionalized AgNCs biosensors, as well as their specific applications in food safety detection including heavy metal, toxin, and foodborne pathogenic bacteria. Furthermore, a brief conclusion and outlook regarding the prospects and challenges of their applications in food safety were drawn in line with the developments in DNA-AgNCs.

Recent Advancements in Molecularly Imprinted Polymers Based Aptasensors: Critical Role of Nanomaterials for the Efficient Food Safety Analysis

Biosensors are being studied extensively for their ability to detect and analyze molecules. There has been a growing interest in combining molecular imprinted polymers (MIPs) and aptamers to create hybrid recognition elements that offer advantages such as target binding, sensitivity, selectivity, and stability. These hybrid elements have been successfully used in identifying a wide range of analytes in food samples. However, the application of MIP-based aptasensors in different sensing approaches is still challenging due to the low conductivity of MIPs-aptamers and limited adsorption capacity of MIPs. To address these limitations, researchers have been exploring the use of nanomaterials (NMs) to design efficient multiple-recognition systems that exploit the synergies between aptamers and MIPs. These hybrid systems can enhance the sensitivity and selectivity of MIP-based aptasensors in quantifying analytical samples. This review provides a comprehensive overview of recent advancements in the field of MIP-based aptasensors. It also introduces technologies that combine MIPs and aptamers to achieve higher sensitivity and selectivity in quantifying analytical samples. The review also highlights potential future trends and practical approaches that can be employed to address the limitations of MIP-based aptasensors, including the use of new NMs, the development of new fabrication techniques, and the integration of MIP-based aptasensors with other analytical tools.

Turn-off enzyme activity of histidine-rich peptides for the detection of lysozyme

An assay that integrates histidine-rich peptides (HisRPs) with high-affinity aptamers was developed enabling the specific and sensitive determination of the target lysozyme. The enzyme-like activity of HisRP is inhibited by its interaction with a target recognized by an aptamer. In the presence of the target, lysozyme molecules progressively assemble on the surface of HisRP in a concentration-dependent manner, resulting in the gradual suppression of enzyme-like activity. This inhibition of HisRP's enzyme-like activity can be visually observed through color changes in the reaction product or quantified using UV-visible absorption spectroscopy. Under optimal conditions, the proposed colorimetric assay for lysozyme had a detection limit as low as 1 nM and exhibited excellent selectivity against other nonspecific interferents. Furthermore, subsequent research validated the practical applicability of the developed colorimetric approach to saliva samples, indicating that the assay holds significant potential for the detection of lysozymes in samples derived from humans.

In vitro selection of a trans aptamer complex for target-responsive fluorescence activation

BACKGROUND

Most biological molecular complexes consist of multiple functional domains, yet rationally constructing such multifunctional complexes is challenging. Aptamers, the nucleic acid-based functional molecules, can perform multiple tasks including target recognition, conformational changes, and enzymatic activities, while being chemically synthesizable and tunable, and thus provide a basis for engineering enhanced functionalities through combination of multiple units. However, the conventional approach of simply combining aptamer units in a serial manner is susceptible to undesired crosstalk or interference between the aptamer units and to false interactions with non-target molecules; besides, the approach would require additional mechanisms to separate the units if they are desired to function independently. It is clearly a challenge to develop multi-aptamer complexes that preserve independent functions of each unit while avoiding undesired interference and non-specific interactions.

RESULTS

By directly in vitro selecting a 'trans' aptamer complex, we demonstrate that one aptamer unit ('utility module') can remain hidden or 'inactive' until a target analyte triggers the other unit ('sensing module') and separates the two aptamers. Since the operation of the utility module occurs free from the sensing module, unnecessary crosstalk between the two units can be avoided. Because the utility module is kept inactive until separated from the complex, non-specific interactions of the hidden module with noncognate targets can be naturally prevented. In our demonstration, the sensing module was selected to detect serotonin, a clinically important neurotransmitter, and the target-binding-induced structure-switching of the sensing module reveals and activates the utility module that turns on a fluorescence signal. The aptamer complex exhibited a moderately high affinity and an excellent specificity for serotonin with ∼16-fold discrimination against common neurotransmitter molecules, and displayed strong robustness to perturbations in the design, disallowing nonspecific reactions against various challenges.

SIGNIFICANCE

This work represents the first example of a trans aptamer complex that was in vitro selected de novo. The trans aptamer complex selected by our strategy does not require chemical modifications or immediate optimization processes to function, because the complex is directly selected to perform desired functions. This strategy should be applicable to a wide range of functional nucleic acid moieties, which will open up diverse applications in biosensing and molecular therapeutics.

Recent Advances in Aptamer-Based Biosensors for Bacterial Detection

The rapid and sensitive detection of pathogenic bacteria is becoming increasingly important for the timely prevention of contamination and the treatment of infections. Biosensors based on nucleic acid aptamers, integrated with optical, electrochemical, and mass-sensitive analytical techniques, have garnered intense interest because of their versatility, cost-efficiency, and ability to exhibit high affinity and specificity in binding bacterial biomarkers, toxins, and whole cells. This review highlights the development of aptamers, their structural characterization, and the chemical modifications enabling optimized recognition properties and enhanced stability in complex biological matrices. Furthermore, recent examples of aptasensors for the detection of bacterial cells, biomarkers, and toxins are discussed. Finally, we explore the barriers to and discuss perspectives on the application of aptamer-based bacterial detection.

Targeted Delivery of Catalase and Photosensitizer Ce6 by a Tumor-Specific Aptamer Is Effective against Bladder Cancer In Vivo

Photodynamic therapy (PDT) is often applied in a clinical setting to treat bladder cancer. However, current photosensitizers report drawbacks such as low efficacy, low selectivity, and numerous side effects, which have limited the clinical values of PDT for bladder cancer. Previously, we developed the first bladder cancer-specific aptamer that can selectively bind to and be internalized by bladder tumor cells versus normal uroepithelium cells. Here, we use an aptamer-based drug delivery system to deliver photosensitizer chlorine e6 (Ce6) into bladder tumor cells. In addition to Ce6, we also incorporate catalase into the drug complex to increase local oxygen levels in the tumor tissue. Compared with free Ce6, an aptamer-guided DNA nanotrain (NT) loaded with Ce6 and catalase (NT-Catalase-Ce6) can specifically recognize bladder cancer cells, produce oxygen locally, induce ROS in tumor cells, and cause mitochondrial apoptosis. In an orthotopic mouse model of bladder cancer, the intravesical instillation of NT-Catalase-Ce6 exhibits faster drug internalization and a longer drug retention time in tumor tissue compared with that in normal urothelium. Moreover, our modified PDT significantly inhibits tumor growth with fewer side effects such as cystitis than free Ce6. This aptamer-based photosensitizer delivery system can therefore improve the selectivity and efficacy and reduce the side effects of PDT treatment in mouse models of bladder cancer, bearing a great translational value for bladder cancer intravesical therapy.

Polymer-DNA assembled nanoflower for targeted delivery of dolastatin-derived microtubule inhibitors

Dolastatin derivatives possess excellent anticancer activity and have been translated into clinical trials for cancer therapy. Drug delivery systems enable dolastatin derivatives to break the limitation of instability during blood circulation and ineffective cell internalization in the application. Nevertheless, their potential has not been thoroughly established because of the limited loading efficacy and complicated chemical modification. Herein, we rationally propose a rolling circle amplification-based polymer-DNA assembled nanoflower for targeted and efficient delivery of dolastatin-derived drugs to achieve efficient anticancer therapy. The polymer-DNA assembled nanoflower with targeted aptamer conjugate is widely applicable for loading dolastatin-derived drugs with high encapsulation efficiency. The developed monomethyl auristatin E (MMAE) loaded PN@M exhibited increased cellular uptake and enhanced inhibitory effect, especially in multidrug-resistant tumor cells. The results of in vivo anticancer effects indicate that nanoflower as a dolastatin derivatives delivery system holds considerable potential for the treatment of malignant cancer.

Treatment-induced and Pre-existing Anti-peg Antibodies: Prevalence, Clinical Implications, and Future Perspectives

Polyethylene glycol (PEG) is a versatile polymer that is used in numerous pharmaceutical applications like the food industry, a wide range of disinfectants, cosmetics, and many commonly used household products. PEGylation is the term used to describe the covalent attachment of PEG molecules to nanocarriers, proteins and peptides, and it is used to prolong the circulation half-life of the PEGylated products. Consequently, PEGylation improves the efficacy of PEGylated therapeutics. However, after four decades of research and more than two decades of clinical applications, an unappealing side of PEGylation has emerged. PEG immunogenicity and antigenicity are remarkable challenges that confound the widespread clinical application of PEGylated therapeutics - even those under clinical trials - as anti-PEG antibodies (Abs) are commonly reported following the systemic administration of PEGylated therapeutics. Furthermore, pre-existing anti-PEG Abs have also been reported in healthy individuals who have never been treated with PEGylated therapeutics. The circulating anti-PEG Abs, both treatment-induced and pre-existing, selectively bind to PEG molecules of the administered PEGylated therapeutics inducing activation of the complement system, which results in remarkable clinical implications with varying severity. These include increased blood clearance of the administered PEGylated therapeutics through what is known as the accelerated blood clearance (ABC) phenomenon and initiation of serious adverse effects through complement activation-related pseudoallergic reactions (CARPA). Therefore, the US FDA industry guidelines have recommended the screening of anti-PEG Abs, in addition to Abs against PEGylated proteins, in the clinical trials of PEGylated protein therapeutics. In addition, strategies revoking the immunogenic response against PEGylated therapeutics without compromising their therapeutic efficacy are important for the further development of advanced PEGylated therapeutics and drug-delivery systems.

Biomacromolecule-tagged nanoscale constructs for crossing the blood-brain barrier

Access to the brain is restricted by the low permeability of the blood-brain barrier (BBB), greatly hampering modern drug delivery efforts. A promising approach to overcome this boundary is to utilize biomacromolecules (peptides, nucleic acids, carbohydrates) as targeting ligands on nanoscale delivery vehicles to shuttle cargo across the BBB. In this mini-review, we highlight the most recent approaches for crossing the BBB using synthetic nanoscale constructs decorated with members of these general classes of biomacromolecules to safely and selectively deliver therapeutic materials to the brain.

Group selective aptamers: Broad-spectrum recognition of target groups in Cronobacter species and implementation of electrochemical biosensors as receptors

Aptamers are a versatile class of receptors with a high affinity and selectivity for specific targets. Although their ability to recognize individual targets has been extensively studied, some scenarios require the development of receptors capable of identifying all target groups. This study investigated the use of aptamers to achieve the broad-spectrum recognition of groups instead of individual targets. Aptamers were screened for selectively distinct groups of Cronobacter species associated with foodborne diseases. Seven Cronobacter spp. were divided into Group A (C. sakazakii, C. malonaticus, C. turicensis, and C. muytjensii) and Group B (C. dublinensis, C. condimenti, and C. universalis). Aptamers with exclusive selectivity for each group were identified, allowing binding to the species within their designated group while excluding those from the other group. The screened aptamers demonstrated reliable affinity and specificity with dissociation constants ranging from 1.3 to 399.7 nM for Group A and 4.0-24.5 nM for Group B. These aptamers have also been successfully employed as receptors in an electrochemical biosensor platform, enabling the selective detection of each group based on the corresponding aptamer (limit of detection was 7.8 and 3.2 CFU for Group A and Group B, respectively). The electrochemical sensor effectively detected the extent of infection in each group in powdered infant formula samples. This study highlights the successful screening and application of group-selective aptamers as sensing receptors, emphasizing their potential for diverse applications in different fields such as food safety, environmental monitoring, and clinical diagnostics, where the selective biosensing of target groups is crucial.

17β-estradiol biosensors based on different bioreceptors and their applications

17β-Estradiol (E2) is a critical sex steroid hormone, which has significant effects on the endocrine systems of both humans and animals. E2 is also believed to play neurotrophic and neuroprotective roles in the brain. Biosensors present a powerful tool to detect E2 because of their small, efficient, and flexible design. Furthermore, Biosensors can quickly and accurately obtain detection results with only a small sampling amount, which greatly meets the detection of the environment, food safety, medicine safety, and human body. This review focuses on previous studies of biosensors for detecting E2 and divides them into non-biometric sensors, enzyme biosensors, antibody biosensors, and aptamer biosensors according to different bioreceptors. The advantages, disadvantages, and design points of various bioreceptors for E2 detection are analyzed and summarized. Additionally, applications of different bioreceptors of E2 detection are presented and highlight the field of environmental monitoring, food and medicine safety, and disease detection in recent years. Finally, the development of E2 detection by biosensor is prospected.

Aptamer-Based Smart Targeting and Spatial Trigger-Response Drug-Delivery Systems for Anticancer Therapy

In recent years, the field of drug delivery has witnessed remarkable progress, driven by the quest for more effective and precise therapeutic interventions. Among the myriad strategies employed, the integration of aptamers as targeting moieties and stimuli-responsive systems has emerged as a promising avenue, particularly in the context of anticancer therapy. This review explores cutting-edge advancements in targeted drug-delivery systems, focusing on the integration of aptamers and stimuli-responsive platforms for enhanced spatial anticancer therapy. In the aptamer-based drug-delivery systems, we delve into the versatile applications of aptamers, examining their conjugation with gold, silica, and carbon materials. The synergistic interplay between aptamers and these materials is discussed, emphasizing their potential in achieving precise and targeted drug delivery. Additionally, we explore stimuli-responsive drug-delivery systems with an emphasis on spatial anticancer therapy. Tumor microenvironment-responsive nanoparticles are elucidated, and their capacity to exploit the dynamic conditions within cancerous tissues for controlled drug release is detailed. External stimuli-responsive strategies, including ultrasound-mediated, photo-responsive, and magnetic-guided drug-delivery systems, are examined for their role in achieving synergistic anticancer effects. This review integrates diverse approaches in the quest for precision medicine, showcasing the potential of aptamers and stimuli-responsive systems to revolutionize drug-delivery strategies for enhanced anticancer therapy.

Dual-color nanospheres based on aggregation-induced emission and catalytic hairpin assembly for simultaneous imaging of acrylamide and miR-21 in living cells

Acrylamide (AA) is a heat-processed potent food carcinogen that is widely used in industry, posing a significant risk to human health. Therefore, it is necessary to investigate the toxic effects and mechanism of AA. miR-21 is a representative biomarker during AA-induced carcinogenesis. Here, dual-color aggregation-induced emission nanoparticles (AIENPs) were developed for the detection and simultaneous imaging of AA and miR-21. AIENPs were synthesized by combining aggregation-induced emission (AIE) dyes and a poly (styrene-co-maleic anhydride) (PSMA) amphiphilic polymer modified with hairpin DNA. Upon AA intervention and aptamer recognition, cDNA was dissociated, leading to miR-21 overexpression and initiating the catalytic hairpin assembly cycle. Consequently, fluorescence quenching was observed due to FRET between AIENPs and labeled quenchers. The relative fluorescence intensities of dual-color AIENPs displayed good linear relationships with logarithmic AA and miR-21 concentrations. Moreover, there was a gradual decrease in dual-color AIENP fluorescence as the HepG2 cell concentration of AA (0-500 μM) and stimulation time (0-12 h) increased, making it possible to simultaneously image AA and AA-induced miR-21. The findings of this work are valuable for revealing the cytotoxic mechanism of AA.

A Universal Aptamer for Influenza A Viruses: Selection, Recognition, and Infection Inhibition

It is crucial to develop universal inhibitors for viral inhibition due to the rapid mutation of viruses. Herein, a universal aptamer inhibitor was developed that enabled a single DNA molecule to recognize several hemeagglutinin (HA) protein subtypes, inducing broad neutralization against influenza A viruses (IAVs). Through a multi-channel enrichment (MCE) strategy, a high-affinity aptamer named UHA-2 was obtained, with its dissociation constants (Kd) for three different HA proteins being 1.5 ± 0.2 nM (H5N1), 3.7 ± 0.4 nM (H7N9), and 10.1 ± 1.1 nM (H9N2). The UHA-2 aptamer had a universal inhibition effect, by which it could broadly neutralize influenza A H5N1, H7N9, H9N2, H1N1, and H3N2 viruses. Universal aptamer inhibitors have the advantages of acquisition in vitro, stability, simple structure, small size, etc. This study not only develops a novel universal aptamer to achieve a broad inhibition effect on various IAVs, but also opens up an efficient strategy for the development of universal inhibitors against viruses.

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.

Enhancing or Quenching of a Mitochondria-Targeted AIEgens-Floxuridine Sensor by the Regulation of pH-Dependent Self-assembly, Efficient Recognition of Hg2+, and Stimulated Response of GSH

Biocompatible fluorescent probes have emerged as essential tools in life sciences for visualizing subcellular structures and detecting specific analytes. Herein, we report the synthesis and characterization of a novel fluorescent probe (TPE-FdU), incorporated with hydrophilic 2'-fluoro-substituted deoxyuridine and hydrophobic ethynyl tetraphenylethene moieties, which possessed typical aggregation-induced emission (AIE) behavior. In comparison to the TPE-FdU (pKa 7.68) treated in neutral conditions, it performed well at pH 4, exhibiting an enhanced 450 nm emission signal of approximately four times stronger. As the pH value was increased to 10, the fluorescence intensity was completely quenched. The TEM images of TPE-FdU in an acidic environment (nanospherical morphology, AIE enhance, pH = 4) and in a basic environment (microrods, fluorescence quenching, pH = 9) revealed that it was a pH-dependent self-assembled probe, which was also illustrated by the interpretation of the NMR spectrum. Furthermore, the TPE-FdU probe exhibited a specific response to trace Hg2+ ions. Interestingly, the quenched fluorescence of the TPE-FdU probe caused by Hg2+ can be recovered by the addition of GSH due to the formation of the Hg-S bond being released away. MTT assay and CLSM images demonstrated that TPE-FdU was nontoxic and selectively visualized in the intracellular mitochondria. These results contributed to the development of advanced fluorescent probes with diverse applications in cell imaging, environment protection, and biomedical research.

Aptamer-functionalized hydrogels promote bone healing by selectively recruiting endogenous bone marrow mesenchymal stem cells

Bone regeneration heavily relies on bone marrow mesenchymal stem cells (BMSCs). However, recruiting endogenous BMSCs for in situ bone regeneration remains challenging. In this study, we developed a novel BMSC-aptamer (BMSC-apt) functionalized hydrogel (BMSC-aptgel) and evaluated its functions in recruiting BMSCs and promoting bone regeneration. The functional hydrogels were synthesized between maleimide-terminated 4-arm polyethylene glycols (PEG) and thiol-flanked PEG crosslinker, allowing rapid in situ gel formation. The aldehyde group-modified BMSC-apt was covalently bonded to a thiol-flanked PEG crosslinker to produce high-density aptamer coverage on the hydrogel surface. In vitro and in vivo studies demonstrated that the BMSC-aptgel significantly increased BMSC recruitment, migration, osteogenic differentiation, and biocompatibility. In vivo fluorescence tomography imaging demonstrated that functionalized hydrogels effectively recruited DiR-labeled BMSCs at the fracture site. Consequently, a mouse femur fracture model significantly enhanced new bone formation and mineralization. The aggregated BMSCs stimulated bone regeneration by balancing osteogenic and osteoclastic activities and reduced the local inflammatory response via paracrine effects. This study's findings suggest that the BMSC-aptgel can be a promising and effective strategy for promoting in situ bone regeneration.

Superanionic DNA: enzymatic synthesis of hypermodified DNA bearing four different anionic substituents at all four nucleobases

We designed and synthesized a set of four 2'-deoxyribonucleoside 5'-O-triphosphates (dNTPs) derived from 5-substituted pyrimidines and 7-substituted 7-deazapurines bearing anionic substituents (carboxylate, sulfonate, phosphonate, and phosphate). The anion-linked dNTPs were used for enzymatic synthesis of modified and hypermodified DNA using KOD XL DNA polymerase containing one, two, three, or four modified nucleotides. The polymerase was able to synthesize even long sequences of >100 modified nucleotides in a row by primer extension (PEX). We also successfully combined two anionic and two hydrophobic dNTPs bearing phenyl and indole moieties. In PCR, the combinations of one or two modified dNTPs gave exponential amplification, while most of the combinations of three or four modified dNTPs gave only linear amplification in asymmetric PCR. The hypermodified ONs were successfully re-PCRed and sequenced by Sanger sequencing. Biophysical studies including hybridization, denaturation, CD spectroscopy and molecular modelling and dynamics suggest that the presence of anionic modifications in one strand decreases the stability of duplexes while still preserving the B-DNA conformation, whilst the DNA hypermodified in both strands adopts a different secondary structure.

Aptamer-Protein Interactions: From Regulation to Biomolecular Detection

Serving as the basis of cell life, interactions between nucleic acids and proteins play essential roles in fundamental cellular processes. Aptamers are unique single-stranded oligonucleotides generated by in vitro evolution methods, possessing the ability to interact with proteins specifically. Altering the structure of aptamers will largely modulate their interactions with proteins and further affect related cellular behaviors. Recently, with the in-depth research of aptamer-protein interactions, the analytical assays based on their interactions have been widely developed and become a powerful tool for biomolecular detection. There are some insightful reviews on aptamers applied in protein detection, while few systematic discussions are from the perspective of regulating aptamer-protein interactions. Herein, we comprehensively introduce the methods for regulating aptamer-protein interactions and elaborate on the detection techniques for analyzing aptamer-protein interactions. Additionally, this review provides a broad summary of analytical assays based on the regulation of aptamer-protein interactions for detecting biomolecules. Finally, we present our perspectives regarding the opportunities and challenges of analytical assays for biological analysis, aiming to provide guidance for disease mechanism research and drug discovery.

Aptamer-modified chitosan-capped mesoporous silica nanoparticles for co-delivery of cytarabine and daunorubicin in leukemia

In this study, surface modified mesoporous silica nanoparticles (MSNs) were prepared for the targeted delivery of the anticancer agents, daunorubicin (DNR) and cytarabine (CTR), against K562 leukemia cancer cell lines. The MSNs were surface-modified with pH-sensitive chitosan (CS) to prevent the burst release of anticancer agents at the physiological pH of 7.4 and to enable a higher drug release at lower pH and higher concentration of glutathione. Finally, the MSNs were surface modified with KK1B10 aptamer (Apt) to enhance their uptake by K562 cells through ligand-receptor interactions. The MSNs were characterized using different methods and both in vitro and in vivo experiments were utilized to demonstrate their suitability as targeted anticancer agents. The resultant MSNs exhibited an average particle size of 295 nm, a surface area of 39.06 m2/g, and a cumulative pore volume of 0.09 cm3/g. Surface modification of MSNs with chitosan (CS) resulted in a more regulated and acceptable continuous release rate of DNR. The drug release rate was significantly higher at pH 5 media enriched with glutathione, compared to pH 7.4. Furthermore, MSNs coated with CS and conjugated with aptamer (MSN-DNR + CTR@CS-Apt) exhibited a lower IC50 value of 2.34 µg/ml, compared to MSNs without aptamer conjugation, which displayed an IC50 value of 12.27 µg/ml. The results of the cell cycle analysis indicated that the administration of MSN-DNR + CTR@CS-Apt led to a significant increase in the population of apoptotic cells in the sub-G1 phase. Additionally, the treatment arrested the remaining cells in various other phases of the cell cycle. Furthermore, the interactions between Apt-receptors were found to enhance the uptake of MSNs by cancer cells. The results of in vivo studies demonstrated that the administration of MSN-DNR + CTR@CS-Apt led to a significant reduction in the expression levels of CD71 and CD235a markers, as compared to MSN-DNR + CTR@CS (p < 0.001). In conclusion, the surface modified MSNs prepared in this study showed lower IC50 against cancer cell lines and higher anticancer activity in animal models.

Modified nucleic acid aptamers: development, characterization, and biological applications

Aptamers are single-stranded oligonucleotides that bind to their targets via specific structural interactions. To improve the properties and performance of aptamers, modified nucleotides are incorporated during or after a selection process such as systematic evolution of ligands by exponential enrichment (SELEX). We summarize the latest modified nucleotides and strategies used in modified (mod)-SELEX and post-SELEX to develop modified aptamers, highlight the methods used to characterize aptamer-target interactions, and present recent progress in modified aptamers that recognize different targets. We discuss the challenges and perspectives in further advancing the methodologies and toolsets to accelerate the discovery of modified aptamers, improve the throughput of aptamer-target characterization, and expand the functional diversity and complexity of modified aptamers.

Arylethynyl- or Alkynyl-Linked Pyrimidine and 7-Deazapurine 2'-Deoxyribonucleoside 3'-Phosphoramidites for Chemical Synthesis of Hypermodified Hydrophobic Oligonucleotides

We designed and synthesized a set of 2'-deoxyribonucleoside 3'-phosphoramidites derived from 5-phenylethynyluracil, 5-(pentyn-1-yl)cytosine, 7-(indol-3-yl)ethynyl-7-deazaadenine, and 7-isopropylethynyl-7-deazaguanine. These nucleoside phosphoramidites were successfully used for automated solid-phase synthesis of oligonucleotides containing one or several modifications, including fully modified sequences where every nucleobase was displaying a modification, and their hybridization was studied. The phosphoramidite building blocks have potential for synthesis of hypermodified aptamers and other functional nucleic acid-based polymers, which sequence-specifically display amino acid-like hydrophobic substituents.

Strict Interactions of Fifth Letters, Hydrophobic Unnatural Bases, in XenoAptamers with Target Proteins

XenoAptamers are DNA fragments containing additional letters (unnatural bases, UBs) that bind specifically to their target proteins with high affinities (sub-nanomolar KD values). One of the UBs is the highly hydrophobic 7-(2-thienyl)imidazo[4,5-b]pyridine (Ds), which significantly increases XenoAptamers' affinities to targets. Originally, Ds was developed as a third base pair with a complementary UB, 2-nitro-4-propynylpyrrole (Px), for replication, and thus it can be used for aptamer generation by an evolutional engineering method involving PCR amplification. However, it is unclear whether the Ds base is the best component as the hydrophobic fifth-letter ligand for interactions with target proteins. To optimize the ligand structure of the fifth letter, we prepared 13 Ds variants and examined the affinities of XenoAptamers containing these variants to target proteins. The results obtained using four XenoAptamers prepared by the replacement of Ds bases with variants indicated that subtle changes in the chemical structure of Ds significantly affect the XenoAptamer affinities. Among the variants, placing either 4-(2-thienyl)pyrrolo[2,3-b]pyridine (Ys) or 4-(2-thienyl)benzimidazole (Bs) at specific Ds positions in each original XenoAptamer greatly improved their affinities to targets. The Ys and Bs bases are variants derived by replacing only one nitrogen with a carbon in the Ds base. These results demonstrate the strict intramolecular interactions, which are not simple hydrophobic contacts between UBs and targets, thus providing a method to mature XenoAptamers' affinities to targets.

Comparative Analysis of pH and Target-Induced Conformational Changes of an Oxytetracycline Aptamer in Solution Phase and Surface-Immobilized Form

To date, numerous aptamer-based biosensing platforms have been developed for sensitive and selective monitoring of target analytes, relying on analyte-induced conformational changes in the aptamer for the quantification of the analyte and the conversion of the binding event into a measurable signal. Despite the impact of these conformational rearrangements on sensor performance, the influence of the environment on the structural conformations of aptamers has rarely been investigated, so the link between parameters directly influencing aptamer folding and the ability of the aptamer to bind to the target analyte remains elusive. Herein, the effect a number of variables have on an aptamer's 3D structure was examined, including the pH of the buffering medium, as well as the anchoring of the aptamer on a solid support, with the use of two label-free techniques. Circular dichroism spectroscopy was utilized to study the conformation of an aptamer in solution along with any changes induced to it by the environment (analyte binding, pH, composition and ionic strength of the buffer solution), while quartz crystal microbalance with dissipation monitoring was employed to investigate the surface-bound aptamer's behavior and performance. Analysis was performed on an aptamer against oxytetracycline, serving as a model system, representative of aptamers selected against small molecule analytes. The obtained results highlight the influence of the environment on the folding and thus analyte-binding capacity of an aptamer and emphasize the need to deploy appropriate surface functionalization protocols in sensor development as a means to minimize the steric obstructions and undesirable interactions of an aptamer with a surface onto which it is tethered.

Profiling extracellular vesicle surface proteins with 10 µL peripheral plasma within 4 h

Extracellular vesicle (EV) surface proteins, expressed by primary tumours, are important biomarkers for early cancer diagnosis. However, the detection of these EV proteins is complicated by their low abundance and interference from non-EV components in clinical samples. Herein, we present a MEmbrane-Specific Separation and two-step Cascade AmpLificatioN (MESS2CAN) strategy for direct detection of EV surface proteins within 4 h. MESS2CAN utilises novel lipid probes (long chains linked by PEG2K with biotin at one end, and DSPE at the other end) and streptavidin-coated magnetic beads, permitting a 49.6% EV recovery rate within 1 h. A dual amplification strategy with a primer exchange reaction (PER) cascaded by the Cas12a system then allows sensitive detection of the target protein at 10 EV particles per microliter. Using 4 cell lines and 90 clinical test samples, we demonstrate MESS2CAN for analysing HER2, EpCAM and EGFR expression on EVs derived from cells and patient plasma. MESS2CAN reports the desired specificity and sensitivity of EGFR (AUC = 0.98) and of HER2 (AUC = 1) for discriminating between HER2-positive breast cancer, triple-negative breast cancer and healthy donors. MESS2CAN is a pioneering method for highly sensitive in vitro EV diagnostics, applicable to clinical samples with trace amounts of EVs.

Screening a DNA Aptamer Specifically Targeting Integrin β3 and Partially Inhibiting Tumor Cell Migration

Due to its key roles in malignant tumor progression and reprograming of the tumor microenvironment, integrin β3 has attracted great attention as a new target for tumor therapy. However, the structure-function relationship of integrins β3 remains incompletely understood, leading to the shortage of specific and effective targeting probes. This work uses a purified extracellular domain of integrin β3 and integrin β3-positive cells to screen aptamers, specifically targeting integrin β3 in the native conformation on live cells through the SELEX approach. Following meticulous truncation and characterization of the initial aptamer candidates, the optimized aptamer S10yh2 was produced, exhibiting a low equilibrium dissociation constant (Kd) in the nanomolar range. S10yh2 displays specific recognition of cancer cells with varying levels of integrin β3 expression and demonstrates favorable stability in serum. Subsequent analysis of docking sites revealed that S10yh2 binds to the seven amino acid residues located in the core region of integrin β3. The S10yh2 aptamer can downregulate the level of integrin heterodimer αvβ3 on integrin β3 overexpressed cancer cells and partially inhibit cell migration behavior. In summary, S10yh2 is a promising probe with a small size, simple synthesis, good stability, high binding affinity, and selectivity. It therefore holds great potential for investigating the structure-function relationship of integrins.

Development of DNA Aptamer-Based PROTACs That Degrade the Estrogen Receptor

Targeted protein degradation (TPD), using chimeric molecules such as proteolysis-targeting chimeras (PROTACs), has attracted attention as a strategy for selective degradation of intracellular proteins by hijacking the ubiquitin-proteasome system (UPS). However, it is often difficult to develop such degraders due to the absence of appropriate ligands for target proteins. In targeting proteins for degradation, the application of nucleic acid aptamers is considered to be effective because these can be explored using systematic evolution of ligand by exponential enrichment (SELEX) methods. In this study, we constructed chimeric molecules in which nucleic acid aptamers capable of binding to the estrogen receptor α (ERα) and E3 ubiquitin ligase ligands were linked via a linker. ERα aptamer-based PROTACs were found to degrade ERα via the UPS. These findings represent the development of novel aptamer-based PROTACs that target intracellular proteins and are potentially applicable to other proteins.

A novel His-tag-binding aptamer for recombinant protein detection and T cell-based immunotherapy

Screening novel aptamers for recombinant protein detection is of great significance in industrial mass production of antibody drugs. In addition, construction of structurally stable bispecific circular aptamers (bc-apts) may provide a tumor-targeted treatment strategy by simultaneously binding two different cell types. In this study, we obtained a high-affinity hexahistidine tag (His-tag)-binding aptamer 20S and explored its application in recombinant protein detection and T cell-based immunotherapy. We developed a new molecular beacon (MB) 20S-MB to detect His-tagged proteins in vitro and in vivo with high sensitivity and specificity, and the results showed high consistency with the enzyme-linked immunosorbent assay (ELISA). Moreover, we constructed two kinds of bc-apts by cyclizing 20S or another His-tag-binding aptamer, 6H5-MU, with Sgc8, which specifically recognizes protein tyrosine kinase 7 (PTK7) on tumor cells. After forming a complex with His-tagged OKT3, an anti-CD3 antibody for T cell activation, we utilized these aptamer-antibody complexes (ap-ab complex) to enhance cytotoxicity of T cells by linking T cells and target cells together, and 20S-sgc8 exhibited antitumor efficacy superior to that of 6H5-sgc8. In conclusion, we screened a novel His-tag-binding aptamer and used it to construct a new type of MB for rapid detection of recombinant proteins, as well as establish a feasible approach for T cell-based immunotherapy.

Customization of aptamer to develop CRISPR/Cas12a-derived ultrasensitive biosensor

The CRISPR/Cas systems have provided wide biosensing applications. Particularly, the aptamer-involved CRISPR/Cas sensor system powerfully expanded to non-nucleic-acid targets. However, tailoring the sequence of the aptamer to explore the relationship between affinity and the activation of CRISPR/Cas12a trans-cleavage activity has not been reported yet. Herein, we developed a series of new aptamers toward the spike protein 1(S1) of SARS-CoV-2. Surface plasmon resonance measurements showed that the affinity of these aptamers to S1 was at the nM level. Subsequently, a "SET" effect (Sequence Essential Trans-cleavage activity) is discovered for the activation of CRISPR/Cas12a trans-cleavage activity. That is, an aptamer, as the activator, sequence needs to be tailored to activate CRISPR/Cas12a efficiently. A balance should be reached between affinity and activation ability. On the one hand, high affinity ensures target recognition performance, and on the other hand, activation can achieve adequate amplification and output of recognition signals. The optimized sequence (with 27 nucleotides, for short 27-nt) not only recognizes the target with a high affinity and specificity but also can trigger the CRISPR/Cas12a trans-cleavage activity efficiently, showing an excellent detection performance in electrochemical biosensors. The detection limit for SARS-CoV-2 S1 can be low at 1.5 pg mL^-1. The new CRISPR/Cas12a-derived aptasensor also displays a remarkable ability to detect Beta, Delta, and Omicron variants but is selective toward other kinds of proteins. Above all, it is robust for point-of-care testing (POCT) in complex biological fluids, such as saliva, urine, and serum, and provides a universal and scalable detecting platform. Our results provide new insights into aptamer development and a different strategy for COVID-19 antigen detection and biosensor development.

An aptamer-based depot system for sustained release of small molecule therapeutics

Delivery of hydrophilic small molecule therapeutics by traditional drug delivery systems is challenging. Herein, we have used the specific interaction between DNA aptamers and drugs to create simple and effective drug depot systems. The specific binding of a phosphorothioate-modified aptamer to drugs formed non-covalent aptamer/drug complexes, which created a sustained release system. We demonstrated the effectiveness of this system with small hydrophilic molecules, the site 1 sodium channel blockers tetrodotoxin and saxitoxin. The aptamer-based delivery system greatly prolonged the duration of local anesthesia and reduced systemic toxicity. The beneficial effects of the aptamers were restricted to the compounds they were specific to. These studies establish aptamers as a class of highly specific, modifiable drug delivery systems, and demonstrate potential usefulness in the management of postoperative pain.

Interactions of Amino Group Functionalized Tetraphenylvinyl and DNA: A Label-Free "On-Off-On" Fluorescent Aptamer Sensor toward Ampicillin

As a type of aggregation-induced emission (AIE) fluorescent probe, tetraphenylvinyl (TPE) or its derivatives are widely used in chemical imaging, biosensing and medical diagnosis. However, most studies have focused on molecular modification and functionalization of AIE to enhance the fluorescence emission intensity. There are few studies on the interaction between aggregation-induced emission luminogens (AIEgens) and nucleic acids, which was investigated in this paper. Experimental results showed the formation of a complex of AIE/DNA, leading to the quenching of the fluorescence of AIE molecules. Fluorescent test experiments with different temperatures proved that the quenching type was static quenching. The quenching constants, binding constants and thermodynamic parameters demonstrated that electrostatic and hydrophobic interactions promoted the binding process. Then, a label-free "on-off-on" fluorescent aptamer sensor for the detection of ampicillin (AMP) was constructed based on the interaction between the AIE probe and the aptamer of AMP. Linear range of the sensor is 0.2-10 nM with a limit of detection 0.06 nM. This fluorescent sensor was applied to detect AMP in real samples.

Detection of saxitoxin by a SERS aptamer sensor based on enzyme cycle amplification technology

Saxitoxin (STX) is a typical toxic guanidinium neurotoxin, one of the paralytic shellfish poisons (PSP), which poses a serious threat to human health. In this paper, a simple and sensitive SERS aptamer sensor (abbreviated as AuNP@4-NTP@SiO₂) for the quantitative determination of STX was developed. Hairpin aptamers of saxitoxin are modified on magnetic beads and used as recognition elements. In the presence of STX, DNA ligase, and the rolling circle template (T1), a rolling circle amplification reaction was triggered to produce long single-stranded DNA containing repetitive sequences. The sequence can be hybridized with the SERS probe to realize the rapid detection of STX. Due to the inherent merits of its components, the obtained AuNP@4-NTP@SiO₂ SERS aptamer sensor manifests excellent sensing performance for STX detection with a wide linear range from 2.0 × 10^-10 mol L^-1 to 5.0 × 10^-4 mol L^-1 and a lower detection limit of 1.2 × 10^-11 mol L^-1. This SERS sensor can provide a strategy for the micro-detection of other biological toxins by changing the aptamer sequence.

Aptamers against cancer drug resistance: Small fighters switching tactics in the face of defeat

Discovering novel cancer therapies has attracted extreme interest in the last decade. In this regard, multidrug resistance (MDR) to chemotherapies is the primary challenge in cancer treatment. Cancerous cells are growingly become resistant to existing chemotherapeutics by employing diverse mechanisms, highlighting the significance of discovering approaches to overcome MDR. One promising strategy is utilizing aptamers as unique tools to target elements or signalings incorporated in resistance mechanisms or develop active targeted drug delivery systems or chimeras enabling the precise delivery of novel agents to inhibit the conventionally undruggable resistance elements. Further, due to their advantages over their proteinaceous counterparts, particularly antibodies, including improved targeting action, enhanced thermal stability, easier production, and superior tumor penetration, aptamers are emerging and have frequently been considered for developing cancer therapeutics. Here, we highlighted significant chemoresistance pathways and thoroughly discussed using aptamers as prospective tools to surmount cancer MDR.

The selection of a hydrophobic 7-phenylbutyl-7-deazaadenine-modified DNA aptamer with high binding affinity for the Heat Shock Protein 70

Nucleic acids aptamers often fail to efficiently target some proteins because of the hydrophilic character of the natural nucleotides. Here we present hydrophobic 7-phenylbutyl-7-deaadenine-modified DNA aptamers against the Heat Shock Protein 70 that were selected via PEX and magnetic bead-based SELEX. After 9 rounds of selection, the pool was sequenced and a number of candidates were identified. Following initial screening, two modified aptamers were chemically synthesised in-house and their binding affinity analysed by two methods, bio-layer interferometry and fluorescent-plate-based binding assay. The binding affinities of the modified aptamers were compared with that of their natural counterparts. The resulting modified aptamers bound with higher affinity (low nanomolar range) to the Hsp70 than their natural sequence (>5 µM) and hence have potential for applications and further development towards Hsp70 diagnostics or even therapeutics.

Recent Advances in Aptamer-Based Sensors for Sensitive Detection of Neurotransmitters

In recent years, there has been an increased demand for highly sensitive and selective biosensors for neurotransmitters, owing to advancements in science and technology. Real-time sensing is crucial for effective prevention of neurological and cardiovascular diseases. In this review, we summarise the latest progress in aptamer-based biosensor technology, which offers the aforementioned advantages. Our focus is on various biomaterials utilised to ensure the optimal performance and high selectivity of aptamer-based biosensors. Overall, this review aims to further aptamer-based biosensor technology.

Biomedical applications of aptamer-modified chitosan nanomaterials: An updated review

Among polysaccharides of environmental and economic interest, chitosan (CS) is receiving much attention, particularly in the food and biotechnology industries to encapsulate active food ingredients and immobilize enzymes. CS nanoparticles (CS NPs) combine the intrinsic beneficial properties of both natural polymers and nanoscale particles such as quantum size effect, biocompatibility, biodegradability, and ease of modification, and have great potential for bioimaging, drug delivery, and biosensing applications. Aptamers are single-stranded oligonucleotides that can fold into predetermined structures and bind to the corresponding biomolecules. They are mainly used as targeting ligands in biosensors, disease diagnostic kits and treatment strategies. They can deliver contrast agents and drugs into cancer cells and tissues, control microorganism growth and precisely target pathogens. Aptamer-conjugated CS NPs can significantly improve the efficacy of conventional therapies, minimize their side effects on normal tissues, and overcome the enhanced permeability retention (EPR) effect. Further, aptamer-conjugated carbohydrate-based nanobiopolymers have shown excellent antibacterial and antiviral properties and can be used to develop novel biosensors for the efficient detection of antibiotics, toxins, and other biomolecules. This updated review aims to provide a comprehensive overview of the bioapplications of aptamer-conjugated CS NPs used as innovative diagnostic and therapeutic platforms, their limitations, and potential future directions.

Electrochemical Aptasensor Based on ZnO-Au Nanocomposites for the Determination of Ochratoxin A in Wine and Beer

Ochratoxin A (OTA) is positively correlated with an increased risk of developing cancer in nephrotoxic and hepatotoxic patients. Therefore, it is of great significance for the highly sensitive, highly selective, and timely detection of OTA. We described here an electrochemical aptasensor for OTA analysis, which took advantage of the favorable properties of gold nanoparticles (AuNPs) functionalized zinc oxide (ZnO) composites and the intercalative binding between methylene blue (MB) and nucleic acid. There were two label-free aptamers: one to capture OTA and another serving as complementary DNA (cDNA), enabling connection to the ZnO-Au composite’s immobilized electrode. Once OTA was present, the aptamer could capture OTA and detach from the electrode interface, thus, preventing MB from accessing electrode surface for efficient electron transfer; a decreased peak current was monitored by differential pulse voltammetry. The aptasensor presented nice analytical performance for OTA detection in the range of 0.1–30,000 pg·mL−1, with a detection limit of 0.05 pg·mL−1. Moreover, the developed biosensor could be applied to actual sample (wine and beer) analysis.

Monitoring Cd2+ in oily wastewater using an aptamer-graphene field-effect transistor with a selective wetting surface

The discharge of oily industrial wastewater containing heavy metal ions with the development of industry severely threatens the environment and human health. Therefore, it is of great significance to monitor the concentration of heavy metal ions in oily wastewater quickly and effectively. Here, an integrated Cd²⁺ monitoring system consisting of an aptamer-graphene field-effect transistor (A-GFET), oleophobic/hydrophilic surface and monitoring-alarm circuits was presented for monitoring the Cd²⁺ concentration in oily wastewater. In the system, oil and other impurities in wastewater are isolated by an oleophobic/hydrophilic membrane before detection. The concentration of Cd²⁺ is then detected by a graphene field-effect transistor with a Cd²⁺ aptamer modifying the graphene channel. Finally, the detected signal is collected and processed by signal processing circuits to judge whether the Cd²⁺ concentration exceeds the standard. Experimental results demonstrated that the separation efficiency of the oleophobic/hydrophilic membrane to an oil/water mixture was up to 99.9%, exhibiting a high oil/water separation ability. The A-GFET detecting platform could respond to changes in the Cd²⁺ concentration within 10 min with a limit of detection (LOD) of 0.125 pM. The sensitivity of this detection platform to Cd²⁺ near 1 nM was 7.643 × 10^-2 nM^-1. Compared with control ions (Cr³⁺, Pb²⁺, Mg²⁺, Fe³⁺), this detection platform exhibited a high specificity to Cd²⁺. Moreover, the system could send out a photoacoustic alarm signal when the Cd²⁺ concentration in the monitoring solution exceeds the preset value. Therefore, the system is practical for monitoring the concentration of heavy metal ions in oily wastewater.

Success probability of high-affinity DNA aptamer generation by genetic alphabet expansion

Nucleic acid aptamers as antibody alternatives bind specifically to target molecules. These aptamers are generated by isolating candidates from libraries with random sequence fragments, through an evolutionary engineering system. We recently reported a high-affinity DNA aptamer generation method that introduces unnatural bases (UBs) as a fifth letter into the library, by genetic alphabet expansion. By incorporating hydrophobic UBs, the affinities of DNA aptamers to target proteins are increased over 100-fold, as compared with those of conventional aptamers with only the natural four letters. However, there is still plenty of room for improvement of the methods for routinely generating high-affinity UB-containing DNA (UB-DNA) aptamers. The success probabilities of the high-affinity aptamer generation depend on the existence of the aptamer candidate sequences in the initial library. We estimated the success probabilities by analysing several UB-DNA aptamers that we generated, as examples. In addition, we investigated the possible improvement of conventional aptamer affinities by introducing one UB at specific positions. Our data revealed that UB-DNA aptamers adopt specific tertiary structures, in which many bases including UBs interact with target proteins for high affinity, suggesting the importance of the UB-DNA library design. This article is part of the theme issue 'Reactivity and mechanism in chemical and synthetic biology'.

Dual-Aptamer-Assisted Ratiometric SERS Biosensor for Ultrasensitive and Precise Identification of Breast Cancer Exosomes

Due to the heterogeneity of breast cancer, its early accurate diagnosis remains a challenge. Exosomes carry abundant genetic materials and proteins and are ideal biomarkers for early cancer detection. Herein, a ratiometric surface-enhanced Raman scattering (SERS) biosensor for exosome detection was constructed using a regularly arranged Au@Ag nanoparticles/graphene oxide (Au@Ag NPs/GO) substrate with 4-nitrothiophenol (4-NTP) molecules as an internal standard. Aptamers of two overexpressed proteins (epithelial cell adhesion molecule and human epidermal growth factor receptor 2) were linked by a short complementary DNA with rhodamine X modified at the 3'-terminal to form V-shaped double-stranded DNA, which attached to the surface of Au@Ag NPs/GO substrate for the selective recognition of breast cancer cell-derived exosomes. In the presence of exosomes, a competitive reaction occurred, resulting in the formation of the V-shaped double-stranded DNA/exosomes complex, and the V-shaped double-stranded DNA separated from the SERS substrate. The SERS signal of rhodamine X on the V-shaped double-stranded DNA decreased with the concentration of exosomes increasing, whereas the SERS signal of 4-NTP on the substrate remained stable. The ratiometric SERS strategy provides huge electromagnetic enhancement and abundant DNA adsorbing sites on the GO layer, achieving a wide detection range of 2.7 × 10² to 2.7 × 10⁸ particles/mL and an ultralow limit of detection down to 1.5 × 10² particles/mL, without the requirement of any nucleic acid amplification. Particularly, the proposed method has significant applications in early cancer diagnosis as it can accurately identify breast cancer cell-derived exosomes in clinical serum samples and can differentiate pancreatic cancer patients and healthy individuals.

Aptamers in cancer therapy: problems and new breakthroughs

Aptamers, a class of oligonucleotides that can bind with molecular targets with high affinity and specificity, have been widely applied in research fields including biosensing, imaging, diagnosing, and therapy of diseases. However, compared with the rapid development in the research fields, the clinical application of aptamers is progressing at a much slower speed, especially in the therapy of cancer. Obstructions including nuclease degradation, renal clearance, a complex selection process, and potential side effects have inhibited the clinical transformation of aptamer-conjugated drugs. To overcome these problems, taking certain measures to improve the biocompatibility and stability of aptamer-conjugated drugs in vivo is necessary. In this review, the obstructions mentioned above are thoroughly discussed and the methods to overcome these problems are introduced in detail. Furthermore, landmark research works and the most recent studies on aptamer-conjugated drugs for cancer therapy are also listed as examples, and the future directions of research for aptamer clinical transformation are discussed.

A novel flower-shaped Ag@ZIF-67 chemiluminescence sensor for sensitive detection of CEA

In this work, a chemiluminescence (CL) aptasensor for sensitive carcinoembryonic antigen (CEA) detection was constructed based on the CL system of luminol-H₂O₂-NaOH. Magnetic carbon nanotubes (MCNTs), as the base material, was modified with CEA-aptamer and DNA1, and was combined with the novel flower-shaped Ag@ZIF-67 of modified with DNA2 through the principle of base complementary pairing. CEA combined with aptamer when it existed in the solution. At the same time, MCNTs was adsorbed at the bottom of the container under the influence of external magnetic field, and Ag@ZIF-67 enhanced the CL signal. The CL aptasensor demonstrated high selectivity and sensitivity for CEA in human serum sample with (1-4): a detection limit of 4.53 × 10^-3 ng/mL in case the detection range was 0.05-500 ng/mL. Furthermore, the proposed method had been shown great potential in cancer diagnosis.