Molecular Aptamer Beacons and Their Applications in Sensing, Imaging, and Diagnostics

Computational Frontiers in Aptamer-Based Nanomedicine for Precision Therapeutics: A Comprehensive Review

In the rapidly evolving landscape of nanomedicine, aptamers have emerged as powerful molecular tools, demonstrating immense potential in targeted therapeutics, diagnostics, and drug delivery systems. This paper explores the computational features of aptamers in nanomedicine, highlighting their advantages over antibodies, including selectivity, low immunogenicity, and a simple production process. A comprehensive overview of the aptamer development process, specifically the Systematic Evolution of Ligands by Exponential Enrichment (SELEX) process, sheds light on the intricate methodologies behind aptamer selection. The historical evolution of aptamers and their diverse applications in nanomedicine are discussed, emphasizing their pivotal role in targeted drug delivery, precision medicine and therapeutics. Furthermore, we explore the integration of artificial intelligence (AI), machine learning (ML), Internet of Things (IoT), Internet of Medical Things (IoMT), and nanotechnology in aptameric development, illustrating how these cutting-edge technologies are revolutionizing the selection and optimization of aptamers for tailored biomedical applications. This paper also discusses challenges in computational methods for advancing aptamers, including reliable prediction models, extensive data analysis, and multiomics data incorporation. It also addresses ethical concerns and restrictions related to AI and IoT use in aptamer research. The paper examines progress in computer simulations for nanomedicine. By elucidating the importance of aptamers, understanding their superiority over antibodies, and exploring the historical context and challenges, this review serves as a valuable resource for researchers and practitioners aiming to harness the full potential of aptamers in the rapidly evolving field of nanomedicine.

Ultrasensitive Optical Detection and Elimination of Residual Microtumors with a Postoperative Implantable Hydrogel Sensor for Preventing Cancer Recurrence

In vivo optical imaging of trace biomarkers in residual microtumors holds significant promise for cancer prognosis but poses a formidable challenge. Here, a novel hydrogel sensor is designed for ultrasensitive and specific imaging of the elusive biomarker. This hydrogel sensor seamlessly integrates a molecular beacon nanoprobe with fibroblasts, offering both high tissue retention capability and an impressive signal-to-noise ratio for imaging. Signal amplification is accomplished through exonuclease I-mediated biomarker recycling. The resulting hydrogel sensor sensitively detects the biomarker carcinoembryonic antigen with a detection limit of 1.8 pg mL-1 in test tubes. Moreover, it successfully identifies residual cancer nodules with a median diameter of less than 2 mm in mice bearing partially removed primary triple-negative breast carcinomas (4T1). Notably, this hydrogel sensor is proven effective for the sensitive diagnosis of invasive tumors in post-surgical mice with infiltrating 4T1 cells, leveraging the role of fibroblasts in locally enriching tumor cells. Furthermore, the residual microtumor is rapidly photothermal ablation by polydopamine-based nanoprobe under the guidance of visualization, achieving ≈100% suppression of tumor recurrence and lung metastasis. This work offers a promising alternative strategy for visually detecting residual microtumors, potentially enhancing the prognosis of cancer patients following surgical interventions.

Green synthesis of silver nanoparticles employing hamdard joshanda extract: putative antimicrobial potential against gram positive and gram negative bacteria

The bio-mediated synthesis of nanoparticles offers a sustainable and eco-friendly approach. In the present study, silver nanoparticles (AgNPs) were synthesized using Joshanda extract, a commercially available herbal formulation derived from a traditional medicinal plant, as a reducing and stabilizing agent. The as-synthesized AgNPs were characterized using UV-Vis spectroscopy, dynamic light scattering (DLS), X-ray Diffraction (XRD) study, and Fourier-transform infrared (FTIR) analysis. UV-Vis spectroscopy exhibited a prominent absorption peak at 430 nm, confirming the formation of AgNPs. DLS analysis revealed the size distribution of the nanoparticles, ranging from 80 to 100 nm, and zeta potential measurements indicated a surface charge of - 14.4 mV. The XRD analysis provide evidence for the presence of a face-centered cubic structure within the silver nanoparticles. FTIR analysis further elucidated the interaction of bioactive compounds from the Joshanda extract with the AgNPs' surface. Strong peaks at 765-829 cm-1 indicated C-Cl stretching vibrations of alkyl halides, while the stretching of alkenes C=C was observed at 1641 cm-1. Moreover, the presence of alcohols and phenol (OH) groups was identified at 3448 cm-1, suggesting their involvement in nanoparticle stabilization. The antimicrobial potential of the synthesized AgNPs was evaluated against both gram-negative Pseudomonas aeruginosa and gram-positive Streptococcus mutans using zone of inhibition assays. The AgNPs exhibited remarkable inhibitory effects against both types of bacteria. Additionally, AgNPs-treated groups demonstrated a significant increase in reactive oxygen species (ROS) levels, indicating potential of as-synthesized AgNPs in disruption of the target microbial membranes. Furthermore, the as-synthesized AgNPs exhibited notable anti-biofilm properties by effectively hindering the development of mature biofilms. This study highlights the efficient green synthesis of AgNPs using Joshanda extract and also provides insights into their physico-chemical properties of as-synthesized nanoparticles. The demonstrated antimicrobial activity against both gram-negative and gram-positive bacteria, along with biofilm inhibition potential, underscores the promising applications of the as-synthesized AgNPs in the field of biomedical and environmental sciences. The study bridges traditional knowledge with contemporary nanotechnology, offering a novel avenue for the development of eco-friendly antimicrobial agents.

Aptamer Based SPREETA Sensor for the Detection of Porphyromonas gingivalis G-Protein

We have developed an aptamer that specifically binds to Porphyromonas gingivalis to reduce the cellular damage caused by P. gingivalis infection and applied it as a biosensor. P. gingivalis is one of the major pathogens causing destructive periodontal disease among the periodontal microorganisms constituting complex biofilms. Porphyromonas gingivalis G-protein (PGP) known to play an important role in the transmission of germs was used as a target protein for the screening of aptamer. The aptamer that has binds to the G-protein of P. gingivalis, was screened and developed through the Systemic Evolution of Ligands by Exponential Energy (SELEX) method. Modified-Western blot analysis was performed with the aptamer which consisted of 38 single-stranded DNA to confirm the selectivity. ELONA (enzyme linked oligonucleotide assay) used to confirm that the aptamer was sensitive to PGP even at low concentration of 1 μg/ml. For the rapid detection of P. gingivalis, we constructed a surface plasmon resonance biosensor with SPREETA using the PGP aptamer. It was confirmed that PGP could be detected as low concentration as at 0.1 pM, which is the minimum concentration of aptamer sensor within 5 min. Based on these results, we have constructed a SPREETA biosensor based on aptamer that can bind to P. gingivalis G-protein. It can be used as an infection diagnosis system to rapidly diagnose and analyze oral diseases caused by P. gingivalis.

Aptamer-Antibody Chimera Sensors for Sensitive, Rapid, and Reversible Molecular Detection in Complex Samples

The development of receptors suitable for the continuous detection of analytes in complex, interferent-rich samples remains challenging. Antibodies are highly sensitive but difficult to engineer in order to introduce signaling functionality, while aptamer switches are easy to construct but often yield only a modest target sensitivity. We present here a programmable antibody and DNA aptamer switch (PANDAS), which combines the desirable properties of both receptors by using a nucleic acid tether to link an analyte-specific antibody to an internal strand-displacement (ISD)-based aptamer switch that recognizes the same target through different epitopes. The antibody increases PANDAS analyte binding due to its high affinity, and the effective concentration between the two receptors further enhances two-epitope binding and fluorescent aptamer signaling. We developed a PANDAS sensor for the clotting protein thrombin and show that a tuned design achieves a greater than 300-fold enhanced sensitivity compared to that of using an aptamer alone. This design also exhibits reversible binding, enabling repeated measurements with a temporal resolution of ∼10 min, and retains excellent sensitivity even in interferent-rich samples. With future development, this PANDAS approach could enable the adaptation of existing protein-binding aptamers with modest affinity to sensors that deliver excellent sensitivity and minute-scale resolution in minimally prepared biological specimens.

Fluorescence Biosensing Based on Bifurcated DNA Scaffold-Aggregated Ag Nanocluster via Responsive Conformation Switch of Quasi-Molecular Beacon

To address the limitations of typical hairpin-structural molecular beacons, exploring the ability of a quasi-molecular beacon (qMB) to create label-free fluorescence biosensors is intriguing and remains a challenge. Herein, we propose the first example of modular qMB with the feature of a stimulation-responsive conformation switch to develop an aggregated Ag nanocluster (aAgNC) in a bifurcated DNA scaffold for fluorescently sensing a specific initiator (I*). This qMB was well designed to program four functional modules: I*-recognizable element adopting metastable stem-loop bihairpin structure and two DNA splits (exposed C3GT4 and locked C4AC4T) of aAgNC template that is separated by a tunable hairpin spacer for the customized combination of selective recognition and signaling readout. When presenting I* in an assay route, the specific hybridization induces the directional disassembly of the bihairpin unit, on which the qMB is configurationally switched to liberate the locked split. Thus, the bifurcated parent template pair of C3GT4/C4AC4T is proximal, affording in situ nucleation and clustering of emissive aAgNC. By collecting the fluorescence signal, the quantitative detection of I* is achieved. Benefiting from the ingenious programming of qMB, the recognizing and signaling integration actuates the construction of a facile and convenient fluorescent biosensor featuring rapid reaction kinetics, a wide linear range, high sensitivity, and specificity. This would provide a new paradigm to exploit versatile qMB-based biosensing platforms via stimulation-responsive conformation switches for developing various DNA-scaffolded Ag clusters.

Aptamer-Based Targeting of Cancer: A Powerful Tool for Diagnostic and Therapeutic Aims

Cancer is known as one of the most significant causes of death worldwide, and, in spite of novel therapeutic methods, continues to cause a considerable number of deaths. Targeted molecular diagnosis and therapy using aptamers with high affinity have become popular techniques for pathological angiogenesis and cancer therapy scientists. In this paper, several aptamer-based diagnostic and therapeutic techniques such as aptamer-nanomaterial conjugation, aptamer-drug conjugation (physically or covalently), and biosensors, which have been successfully designed for biomarkers, were critically reviewed. The results demonstrated that aptamers can potentially be incorporated with targeted delivery systems and biosensors for the detection of biomarkers expressed by cancer cells. Aptamer-based therapeutic and diagnostic methods, representing the main field of medical sciences, possess high potential for use in cancer therapy, pathological angiogenesis, and improvement of community health. The clinical use of aptamers is limited due to target impurities, inaccuracy in the systematic evolution of ligands via exponential enrichment (SELEX)stage process, and in vitro synthesis, making them unreliable and leading to lower selectivity for in vivo targets. Moreover, size, behavior, probable toxicity, low distribution, and the unpredictable behavior of nanomaterials in in vivo media make their usage in clinical assays critical. This review is helpful for the implementation of aptamer-based therapies which are effective and applicable for clinical use and the design of future studies.

Application of a Novel Aptamer Beacon for Rapid Detection of IgG1 Antibody Drugs

Antibody drugs have been widely used to treat many diseases and are the fastest-growing drug class. IgG1 is the most common type of antibody because of its good serum stability; however, effective methods for the rapid detection of IgG1-type antibodies are lacking. In this study, we designed two aptamer molecules derived from the reported aptamer probe that has been proven to bind to the Fc fragment of the IgG1 antibody. The results showed that Fc-1S could specifically bind to the human IgG1 Fc proteins. In addition, we modified the structure of Fc-1S and constructed three aptamer molecular beacons that could quantitatively detect IgG1-type antibodies within a short time. Furthermore, we unveiled that the Fc-1S37R beacon has the highest sensitivity for IgG1-type antibodies with a detection limit of 48.82813 ng/mL and can accurately detect serum antibody concentrations in vivo with consistent results to ELISA. Therefore, Fc-1S37R is an efficient method for the production monitoring and quality control of IgG1-type antibodies to enable the large-scale production and application of antibody drugs.

Recent Progress in Micro- and Nanotechnology-Enabled Sensors for Biomedical and Environmental Challenges

Micro- and nanotechnology-enabled sensors have made remarkable advancements in the fields of biomedicine and the environment, enabling the sensitive and selective detection and quantification of diverse analytes. In biomedicine, these sensors have facilitated disease diagnosis, drug discovery, and point-of-care devices. In environmental monitoring, they have played a crucial role in assessing air, water, and soil quality, as well as ensured food safety. Despite notable progress, numerous challenges persist. This review article addresses recent developments in micro- and nanotechnology-enabled sensors for biomedical and environmental challenges, focusing on enhancing basic sensing techniques through micro/nanotechnology. Additionally, it explores the applications of these sensors in addressing current challenges in both biomedical and environmental domains. The article concludes by emphasizing the need for further research to expand the detection capabilities of sensors/devices, enhance sensitivity and selectivity, integrate wireless communication and energy-harvesting technologies, and optimize sample preparation, material selection, and automated components for sensor design, fabrication, and characterization.

Complementary DNA Significantly Enhancing Signal Response and Sensitivity of a Molecular Beacon Probe to Aflatoxin B1

This paper reported an improved molecular beacon method for the rapid detection of aflatoxin B1 (AFB1), a natural mycotoxin with severe carcinogenicity. With the assistance of a complementary DNA (cDNA) chain, the molecular beacon which consists of a DNA aptamer flanked by FAM and BHQ1 displayed a larger fluorescent response to AFB1, contributing to the sensitive detection of AFB1. Upon optimization of some key experimental factors, rapid detection of AFB1 ranging from 1 nM to 3 μM, within 20 min, was realized by using this method. A limit of detection (LoD) of 1 nM was obtained, which was lower than the LoD (8 nM) obtained without cDNA assistance. This aptamer-based molecular beacon detection method showed advantages in easy operation, rapid analysis and larger signal response. Good specificity and anti-interference ability were demonstrated. This method showed potential in real-sample analysis.

Novel Molecular Aptamer Beacon for the Specific Simultaneous Analysis of Circulating Tumor Cells and Exosomes of Colorectal Cancer Patients

Liquid biopsy provides non-invasive and real-time detection for cancer diagnosis, but the lack of specific markers targeted to liquid biopsy components, such as circulating tumor cells (CTCs) and exosomes, has impeded its effective utilization in clinical settings. W3 is an aptamer, and its target has been previously demonstrated to be a predictor of colorectal cancer (CRC) metastasis. Herein, we developed a W3-based molecular beacon (MAB-W3-3G) to specifically detect CTCs and exosomes derived from CRC patients by modifying the W3 sequence and adding a fluorescent group FAM at the 5' end and a quencher group BHQ1 at the 3' end, resulting in a detectable green fluorescence only in the presence of the target. MAB-W3-3G retained features similar to those of the original W3, including high specificity and affinity for metastatic CRC cells, as well as excellent plasma stability. Notably, W3 target-positive CTCs were visualized, positive exosomes were quantified in CRC patients' whole blood without any sample pretreatment, and both detections could be finished in one step without any routine washing procedures. For CRC, the W3 target-positive CTC enumeration in metastasis was higher than that in non-metastasis (p < 0.01), and the quantitation of positive exosomes was correlated with CRC patients (p < 0.0001). Moreover, the MAB-W3-3G-based simultaneous detection of CTCs and exosomes was proven to have the potential for more precise clinical diagnosis. In conclusion, MAB-W3-3G could detect CTCs and exosomes in the blood samples of tumor patients with simple manipulation, rapid analysis, and high specificity, providing an effective liquid biopsy tool for the prediction of CRC.

DNA Nanomaterial-Based Optical Probes for Exosomal miRNA Detection

Micro ribonucleic acids (miRNAs) in exosomes have been proven as reliable biomarkers to detect disease progression. In recent years, deoxyribonucleic acid (DNA)-based nanomaterials show great potential in the field of diagnosis due to the programmable sequence, various molecule recognition and predictable assembly/disassembly of DNA. In this review, we focus on the molecular design and detection mechanism of DNA nanomaterials, and the developed DNA nanomaterial-based optical probes for exosomal miRNA detection are summarized and discussed. The rationally-designed DNA sequences endows these probes with low background signal and high sensitivity in exosomal miRNA detection, and the detection mechanisms based on different DNA nanomaterials are detailly introduced. At the end, the challenges and future opportunities of DNA nanomaterial-based optical probes in exosomal miRNA detection are discussed. We envision that DNA nanomaterial-based optical probes will be promising in precise biomedicine.

Aptamer Molecular Beacon Sensor for Rapid and Sensitive Detection of Ochratoxin A

Ochratoxin A (OTA) is a carcinogenic fungal secondary metabolite which causes wide contamination in a variety of food stuffs and environments and has a high risk to human health. Developing a rapid and sensitive method for OTA detection is highly demanded in food safety, environment monitoring, and quality control. Here, we report a simple molecular aptamer beacon (MAB) sensor for rapid OTA detection. The anti-OTA aptamer has a fluorescein (FAM) labeled at the 5' end and a black hole quencher (BHQ1) labeled at the 3' end. The specific binding of OTA induced a conformational transition of the aptamer from a random coil to a duplex-quadruplex structure, which brought FAM and BHQ1 into spatial proximity causing fluorescence quenching. Under the optimized conditions, this aptamer sensor enabled OTA detection in a wide dynamic concentration range from 3.9 nM to 500 nM, and the detection limit was about 3.9 nM OTA. This method was selective for OTA detection and allowed to detect OTA spiked in diluted liquor and corn flour extraction samples, showing the capability for OTA analysis in practical applications.

Enzyme-Linked Aptamer Kits for Rapid, Visual, and Sensitive Determination of Lactoferrin in Dairy Products

Lactoferrin (Lf), as a popular nutritional fortification in dairy products, has the ability regulate the body's immune system and function as a broad-spectrum antibacterial, which is of great significance to the growth and development of infants and children. Herein, an indirect competitive enzyme-linked aptamer assay (ELAA) kit was established for rapid, sensitive, and visual determination of Lf in dairy products. In the construction, the Lf aptamer was conjugated with horseradish peroxidase (HRP) as the recognition probe and aptamer complementary strand (cDNA) were anchored onto the microplate as the capture probe. The recognition probes were first mixed with a sample solution and specifically bound with the contained Lf, then added into the microplate in which the free recognition probes in the mixture were captured by the capture probe. After washing, the remaining complex of cDNA/Aptamer/HRP in the microplate was conducted with a chromogenic reaction through HRP, efficiently catalyzing the substrate 3, 3', 5, 5'-tetramethylbenzidine (TMB), therefore the color shade would directly reflect Lf concentration. Under the optimization conditions, a good linear relationship (R², 0.9901) was obtained in the wide range of 25-500 nM with the detection limit of 14.01 nM and a good specificity, as well as the reliable recoveries. Furthermore, the ELAA kits achieved the Lf determination with an accuracy of 79.71~116.99% in eleven samples, which consisted of three kinds of dairy products: including goat milk powder, cow milk powder, and nutrition drop. Moreover, the results were also validated by the high-performance capillary electrophoresis (HPCE) method. The ELAA kit provides a simple and convenient determination for Lf in dairy products, and it is highly expected to be commercialized.

Selection of an Aptamer against the Enzyme 1-deoxy-D-xylulose-5-phosphate Reductoisomerase from Plasmodium falciparum

The methyl erythritol phosphate (MEP) pathway of isoprenoid biosynthesis is essential for malaria parasites and also for several human pathogenic bacteria, thus representing an interesting target for future antimalarials and antibiotics and for diagnostic strategies. We have developed a DNA aptamer (D10) against Plasmodium falciparum 1-deoxy-D-xylulose-5-phosphate reductoisomerase (DXR), the second enzyme of this metabolic route. D10 binds in vitro to recombinant DXR from P. falciparum and Escherichia coli, showing at 10 µM a ca. 50% inhibition of the bacterial enzyme. In silico docking analysis indicates that D10 associates with DXR in solvent-exposed regions outside the active center pocket. According to fluorescence confocal microscopy data, this aptamer specifically targets in P. falciparum in vitro cultures the apicoplast organelle where the MEP pathway is localized and is, therefore, a highly specific marker of red blood cells parasitized by Plasmodium vs. naïve erythrocytes. D10 is also selective for the detection of MEP+ bacteria (e.g., E. coli and Pseudomonas aeruginosa) vs. those lacking DXR (e.g., Enterococcus faecalis). Based on these results, we discuss the potential of DNA aptamers in the development of ligands that can outcompete the performance of the well-established antibody technology for future therapeutic and diagnostic approaches.

Critical Design Factors for Electrochemical Aptasensors Based on Target-Induced Conformational Changes: The Case of Small-Molecule Targets

Nucleic-acid aptamers consisting in single-stranded DNA oligonucleotides emerged as very promising biorecognition elements for electrochemical biosensors applied in various fields such as medicine, environmental, and food safety. Despite their outstanding features, such as high-binding affinity for a broad range of targets, high stability, low cost and ease of modification, numerous challenges had to be overcome from the aptamer selection process on the design of functioning biosensing devices. Moreover, in the case of small molecules such as metabolites, toxins, drugs, etc., obtaining efficient binding aptamer sequences proved a challenging task given their small molecular surface and limited interactions between their functional groups and aptamer sequences. Thus, establishing consistent evaluation standards for aptamer affinity is crucial for the success of these aptamers in biosensing applications. In this context, this article will give an overview on the thermodynamic and structural aspects of the aptamer-target interaction, its specificity and selectivity, and will also highlight the current methods employed for determining the aptamer-binding affinity and the structural characterization of the aptamer-target complex. The critical aspects regarding the generation of aptamer-modified electrodes suitable for electrochemical sensing, such as appropriate bioreceptor immobilization strategy and experimental conditions which facilitate a convenient anchoring and stability of the aptamer, are also discussed. The review also summarizes some effective small molecule aptasensing platforms from the recent literature.

Multiple amplification-based fluorometric aptasensor for highly sensitive detection of Staphylococcus aureus

Rapid and accurate detection and identification of Staphylococcus aureus (S. aureus) are of great significance for food safety, environmental monitoring, early clinical diagnosis, and prevention of the spread of drug-resistant bacteria. Herein, we design a fluorometric aptasensor for ultra-sensitive, specific, and rapid detection of S. aureus. The apasensor combines the enrichment and separation of magnetic nanoparticles (MNPs), the biotin-streptavidin conjugation system, and a single S. aureus can release four signaling probes for signal amplification. Aptamer acts as a specific biorecognition element of S. aureus. Four FAM-labeled partially complementary sequences (FAM-pcDNAs) were used as signaling probes. The aptamers were sequential hybridized with the four FAM-pcDNAs to form aptamer&pcDNAs, which were then bound to MNPs via the biotin-streptavidin. When the aptamer specifically recognizes and binds to S. aureus, the FAM-pcDNAs signaling probes are replaced and released into the supernatant. The concentration of S. aureus can be quantified by measuring the fluorescence intensity (λexc/em = 492/520 nm) of the replaced signaling probe FAM-pcDNAs. The results show that the proposed fluorometric aptasensor displays good specificity, ultra-high sensitivity (1.23 cfu/mL), wide linear range (1 ~ 10⁸ cfu/mL), and fast detection speed (~ 1.5 h). The recovery test verifies further that the proposed fluorometric aptasensor can detect S. aureus in spiked blood samples. Since aptamers are easy to customize, we believe that fluorometric aptasensors based on multiple amplification have broad prospects in the construction of practical high-performance biosensors for bacterial detection. KEY POINTS: • Multiple amplification-based fluorometric aptasensor for S. aureus is developed • The aptasensor displays high specificity with a LOD of 1.23 CFU/mL • The aptasensor can directly detect S. aureus in spiked blood samples.

Radiolabeling of functional oligonucleotides for molecular imaging

Molecular imaging has greatly advanced basic biology and translational medicine through visualization and quantification of molecular events in a cellular context and living organisms. Nuclear medicine, including positron emission tomography (PET) and single-photon emission tomography (SPECT), is one of the most representative molecular imaging modalities which is widely used in clinical theranostics. Recently, numerous molecular imaging agents have been developed to improve the quality and expand the applicable diseases of molecular imaging. Based on the choice of specific imaging agents, molecular imaging is capable of studying tumor biological activities, detecting tumor metastasis, and imaging Alzheimer’s disease-related amyloid proteins. Among these imaging agents, functional oligonucleotides-based imaging probes are becoming increasingly important due to their unique features. Antisense oligonucleotides, small interfering RNA, and aptamers are privileged molecular tools in precision medicine for cancer diagnosis and treatment. These chemically synthesized oligonucleotides without batch-to-batch variations are flexible to incorporate with other molecules without affecting their functionalities. Therefore, through the combination of oligonucleotides with radioisotopes, a series of molecular imaging agents were developed in the past decades to achieve highly sensitive and accurate biomedical imaging modalities for clinical theranostic. Due to the nature of oligonucleotides, the strategies of oligonucleotide radiolabeling are different from conventional small molecular tracers, and the radiolabeling strategy with rational design is highly correlated to the imaging quality. In this review, we summarize recent advancements in functional oligonucleotide radiolabeling strategies and respective molecular imaging applications. Meanwhile, challenges and future development insights of functional oligonucleotide-based radiopharmaceuticals are discussed in the end.

Multimodal Ochratoxin A-Aptasensor Using 3'-FAM-Enhanced Exonuclease I Tool and Magnetic Microbead Carrier

Thanks to its preparatory ease, close affinity, and low cost, the aptasensor can serve as a promising substitute for antibody-dependent biosensors. However, the available aptasensors are mostly subject to a single-mode readout and the interference of unbound aptamers in solution and non-target-induced transition events. Herein, we proposed a multimodal aptasensor for multimode detection of ochratoxin A (OTA) with cross-validation using the 3'-6-carboxyfluorescein (FAM)-enhanced exonuclease I (Exo I) tool and magnetic microbead carrier. Specifically, the 3'-FAM-labeled aptamer/biotinylated-cDNA hybrids were immobilized onto streptavidin-magnetic microbeads via streptavidin-biotin interaction. With the presence of OTA, an antiparallel G-quadruplex conformation was formed, protecting the 3'-FAM labels from Exo I digestion, and then anti-FAM-horseradish peroxidase (HRP) was bound via specific antigen-antibody affinity; for the aptamers without the protection of OTA, the distal ssDNA was hydrolyzed from 3' → 5', releasing 3'-FAM labels to the solution. Therefore, the OTA was detected by analyzing the "signal-off" fluorescence of the supernatant and two "signal-on" signals in electrochemistry and colorimetry through the detection of the coating magnetic microbeads in HRP's substrate. The results showed that the 3'-FAM labels increased the activity of Exo I, producing a low background due to a more thorough digestion of unbound aptamers. The proposed multimodal aptasensor successfully detected the OTA in actual samples. This work first provides a novel strategy for the development of aptasensors with Exo I and 3'-FAM labels, broadening the application of aptamer in the multimode detection of small molecules.

Thermal Probing Techniques for a Single Live Cell

Temperature is a significant factor in determining and characterizing cellular metabolism and other biochemical activities. In this study, we provide a brief overview of two important technologies used to monitor the local temperatures of individual living cells: fluorescence nano-thermometry and an array of micro-/nano-sized thin-film thermocouples. We explain some key technical issues that must be addressed and optimised for further practical applications, such as in cell biology, drug selection, and novel antitumor therapy. We also offer a method for combining them into a hybrid measuring system.

A Simple and Rapid “Signal On” Fluorescent Sensor for Detecting Mercury (II) Based on the Molecular Beacon Aptamer

Biosensors for mercury (II) (Hg2+) with high sensitivity are urgently required for food safety, ecosystem protection and disease prevention. In this study, a simple and fast detection method of Hg2+ based on the molecular beacon aptamer was established, according to the principle that Hg2+ could change the structure of the molecular beacon aptamer, resulting in the changed fluorescence intensity. All of the detection conditions were optimized. It was found that an optimal molecular beacon aptamer MB3 showed the optimal response signal in the optimized reaction environment, which was 0.08 μmol/L MB3, 50 mmol/L tris buffer (40 mmol/L NaCl, 10 mmol/L MgCl2, pH 8.1), and a 10 min reaction. Under the optimal detection conditions, the molecular beacon aptamer sensor showed a linear response to Hg2+ concentration within a range from 0.4 to 10 μmol/L and with a detection limit of 0.2254 μmol/L and a precision of 4.9%. The recovery rates of Hg2+ in water samples ranged from 95.00% to 99.25%. The method was convenient and rapid, which could realize the rapid detection of mercury ions in water samples.

Nucleic Acid Aptamers Emerging as Modulators of G-Protein-Coupled Receptors: Challenge to Difficult Cell Surface Proteins

G-protein-coupled receptors (GPCRs), among various cell surface proteins, are essential targets in the fields of basic science and drug discovery. The discovery and development of modulators for the receptors have provided deep insights into the mechanism of action of receptors and have led to a new therapeutic option for human diseases. Although various modulators against GPCRs have been developed to date, the identification of new modulators for GPCRs remains a challenge due to several technical problems and limitations. To overcome this situation, a variety of strategies have been developed by several modalities, including nucleic acid aptamers, which are emerging as unique molecules isolated by a repetitive selection process against various types of targets from an enormous combinatorial library. This review summarized the achievements in the development of aptamers targeting GPCRs, and discussed their isolation methods and the diverse functional features of aptamers against GPCRs.

Recent advances in aptamer applications for analytical biochemistry

Aptamers are typically defined as relatively short (20-60 nucleotides) single-stranded DNA or RNA molecules that bind with high affinity and specificity to various types of targets. Aptamers are frequently referred to as "synthetic antibodies" but are easier to obtain, less expensive to produce, and in several ways more versatile than antibodies. The beginnings of aptamers date back to 1990, and since then there has been a continual increase in aptamer publications. The intent of the present account was to focus on recent original research publications, i.e., those appearing in 2019 through April 2020, when this account was written. A Google Scholar search of this recent literature was performed for relevance-ranking of articles. New methods for selection of aptamers were not included. Nine categories of applications were organized and representative examples of each are given. Finally, an outlook is offered focusing on "faster, better, cheaper" application performance factors as key drivers for future innovations in aptamer applications.

Sandwich Fluorescence Detection of Foodborne Pathogen Staphylococcus aureus with CD Fluorescence Signal Amplification in Food Samples

Timely detection of Staphylococcus aureus (S. aureus) is critical because it can multiply to disease−causing levels in a matter of hours. Herein, a simple and sensitive DNA tetrahedral (Td) fluorescence signal amplifier with blue carbon quantum dots (bCDs) was prepared for sandwich detection of S. aureus. bCD was modified at the apex of Td, and an aptamer on Td was used to accurately identify and “adsorb” the amplifier to the surface of S. aureus. Atomic force microscopy (AFM) demonstrates the successful preparation of this signal amplifier. The fluorescence intensity emitted in this strategy increased 4.72 times. The strategy showed a stronger fluorescence intensity change, sensitivity (linear range of 7.22 × 10⁰–1.44  × 10⁹ CFU/mL with a LOD of 4 CFU/mL), and selectivity. The recovery rate in qualified pasteurized milk and drinking water samples was 96.54% to 104.72%. Compared with simple aptamer sandwich detection, these fluorescence signal amplifiers have improved fluorescence detection of S. aureus. Additionally, this fluorescent signal amplification strategy may be applied to the detection of other food pathogens or environmental microorganisms in the future.

Enzymatic Beacons for Specific Sensing of Dilute Nucleic Acid

Enzymatic beacons, or E-beacons, are 1 : 1 bioconjugates of the nanoluciferase enzyme linked covalently at its C-terminus to hairpin forming ssDNA equipped with a dark quencher. We prepared E-beacons biocatalytically using HhC, the promiscuous Hedgehog C-terminal protein-cholesterol ligase. HhC attached nanoluciferase site-specifically to mono-sterylated hairpin oligonucleotides, called steramers. Three E-beacon dark quenchers were evaluated: Iowa Black, Onyx-A, and dabcyl. Each quencher enabled sensitive, sequence-specific nucleic acid detection through enhanced E-beacon bioluminescence upon target hybridization. We assembled prototype dabcyl-quenched E-beacons specific for SARS-CoV-2. Targeting the E484 codon of the virus Spike protein, E-beacons (80×10^-12  M) reported wild-type SARS-CoV-2 nucleic acid at ≥1×10^-9  M by increased bioluminescence of 8-fold. E-beacon prepared for the SARS-CoV-2 E484K variant functioned with similar sensitivity. Both E-beacons could discriminate their target from the E484Q mutation of the SARS-CoV-2 Kappa variant. Along with mismatch specificity, E-beacons are two to three orders of magnitude more sensitive than synthetic molecular beacons.

Continuous monitoring of molecular biomarkers in microfluidic devices

The ability to monitor molecular targets is crucial in fields ranging from healthcare to industrial processing to environmental protection. Devices employing biomolecules to achieve this goal are called biosensors. Over the last half century researchers have developed dozens of different biosensor approaches. In this chapter we analyze recent advances in the biosensing field aiming at adapting these to the problem of continuous molecular monitoring in complex sample streams, and how the merging of these sensors with lab-on-a-chip technologies would be beneficial to both. To do so we discuss (1) the components that comprise a biosensor, (2) the challenges associated with continuous molecular monitoring in complex sample streams, (3) how different sensing strategies deal with (or fail to deal with) these challenges, and (4) the implementation of these technologies into lab-on-a-chip architectures.

Utilizing the DNA Aptamer to Determine Lethal α-Amanitin in Mushroom Samples and Urine by Magnetic Bead-ELISA (MELISA)

Amanita poisoning is one of the most deadly types of mushroom poisoning. α-Amanitin is the main lethal toxin in amanita, and the human-lethal dose is about 0.1 mg/kg. Most of the commonly used detection techniques for α-amanitin require expensive instruments. In this study, the α-amanitin aptamer was selected as the research object, and the stem-loop structure of the original aptamer was not damaged by truncating the redundant bases, in order to improve the affinity and specificity of the aptamer. The specificity and affinity of the truncated aptamers were determined using isothermal titration calorimetry (ITC) and gold nanoparticles (AuNPs), and the affinity and specificity of the aptamers decreased after truncation. Therefore, the original aptamer was selected to establish a simple and specific magnetic bead-based enzyme linked immunoassay (MELISA) method for α-amanitin. The detection limit was 0.369 μg/mL, while, in mushroom it was 0.372 μg/mL and in urine 0.337 μg/mL. Recovery studies were performed by spiking urine and mushroom samples with α-amanitin, and these confirmed the desirable accuracy and practical applicability of our method. The α-amanitin and aptamer recognition sites and binding pockets were investigated in an in vitro molecular docking environment, and the main binding bases of both were T3, G4, C5, T6, T7, C67, and A68. This study truncated the α-amanitin aptamer and proposes a method of detecting α-amanitin.

Synthesis of fluorescence labelled aptamers for use as low-cost reagents in HIV/AIDS research and diagnostics

Aptamers are nucleic acids selected by systematic evolution of ligands by exponential enrichment. They have potential as alternatives to antibodies in medical research and diagnostics, with the advantages of being non-immunogenic and relatively inexpensive to produce. In the present study, gp120 aptamers conjugated with fluorescein isothiocyanate (FITC) were generated, which could interact with HIV-1 gp120. A previously isolated gp120 aptamer, CSIR 1.1, was conjugated with FITC by incubation with 1-ethyl-3-(3-dimethylaminopropyl) carbodiimide and imidazole. The conjugation and binding to the glycoprotein were confirmed by flow cytometry. FITC conjugated aptamers showed an increase in fluorescence emission 24-fold higher than baseline, and this difference was statistically significant (P=0.0016). Compared with a commercially available biotinylated anti-gp120 antibody, detected using FITC conjugated streptavidin, the emission of fluorescence obtained from the FITC-conjugated aptamer was 8-fold higher, suggesting a stronger interaction with gp120. In addition, the FITC conjugated aptamer neutralized HIV-1 pseudoviruses with an average IC₅₀ of 21.3 nM, similar to the parent aptamer that had an IC₅₀ of 19.2 nM. However, the difference in inhibition between the two aptamers was not statistically significant (P=0.784). These results indicate that the FITC-conjugated aptamer generated in the present study could potentially be used as a low-cost reagent in HIV/AIDS research and diagnostics.

Versatile Integration of Liquid-Phase Microextraction and Fluorescent Aptamer Beacons: A Synergistic Effect for Bioanalysis

Fluorescent aptamer beacons (FABs) are a major category of biosensors widely used in environmental analysis. However, due to their low compatibility, it is difficult to use the common FABs for biological samples. To overcome this challenge, construction of FABs with complex structures to adapt the nature of biological samples is currently in progress in this field. Unlike previous works, we moved our range of vision from the FAB itself to the biological sample. Inspired by this idea, in this work, flat membrane-based liquid-phase microextraction (FM-LPME) with sufficient sample cleanup and preconcentration capacities was integrated with FABs. With the merits of both FM-LPME and FABs, the integrated LPME-FAB system displayed a clear synergistic enhancement for target analysis. Specifically, LPME in the LPME-FAB system provided purified and enriched Hg²⁺ for the FAB recognition, while the FAB recognition event promoted the extraction efficiency of LPME. Due to superior performances, the LPME-FAB system achieved highly sensitive analysis of Hg²⁺ in urine samples with a detection limit of 27 nM and accuracies in the range of 98-113%. To the best of our knowledge, this is the first time that an integrated LPME-FAB system was constructed for target analysis in biological samples. We believe that this study will provide a new insight into the next generation of biosensors, where the integration of sample preparation with detection probes is as important as the design of complex probes in the field of bioanalysis.

Enzymatic Beacons for Specific Sensing of Dilute Nucleic Acid and Potential Utility for SARS-CoV-2 Detection

Enzymatic beacons, or E-beacons, are 1:1 bioconjugates of the nanoluciferase enzyme linked covalently at its C-terminus to hairpin forming DNA oligonucleotides equipped with a dark quencher. We prepared E-beacons biocatalytically using the promiscuous “hedgehog” protein-cholesterol ligase, HhC. Instead of cholesterol, HhC attached nanoluciferase site-specifically to mono-sterylated hairpin DNA, prepared in high yield by solid phase synthesis. We tested three potential E-beacon dark quenchers: Iowa Black, Onyx-A, and dabcyl. Prototype E-beacon carrying each of those quenchers provided sequence-specific nucleic acid sensing through turn-on bioluminescence. For practical application, we prepared dabcyl-quenched E-beacons for potential use in detecting the COVID-19 virus, SARS-CoV-2. Targeting the E484 codon of the SARS-CoV-2 Spike protein, E-beacons (80 × 10⁻¹² M) reported wild-type SARS-CoV-2 nucleic acid at ≥1 × 10⁻⁹ M with increased bioluminescence of 8-fold. E-beacon prepared for the E484K variant of SARS-CoV-2 functioned with similar sensitivity. These E-beacons could discriminate their complementary target from nucleic acid encoding the E484Q mutation of the SARS-CoV-2 Kappa variant. Along with specificity, detection sensitivity with E-beacons is two to three orders of magnitude better than synthetic molecular beacons, rivaling the most sensitive nucleic acid detection agents reported to date.

A kinetically controlled platform for ligand-oligonucleotide transduction

Ligand-oligonucleotide transduction provides the critical pathway to integrate non-nucleic acid molecules into nucleic acid circuits and nanomachines for a variety of strand-displacement related applications. Herein, a general platform is constructed to convert the signals of ligands into desired oligonucleotides through a precise kinetic control. In this design, the ligand-aptamer binding sequence with an engineered duplex stem is introduced between the toehold and displacement domains of the invading strand to regulate the strand-displacement reaction. Employing this platform, we achieve efficient transduction of both small molecules and proteins orthogonally, and more importantly, establish logical and cascading operations between different ligands for versatile transduction. Besides, this platform is capable of being directly coupled with the signal amplification systems to further enhance the transduction performance. This kinetically controlled platform presents unique features with designing simplicity and flexibility, expandable complexity and system compatibility, which may pave a broad road towards nucleic acid-based developments of sophisticated transduction networks.

The Multifunctionally Graded System for a Controlled Size Effect on Iron Oxide-Gold Based Core-Shell Nanoparticles

We report that Fe3O4@Au core-shell nanoparticles (NPs) serve as a multifunctional molecule delivery platform. This platform is also suitable for sensing the doxorubicin (DOX) through DNA hybridization, and the amount of carried DOX molecules was determined by size-dependent Fe3O4@Au NPs. The limits of detection (LODs) for DOX was found to be 1.839 nM. In our approach, an Au nano-shell coating was coupled with a specially designed DNA sequence using thiol bonding. By means of a high-frequency magnetic field (HFMF), a high release percentage of such a molecule could be efficiently achieved in a relatively short period of time. Furthermore, the thickness increase of the Au nano-shell affords Fe3O4@Au NPs with a larger surface area and a smaller temperature increment due to shielding effects from magnetic field. The change of magnetic property may enable the developed Fe3O4@Au-dsDNA/DOX NPs to be used as future nanocarrier material. More importantly, the core-shell NP structures were demonstrated to act as a controllable and efficient factor for molecule delivery.

Recent Advances and a Roadmap to Aptamer-Based Sensors for Bloodstream Infections

The present review is intended to describe bloodstream infections (BSIs), the major pathogens responsible for BSIs, conventional tests and their limitations, commercially available methods used, and the aptamer and nanomaterials-based approaches developed so far for the detection of BSIs. The advantages associated with aptamers and the aptamer-based sensors, the comparison between the aptamers and the antibodies, and the various types of aptasensors developed so far for the detection of bloodstream infections have been described in detail in the present review. Also, the future outlook and roadmap toward aptamer-based sensors and the challenges associated with the aptamer development have also been concluded in this review.

Aptamer-based strategies for recognizing adenine, adenosine, ATP and related compounds

Adenine is a key nucleobase, adenosine is an endogenous regulator of the immune system, while adenosine triphosphate (ATP) is the energy source of many biological reactions. Selective detection of these molecules is useful for understanding biological processes, biochemical reactions and signaling. Since 1993, various aptamers have been reported to bind to adenine and its derivatives. In addition, the adenine riboswitch was later discovered. This review summarizes the efforts for the selection of RNA and DNA aptamers for adenine derivatives, and we pay particular attention to the specificity of binding. In addition, other molecular recognition strategies based on rational sequence design are also introduced. Most of the work in the field was performed on the classic DNA aptamer for adenosine and ATP reported by the Szostak group. Based on this aptamer, some representative applications such as the design of fluorescent, colorimetric and electrochemical biosensors, intracellular imaging, and ATP-responsive materials are also described. In addition, we critically review the limit of the reported aptamers and also important problems in the field, which can give future research opportunities.

Comparative evaluation and design of a G-triplex/thioflavin T-based molecular beacon

Both G-quadruplex (G4) and G-triplex (G3) can bind thioflavin T (ThT) to light up the fluorescence of ThT. G4/ThT and G3/ThT can be used as fluorescent indicators to construct a label-free molecular beacon (MB). In this work, we present a comparative perspective of G3/ThT-based MB and G4/ThT-based MB. The results showed that the G3/ThT-based MB had higher sensitivity and faster response speed than the G4/ThT-based MB. Furthermore, we systematically studied the effect of stem length and varying pairs on the response of the G3/ThT-based MB, and then proposed one rational design of the G3/ThT-based MB. This work demonstrates that the shorter G3 is more suitable for constructing the MB stem. This present work opens a promising way to develop a sensitive, simple and homogeneous biosensing method.

Recent Developments in Aptasensors for Diagnostic Applications

Aptamers are exciting smart molecular probes for specific recognition of disease biomarkers. A number of strategies have been developed to convert target-aptamer binding into physically detectable signals. Since the aptamer sequence was first discovered, a large variety of aptamer-based biosensors have been developed, with considerable attention paid to their potential applications in clinical diagnostics. So far, a variety of techniques in combination with a wide range of functional nanomaterials have been used for the design of aptasensors to further improve the sensitivity and detection limit of target determination. In this paper, the advantages of aptamers over traditional antibodies as the molecular recognition components in biosensors for high-throughput screening target molecules are highlighted. Aptamer-target pairing configurations are predominantly single- or dual-site binding; the design of recognition modes of each aptamer-target pairing configuration is described. Furthermore, signal transduction strategies including optical, electrical, mechanical, and mass-sensitive modes are clearly explained together with examples. Finally, we summarize the recent progress in the development of aptamer-based biosensors for clinical diagnosis, including detection of cancer and disease biomarkers and in vivo molecular imaging. We then conclude with a discussion on the advanced development and challenges of aptasensors.

X-aptamers targeting Thy-1 membrane glycoprotein in pancreatic ductal adenocarcinoma

Modified DNA aptamers incorporated with amino-acid like side chains or drug-like ligands can offer unique advantages and enhance specificity as affinity ligands. Thy-1 membrane glycoprotein (THY1 or CD90) was previously identified as a biomarker candidate of neovasculature in pancreatic ductal adenocarcinoma (PDAC). The current study developed and evaluated modified DNA X-aptamers targeting THY1 in PDAC. The expression and glycosylation of THY1 in PDAC tumor tissues were assessed using immunohistochemistry and quantitative proteomics. Bead-based X-aptamer library that contains 108 different sequences was used to screen for high affinity THY1 X-aptamers. The sequences of the X-aptamers were analyzed with the next-generation sequencing. The affinities of the selected X-aptamers to THY1 were quantitatively evaluated with flow cytometry. Three high affinity THY1 X-aptamers, including XA-B217, XA-B216 and XA-A9, were selected after library screening and affinity binding evaluation. These three X-aptamers demonstrated a high binding affinity and specificity to THY1 protein and the THY1 expressing cell lines, using THY1 antibody as a comparison. The development of these X-aptamers provides highly specific and non-immunogenic affinity ligands for THY1 binding in the context of biomarker development and clinical applications. They could be further exploited to assist molecular imaging of PDAC targeting THY1.

DNA pom-pom nanostructure as a multifunctional platform for pathogenic bacteria determination and inactivation

Pathogenic bacteria levels are significantly related with disease control, clinical diagnosis, and even environmental monitoring. It is becoming highly urgent to achieve ultrasensitive detection of pathogenic bacteria and efficient combat of bacterial infection. Toward this end, we have assembled a DNA Pom-Pom nanostructure (PP-N) based multifunctional platform for pathogenic bacteria determination and inactivation. In particular, one DNA oligonucleotide probe that serve as a trigger was specifically designed for the autonomous cross-opening of metastable DNA hairpin probes and long dsDNA structure formation, achieving a catalytic self-assembly of DNA nanostructure. Numerous DNA strands in this PP-N assembly provide sufficient interaction sites for functional domains and connector, showing high programmability, excellent biostability, as well as selective target recognition. With these properties, the fluorescence dyes modified PP-N platform showed excellent bacteria analysis with both excellent selectivity and ultrasensitive determination limit as low as 2.0 CFU/mL. Furthermore, the aptamer-functionalized and antibiotics loaded PP-N platform demonstrate excellent merits of high antibiotics-loading capacity and negligible cytotoxicity to targets. Therefore, this DNA PP-N assembly based multifunctional platform promise its great application in targeted sensing, combating bacterial infection, and potential clinic therapy.

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

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

MUC-1 aptamer conjugated InP/ZnS quantum dots/nanohydrogel fluorescent composite for mitochondria-mediated apoptosis in MCF-7 cells

The combined use of nanohydrogels (NHGs) and quantum dots (QDs) has resulted in the development of a nanoscaled drug delivery system (DDS) with fluorescence imaging potential. NHG-QDs composite loaded with anti-cancer drugs could be applied as an effective theranostics for simultaneous diagnosis and therapy of cancer cells. Here, we report on the synthesis of NHG-QDs nanosystem (NS) conjugated with an amino-modified MUC-1 aptamer (Ap) and loaded with hydrophobic paclitaxel (PTX). To effectively target and eradicate breast cancer MCF-7 cells, the nanocomposite was further loaded with the inhibitor of lactate dehydrogenase (LDH), sodium oxamate (SO) (Ap-NHG-QDs-PTX-SO) to inhibit the conversion of pyruvate to lactate via LDH and disrupting glycolysis. Results obtained from in vitro analysis (MTT assay, apoptosis/necrosis assessment, evaluation of mitochondria targeting, and gene expression profiling) revealed that Ap-NHG-QDs-PTX-SO NS could significantly target and inhibit MCF-7 cells and also induce mitochondria-mediated apoptosis. Collectively, the Ap-NHG-QDs-PTX-SO NS is proposed to serve as a robust theranostics for simultaneous imaging and therapy of breast cancer and other types of solid tumors.

Wettability read-out strategy for aptamer target binding based on a recognition/hydrophobic bilayer surface

We established a wettability read-out strategy for an aptasensor with a bilayer surface, using hydrophobicity reduction as the signal. The signal was induced by a fracture of the nanoneedle layer resulting from recognition by the supporting aptamer layer. The kinetics and influencing factors of this process were investigated with time curves.

Smart Biomimetic Nanocomposites Mediate Mitochondrial Outcome through Aerobic Glycolysis Reprogramming: A Promising Treatment for Lymphoma

Toxicity and drug resistance caused by chemotherapeutic drugs have become bottlenecks in treating tumors. The delivery of anticancer drugs based on nanocarriers is regarded as an ideal way to solve the aforementioned problems. In this study, a new antilymphoma nanodrug CD20 aptamer-RBCm@Ag-MOFs/PFK15 (A-RAMP) is designed and constructed, and it consists of two parts: (1) metal-organic frameworks Ag-MOFs (AM) loaded with tumor aerobic glycolysis inhibitor PFK15 (P), forming a core part (AMP); (2) targeted molecule CD20 aptamer (A) is inserted into the red blood cell membrane (RBCm) to form the shell part (A-R). A-RAMP under the guidance of CD20 aptamer actively targets B-cell lymphoma both in vitro and in vivo. As a result, A-RAMP not only significantly inhibits the effect on tumor growth but also shows no obvious side effects on the treated nude mice, indicating that A-RAMP can accurately target tumor cells, reprogram aerobic glycolysis, and exert synergistic antitumor effect by Ag⁺ and PFK 15. Furthermore, the antitumor mechanism of A-RAMP in vivo by apoptotic pathway and targeting metabonomics are explored. These results suggest that A-RAMP has a promising application prospect as an smart, safe, effective, and synergistic antilymphoma agent.

Diagnostic and Therapeutic Value of Aptamers in Envenomation Cases

It is now more than a century since Albert Calmette from the Institut Pasteur changed the world of envenomation by demonstrating that antibodies raised against animal venoms have the ability to treat human victims of previously fatal bites or stings. Moreover, the research initiated at that time effectively launched the discipline of toxicology, first leading to the search for toxic venom components, followed by the demonstration of venoms that also contained compounds of therapeutic value. Interest from pharmaceutical companies to treat envenomation is, however, declining, mainly for economic reasons, and hence, the World Health Organization has reclassified this public health issue to be a highest priority concern. While the production, storage, and safety of antivenom sera suffer from major inconveniences, alternative chemical and technological approaches to the problem of envenomation need to be considered that bypass the use of antibodies for toxin neutralization. Herein, we review an emerging strategy that relies on the use of aptamers and discuss how close—or otherwise—we are to finding a viable alternative to the use of antibodies for the therapy of human envenomation.

Olax scandens Mediated Biogenic Synthesis of Ag-Cu Nanocomposites: Potential Against Inhibition of Drug-Resistant Microbes

In the present study, we have synthesized silver-copper nanocomposites (Ag-Cu NCs) using an Olax scandens leaf extract (green synthesis method) and evaluated their antimicrobial potential against less susceptible pathogens. The kinetics of Ag-Cu NCs synthesis was followed by UV-VIS and fluorescence spectroscopy. The physicochemical characterization of as-synthesized Ag-Cu NCs was executed using electron microscopy, Energy Dispersive X-Ray, Fourier Transform Infrared Spectroscopy, and a Differential Light Scattering method. As-synthesized Ag-Cu NCs induced the formation of Reactive Oxygen Species (ROS), thereby causing alteration and decrementation of cellular proteins, DNA, lipids, etc., and eventually leading to cell death, as determined by a Live/Dead assay. Next, we assessed the anti-biofilm potential of as-synthesized Ag-Cu NCs against biofilm forming bacteria. The as-synthesized Ag-Cu NCs, when compared to monometallic silver nanoparticles, exhibited significantly higher anti-microbial activity against both sensitive as well as drug resistant microbial isolates.

Aptamer-guided extracellular vesicle theranostics in oncology

In the past decade, the study of exosomes, nanosized vesicles (50-150 nm) released into the extracellular space via the fusion of multivesicular bodies with the plasma membrane, has burgeoned with impressive achievements in theranostics applications. These nanosized vesicles have emerged as key players in homeostasis and in the pathogenesis of diseases owing to the variety of the cargos they can carry, the nature of the molecules packaged inside the vesicles, and the robust interactions between exosomes and target cells or tissues. Accordingly, the development of exosome-based liquid biopsy techniques for early disease detection and for monitoring disease progression marks a new era of precision medicine in the 21st century. Moreover, exosomes possess intrinsic properties - a nanosized structure and unique "homing effects" - that make them outstanding drug delivery vehicles. In addition, targeted exosome-based drug delivery systems can be further optimized using active targeting ligands such as nucleic acid aptamers. Indeed, the aptamers themselves can function as therapeutic and/or diagnostic tools based on their attributes of unique target-binding and non-immunogenicity. This review aims to provide readers with a current picture of the research on exosomes and aptamers and their applications in cancer theranostics, highlighting recent advances in their transition from the bench to the clinic.

Novel Chemiluminescence Sensor for Thrombin Detection Based on Dual-Aptamer Biorecognition and Mesoporous Silica Encapsulated with Iron Porphyrin

Thrombin is a marker of blood-related diseases, and its detection is of great significance in the fields of medical and biological research. Herein, a novel chemiluminescence (CL) sensor for thrombin detection was prepared based on dual-aptamer biorecognition and mesoporous silica encapsulated with iron porphyrin. Mesoporous silica encapsulated with hematin by aptamer1 (Apt1/hematin/M-SiO₂) and magnetic microspheres modified with aptamer2 (Apt2/NH₂-MS) were successfully prepared, and the two materials were used to construct a CL sensor to detect thrombin. Primarily, Apt2/NH₂-MS is used for pretreatment separation of thrombin samples by the biorecognition effect between the aptamer (Apt2) and target (thrombin). Then, thrombin/Apt2/NH₂-MS is again recognized with Apt1 on the surface of Apt1/hematin/M-SiO₂ and Apt1/thrombin/Apt2/NH₂-MS is formed, so dual-aptamer biorecognition is realized. Meanwhile, the generated Apt1/thrombin/Apt2/NH₂-MS makes Apt1 shed off the surface of M-SiO₂ and release hematin. The released hematin can catalyze the luminol-H₂O₂ CL reaction. Therefore, a sandwich-type CL sensor was constructed based on dual-aptamer biorecognition and hematin catalysis for the detection of thrombin. The sensor has a linear range of 7.5 × 10^-15 to 2.5 × 10^-10 mol·L^-1 and a detection limit of 2.2 × 10^-15 mol·L^-1 and also exhibits excellent selectivity, reproducibility, and stability. The sensor was successfully used for the detection of thrombin in serum samples, which makes it possible to apply the sensor in the detection of thrombin in actual samples.