Aptamers Chemistry: Chemical Modifications and Conjugation Strategies

Design of hybrid aptamer-molecularly imprinted polymer nanoparticles for selective binding of oxidized low-density lipoprotein in an ELISA-mimic system

Oxidized low-density lipoprotein (oxLDL) is the leading cause of atherosclerosis and cardiovascular disease development. An enzyme-linked immunosorbent assay (ELISA)-mimic system for sensitive and specific oxLDL determination was developed using selective aptamer-molecularly imprinted polymer nanoparticles (AP-MIP NP) coupled with an immunology-based colorimetric assay. The AP-MIP NP were synthesized using solid-phase molecular imprinting by incorporating aptamers into the MIP NP cavities. This resulted in AP-MIP NP with diameters of 108 ± 28 nm. For AP-MIP NP-ELISA-mimic assay development, the surface of a microplate was coated with the novel AP-MIP NP capture receptors at a concentration of 0.1 mg mL-1 to capture oxLDL. The reaction time between AP-MIP NP and oxLDL was 20 min. Horseradish peroxidase conjugated anti-oxLDL polyclonal antibody at a concentration of 0.6 μg mL-1 was used as the detection antibody, with a linear response ranging from 24.72 to 1,600 μg dL-1. The recovery accuracy was 89-106 %. Within-run precision was 3.3-6.7 % of the coefficient of variation, while between-day precision was 3.8-7.1 %. The AP-MIP NP-coated wells were stored at room temperature for one month without a loss of binding ability, retaining over 91 % binding ability after three regeneration cycles. Human serum diluted 1:10 and analyzed by the AP-MIP NP-ELISA-mimic assay showed high correlation with conventional ELISA (R2 = 0.9779). This assay achieved rapid results within 95 min, compared to ELISA at 195 min. The high binding ability and selectivity of the AP-MIP NP shows promise as a selective material against oxLDL for the ELISA-mimic system and other applications.

Exploring the diagnostic landscape: Portable aptasensors in point-of-care testing

Aptamers, discovered in the 1990s, have marked a significant milestone in the fields of therapeutics and diagnostics. This review provides a comprehensive survey of aptamers, focusing on their diagnostic applications. It especially encapsulates a decade of aptamer, encompassing research, patents, and market trends. The unique properties and inherent stability of aptamers are discussed, highlighting their potential for various clinical applications. It goes on to introduce biosensor design, emphasizing the advantages of aptamers over antibodies as conventional molecular recognition interface. The operation and design of aptasensors are examined, with a focus on single- and dual-site binding configurations and their respective recognition modes. Paper-based sensors are highlighted as cost-effective, user-friendly alternatives that are gaining widespread adoption, particularly in point-of-care platforms.

Nanostructured aptasensors for ricin detection and tumor therapy: exploring aptamer-protein interactions and conformational stability in biological complexities

Aptamers are distinctive single-stranded oligonucleotides derived through in vitro evolution, and exhibit exceptional ability in binding to target proteins. Structural modifications of aptamers can profoundly regulate their interactions with proteins, thereby influencing associated cellular behavior. Recent research focused on modulating aptamer-protein interaction in complex biological environments to regulate various biological processes. However, in such crowded conditions, aptamer conformation and stability are susceptible to nuclease degradation, which can impair stable binding to target. Ricin is recognized as a significant biological toxin protein, distinguished by its widespread availability, remarkable dissemination, and resilience including wide pH tolerance, remarkable thermostability, and solubility. RTA is an enzymatic subunit of ricin, that can inactivate approximately 2000 ribosomes per minute, rapidly halting protein synthesis, making it a powerful candidate for tumor therapy. By leveraging the potent cytotoxicity of ricin, coupled with the targeting precision of aptamers and the versatility of nanomaterials, a powerful approach emerges for both targeted tumor therapy and highly sensitive detection of ricin. Although there have been some insightful reports on aptamers applied in ricin detection, a systematic discussion remains limited. In this context, we provide an in-depth overview of techniques used to analyze aptamer-ricin interactions and explore the potential of ricin-aptamer interactions in clinical diagnosis.

Unravelling the therapeutic properties of aptamer-modified exosome nanocomposite

Exosomes are naturally occurring nanocarriers derived from various cells. In recent years, they have attained significant attention for their potential in precise drug delivery and therapeutic applications. Exosomes exhibit several advantages, remarkably improved stability, bioavailability, and delivery efficiency, which are further augmented by integration with nanomaterials. Functionalizing the aptamer and nanomaterial on the exosomal surface significantly improves the binding affinity and specificity. Here in this review, we examine the synergistic therapeutic effect of exosome-nanomaterial-aptamer conjugate with particular attention to their uses in cancer therapy, bone fracture regeneration, wound healing, etc. Recent advances in the field demonstrated that the amalgamation of different nanomaterials, aptamers, and exosomes has proven to be a transformative approach in the field of therapeutics. Here in the nanocomposite, the aptamer is exclusively used as a recognition molecule to provide specificity to the target cells. Exosomes serve as biocompatible nanocarriers, and different nanomaterials (AuNPs, AuNRs, SiNPs, Graphene, etc.) complement the therapeutic efficiency by PTT/PDT/ROS generation/SO generation, etc. Briefly, the above-mentioned nanocomposite serves as the perfect therapeutic agent by utilizing the exosome's biocompatibility, aptamer's high affinity and nanomaterial's multifunctionality. Furthermore, the challenges and limitations of this nanocomposite have been discussed, along with its prospects in clinical practices.

Aptamers as Diagnostic and Therapeutic Agents for Aging and Age-Related Diseases

In the 21st century, the demographic shift toward an aging population has posed a significant challenge, particularly with respect to age-related diseases, which constitute a major threat to human health. Accordingly, the detection, prevention, and treatment of aging and age-related diseases have become critical issues, and the introduction of novel molecular recognition elements, called aptamers, has been considered. Aptamers, a class of oligonucleotides, can bind to target molecules with high specificity. In addition, aptamers exhibit superior stability, biocompatibility, and applicability, rendering them promising tools for the diagnosis and treatment of human diseases. In this paper, we present a comprehensive overview of aptamers, systematic evolution of ligands by exponential enrichment (SELEX), biomarkers associated with aging, as well as aptamer-based diagnostic and therapeutic platforms. Finally, the limitations associated with predicting and preventing age-related conditions are discussed, along with potential solutions based on advanced technologies and theoretical approaches.

Using aptamers for targeted delivery of RNA therapies

RNA-based treatments that can silence, introduce, or restore gene expression to target human diseases are emerging as a new class of therapeutics. Despite their potential for use in broad applications, their clinical translation has been hampered by a need for delivery to specific cells and tissues. Cell targeting based on the use of aptamers provides an approach for improving their delivery to the desired sites of action. Aptamers are nucleic acid oligonucleotides with structural conformations that provide a robust capacity for the recognition of cell surface molecules and that can be used for directed targeting. Aptamers can be directly conjugated to therapeutic RNA molecules, in the form of aptamer-oligonucleotide chimeras, or incorporated into nanoparticles used as vehicles for the delivery of these therapeutics. Herein, we discuss the use of aptamers for cell-directed RNA therapies, provide an overview of different types of aptamer-targeting RNA therapeutics, and review examples of their therapeutic applications. Challenges associated with manufacturing and scaling up production, and key considerations for their clinical implementation, are also outlined.

DNA Aptamers with Chemically Locked Ends for Virus Infection Inhibition

Nucleic acid aptamers, known as chemical antibodies, demonstrate remarkable affinity and specificity for targets. Therefore, aptamers are proposed as an alternative to an antibody in extensive applications. However, nucleic acid aptamers exhibit poor tolerance to degradation by nucleases, which severely hampers their biological applications. Herein, we developed a biological regulation pattern for aptamers by utilizing small-molecule-mediated terminal manipulation, which could prevent the interaction of DNA aptamers with exonucleases and help aptamers persist in the desired conformation with high stability. Diagonal T-T bases were designed in the ends of aptamers and could be chemically cross-linked with trioxsalen via photocatalyzed cycloaddition. Aptamers with different patterns of terminal T-T cross-linking sites were synthesized. Experimental investigation and molecular dynamics simulations combinedly revealed that the cross-linking efficiency of ends depended on multiple factors: (i) the number of T-T cross-linking sites in the terminal sequences, (ii) the spatial conformation of aptamers, and (iii) the competitive binding ability of the T-T sites with trioxsalen compared to other base sites. The aptamers with locked ends exhibited superior exonuclease resistance, especially with both 3'- and 5'-cross-linked ends, thus demonstrating a great target binding capability. Notably, in the application exploration, the terminal locked aptamers, which bound to receptor-binding domains on SARS-CoV-2, showed superior performance in virus infection inhibition. This work puts forward a paradigm to develop a biological regulation pattern for aptamers based on chemical terminal manipulation of DNA, potentially promoting the clinical applications of nucleic acid drugs.

Incorporation of polymerizable linkers into aptamers for high-affinity nanoscale molecularly imprinted polymer hybrids: analysis of positional selectivity

Aptamers are short single strand nucleic acid sequences that exhibit high-affinity molecular recognition towards non nucleic acid targets. They offer many benefits over antibodies, but still suffer from variable affinities and stability issues. Recently, aptamers have been incorporated as functional recognition agents into molecularly imprinted polymers, a competing recognition technology, to create hybrid materials, AptaMIPs, that exhibit the benefits of both classes. Specifically, this process can increase target affinity while preventing aptamer degradation. For the first time, using a lysozyme aptamer as an exemplar, we have undertaken a systematic and fundamental study to identify the optimal number and location of polymer connection points on an aptameric sequence for boosting AptaMIP target affinity and selectivity creating high affinity recognition elements. Clear patterns have emerged showing "fixing" throughout the molecule is required, but only in particular regions of the sequence. The results suggest that conformationally flexible regions within the polymer-bound aptameric sequence are detrimental to strong target binding, supporting the hypothesis that a successful imprinting process must lock the aptamer into its ideal binding conformation to achieve observable marked improvement in recognition. Conversely, too much flexibility in the embedded oligo (demonstrated through limited binding points) leads to poor performance. These findings offer a clear direction for development of aptamer-polymer hybrids. We also demonstrate the effectiveness of the developed materials in sensitive detection of the template using surface plasmon resonance, through improved quality of the recognition element.

Effect of cucurbit[7]uril on DPPC-containing liposomes: Interactions with the lipid bilayer

Liposomes, which are bilayer lipidic nanocarriers, have been utilized in many pharmaceutical applications to enhance the solubility and therapeutic index of drugs. Liposomes have also been used as carriers for smaller drug carriers, such as cucurbiturils, to achieve a more controlled release of the drug into the targeted site in the body. In this study, we investigated the effects of cucurbit[7]uril, a macrocyclic organic compound, on the integrity of liposome lipid membranes. The average liposome size, measured by dynamic light scattering, increased with increasing concentrations of cucurbit[7]uril. In addition, fluorescence spectroscopy was used to calculate an association constant (Ka) between cucurbit[7]uril and cholesterol of 3 × 10 6 / M . This high Ka value demonstrated the ability of cucurbit[7]uril to reduce liposome stability by extracting cholesterol molecules from the lipid bilayer. Thermogravimetric analysis demonstrated the localization of cucurbit[7]uril molecules on the surface of the liposomes. As the concentration of cucurbit[7]uril increased, the thermal stability increased, i.e. the mass loss of the liposomal suspension decreased. The biocompatibility of cucurbit[7]uril was also investigated using a hemolysis test on human red blood cells. In conclusion, the current study is the first to explain the relationship between lipid membranes and cucurbit[7]uril. The results of this study can be used to develop a new drug delivery system comprising liposomes and cucurbit[7]uril.

DNA-based hydrogels for bone regeneration: A promising tool for bone organoids

DNA-based hydrogels stand out for bone regeneration due to their exceptional biocompatibility and programmability. These hydrogels facilitate the formation of spatial bone structures through bulk hydrogel fabricating, microsphere formatting, and 3D printing. Furthermore, the bone microenvironment can be finely tuned by leveraging the degradation products, nanostructure, targeting, and delivery capabilities inherent to DNA-based materials. In this review, we underscore the advantages of DNA-based hydrogels, detailing their composition, gelation techniques, and structure optimization. We then delineate three critical elements in the promotion of bone regeneration using DNA-based hydrogels: (i) osteogenesis driven by phosphate ions, plasmids, and oligodeoxynucleotides (ODNs) that enhance mineralization and promote gene and protein expression; (ii) vascularization facilitated by tetrahedral DNA nanostructures (TDNs) and aptamers, which boosts gene expression and targeted release; (iii) immunomodulation achieved through loaded factors, TDNs, and bound ions that stimulate macrophage polarization and exhibit antibacterial properties. With these advantages and properties, these DNA-based hydrogels can be used to construct bone organoids, providing an innovative tool for disease modeling and therapeutic applications in bone tissue engineering. Finally, we discuss the current challenges and future prospects, emphasizing the potential impacts and applications in regenerative medicine.

Microfluidic rapid isolation and electrochemical detection of S. pneumonia via aptamer-decorated surfaces

BACKGROUND

S. pneumoniae is widely recognized as a leading cause of respiratory infections worldwide, often resulting in high mortality rates. However, the advent of microfluidic technologies has brought significant advancements, including the simplified, sensitive, cost-effective, and rapid approach to pneumococcal bacteremia detection. In this study, a microfluidic magnetic platform is presented for rapid isolation, and an electrode array is utilized for the electrochemical detection of S. pneumoniae. Aptamer-decorated surfaces were employed for both isolation and detection. For isolation, silica magnetic microparticles were synthesized and decorated with aptamer.

RESULTS

Isolation performance was assessed for phosphate-buffered saline (PBS) and blood samples for different concentrations of S. pneumoniae. Electrical impedance spectroscopy (EIS) with fabricated gold interdigitated electrodes (IDEs) decorated with aptamer was implemented for the detection of S. pneumoniae at different bacteria concentrations. The microfluidic platform performed bacteria isolation at comparable isolation efficiency with batch systems but at a much faster rate (isolation took about a minute, and the aptamer-decorated electrode array exhibited a limit of detection (LOD) at 962 CFU/mL and linear range between 104 and 107 CFU/mL.

SIGNIFICANCE

Our method represents a significant advancement compared to previous reports. Our microfluidic platform can efficiently isolate 60 μL of the bacteria sample within about one minute. The entire process takes about two minutes including the detection step. Furthermore, our method achieves a notable improvement in the detection limit for S. pneumoniae compared to conventional ELISA and magnetic microfluidics ELISA.

The Progress and Evolving Trends in Nucleic-Acid-Based Therapies

Nucleic-acid-based therapies have emerged as a pivotal domain within contemporary biomedical science, marked by significant advancements in recent years. These innovative treatments primarily operate through the precise binding of DNA or RNA molecules to discrete target genes, subsequently suppressing the expression of the target proteins. The spectrum of nucleic-acid-based therapies encompasses antisense oligonucleotides (ASOs), small interfering RNAs (siRNAs), microRNAs (miRNAs), and messenger RNAs (mRNAs), etc. Compared to more traditional medicinal approaches, nucleic-acid-based therapies stand out for their highly targeted action on specific genes, as well as their potential for chemical modification to improve resistance to nucleases, ensuring sustained therapeutic activity and mitigating immunogenicity concerns. Nevertheless, these molecules' limited cellular permeability necessitates the deployment of delivery vectors to enhance their intracellular uptake and stability. As nucleic-acid-based therapies progressively display promising pharmacodynamic profiles, there has been a burgeoning interest in these treatments for applications in clinical research. This review aims to summarize the variety of nucleic acid drugs and their mechanisms, evaluate the present status in research and application, discourse on prospective trends, and potential challenges ahead. These innovative therapeutics are anticipated to assume a pivotal role in the management of a wide array of diseases.

Functional Aptamers In Vitro Evolution for Protein-Protein Interaction Blockage

As aptamer development progresses, their applications have expanded significantly beyond high affinity to include functional capabilities. Currently, the identification of functional aptamers relies on traditional SELEX techniques, followed by functional validation and computer-assisted redesign of high-affinity aptamers. However, high affinity does not guarantee optimal functionality, making the search for functional aptamers from binding pools time-consuming and labor-intensive. Addressing this challenge, we introduce functional aptamers in vitro evolution (FAIVE), a novel screening method that links sequence functionality to fluorescence intensity. We demonstrated the effectiveness of FAIVE by obtaining modified DNA aptamers capable of disrupting the interaction between the SARS-CoV-2 spike receptor-binding domain (RBD) and hACE2, targeting protein-protein interaction inhibition. Furthermore, we investigated the criteria for validating the quality of the bead library generated for selection by modeling the emulsion PCR process, providing theoretical insights for future applications. The concept of incorporating fluorescent signal reporting of aptamer functionality into the aptamer selection process holds the potential to facilitate the identification of aptamers with diverse functionalities and is readily adaptable to various research contexts.

A review of RNA nanoparticles for drug/gene/protein delivery in advanced therapies: Current state and future prospects

Nanotechnology involves the utilization of materials with exceptional properties at the nanoscale. Over the past few years, nanotechnologies have demonstrated significant potential in improving human health, particularly in medical treatments. The self-assembly characteristic of RNA is a highly effective method for designing and constructing nanostructures using a combination of biological, chemical, and physical techniques from different fields. There is great potential for the application of RNA nanotechnology in therapeutics. This review explores various nano-based drug delivery systems and their unique features through the impressive progress of the RNA field and their significant therapeutic promises due to their unique performance in the COVID-19 pandemic. However, a significant hurdle in fully harnessing the power of RNA drugs lies in effectively delivering RNA to precise organs and tissues, a critical factor for achieving therapeutic effectiveness, minimizing side effects, and optimizing treatment outcomes. There have been many efforts to pursue targeting, but the clinical translation of RNA drugs has been hindered by the lack of clear guidelines and shared understanding. A comprehensive understanding of various principles is essential to develop vaccines using nucleic acids and nanomedicine successfully. These include mechanisms of immune responses, functions of nucleic acids, nanotechnology, and vaccinations. Regarding this matter, the aim of this review is to revisit the fundamental principles of the immune system's function, vaccination, nanotechnology, and drug delivery in relation to the creation and manufacturing of vaccines utilizing nanotechnology and nucleic acids. RNA drugs have demonstrated significant potential in treating a wide range of diseases in both clinical and preclinical research. One of the reasons is their capacity to regulate gene expression and manage protein production efficiently. Different methods, like modifying chemicals, connecting ligands, and utilizing nanotechnology, have been essential in enabling the effective use of RNA-based treatments in medical environments. The article reviews stimuli-responsive nanotechnologies for RNA delivery and their potential in RNA medicines. It emphasizes the notable benefits of these technologies in improving the effectiveness of RNA and targeting specific cells and organs. This review offers a comprehensive analysis of different RNA drugs and how they work to produce therapeutic benefits. Recent progress in using RNA-based drugs, especially mRNA treatments, has shown that targeted delivery methods work well in medical treatments.

Recent Advances in Aptamers-Based Nanosystems for Diagnosis and Therapy of Cardiovascular Diseases: An Updated Review

The increasing global prevalence of cardiovascular diseases highlights the urgent need for innovative diagnostic and therapeutic strategies. Aptamers, small single-stranded nucleic acid molecules with exceptional specificity and affinity for target biomolecules, have emerged as promising tools for precise diagnostics and targeted therapies. Their selective binding capabilities provide valuable insights into the molecular mechanisms underlying cardiovascular conditions. When integrated into nanosystems, aptamers enhance the delivery, bioavailability, and stability of diagnostic and therapeutic agents, addressing challenges of solubility and degradation. This integration enables more targeted drug delivery, advanced imaging techniques, and improved therapeutic interventions, ultimately improving the management of cardiovascular diseases. Recent advancements in aptamer selection methodologies, coupled with their unique three-dimensional structures, have significantly expanded their application potential in cardiovascular health. By combining aptamers with nanosystems, novel approaches to cardiovascular disease diagnosis and treatment are emerging, promising enhanced efficacy, safety, and precision. This review explores recent progress in the development and application of aptamer-based nanosystems in cardiovascular diagnostics and therapies.

Aptamer based immunotherapy: a potential solid tumor therapeutic

Aptamer-based immunotherapy can be a new hope for treating solid tumors with personalized and specific approaches toward cancer therapies. Aptamers are small synthetic single-stranded nucleic acids that may bring in a paradigm shift in treating solid tumors. These are highly selective drugs applied in cellular immunotherapy, cytokine modulation, and immune checkpoint suppression. This review provides an overview of the recent advances in aptamer-based technologies with specific key clinical trials involving AON-D21 and AM003. Aptamers are potently active in immune regulation and tumor targeting. However, aptamer stability and bioavailability are seriously compromised by the issues relating to renal clearance and rapid degradation through nucleases. The latter are reviewed here along with novel improvements, some of which involve chemical modifications that greatly enhance stability and prolong the circulation time; exemplary such modifications are PEGylation, cholesterol conjugation, and the synthesis of circular nucleic acids. The regulatory aspect is also crucial. For example, in addition to specific strategies to prevent drug-drug interactions (DDIs) in cancer remediation medications, this paper underscores the need of risk assessment, particularly because of immunogenicity and organ failure. The use of aptamers is expanded by the development of SOMAmers, X-aptamers, and bioinformatics. To make aptamer-based drugs a major part of cancer treatment, future research should concentrate more on resolving existing issues and expanding their beneficial uses.

PROTACs coupled with oligonucleotides to tackle the undruggable

Undruggable targets account for roughly 85% of human disease-related targets and represent a category of therapeutic targets that are difficult to tackle with traditional methods, but their considerable clinical importance. These targets are generally defined by planar functional interfaces and the absence of efficient ligand-binding pockets, making them unattainable for conventional pharmaceutical strategies. The advent of oligonucleotide-based proteolysis-targeting chimeras (PROTACs) has instilled renewed optimism in addressing these challenges. These PROTACs facilitate the targeted degradation of undruggable entities, including transcription factors (TFs) and RNA-binding proteins (RBPs), via proteasome-dependent mechanisms, thereby presenting novel therapeutic approaches for diseases linked to these targets. This review offers an in-depth examination of recent progress in the integration of PROTAC technology with oligonucleotides to target traditionally undruggable proteins, emphasizing the design principles and mechanisms of action of these innovative PROTACs.

Lipid-Based Nanocarriers for Targeted Gene Delivery in Lung Cancer Therapy: Exploring a Novel Therapeutic Paradigm

Lung cancer is a significant cause of cancer-related death worldwide. It can be broadly categorised into small-cell lung cancer (SCLC) and Non-small cell lung cancer (NSCLC). Surgical intervention, radiation therapy, and the administration of chemotherapeutic medications are among the current treatment modalities. However, the application of chemotherapy may be limited in more advanced stages of metastasis due to the potential for adverse effects and a lack of cell selectivity. Although small-molecule anticancer treatments have demonstrated effectiveness, they still face several challenges. The challenges at hand in this context comprise insufficient solubility in water, limited bioavailability at specific sites, adverse effects, and the requirement for epidermal growth factor receptor inhibitors that are genetically tailored. Bio-macromolecular drugs, including small interfering RNA (siRNA) and messenger RNA (mRNA), are susceptible to degradation when exposed to the bodily fluids of humans, which can reduce stability and concentration. In this context, nanoscale delivery technologies are utilised. These agents offer encouraging prospects for the preservation and regulation of pharmaceutical substances, in addition to improving the solubility and stability of medications. Nanocarrier-based systems possess the notable advantage of facilitating accurate and sustained drug release, as opposed to traditional systemic methodologies. The primary focus of scientific investigation has been to augment the therapeutic efficacy of nanoparticles composed of lipids. Numerous nanoscale drug delivery techniques have been implemented to treat various respiratory ailments, such as lung cancer. These technologies have exhibited the potential to mitigate the limitations associated with conventional therapy. As an illustration, applying nanocarriers may enhance the solubility of small-molecule anticancer drugs and prevent the degradation of bio-macromolecular drugs. Furthermore, these devices can administer medications in a controlled and extended fashion, thereby augmenting the therapeutic intervention's effectiveness and reducing adverse reactions. However, despite these promising results, challenges remain that must be addressed. Multiple factors necessitate consideration when contemplating the application of nanoparticles in medical interventions. To begin with, the advancement of more efficient delivery methods is imperative. In addition, a comprehensive investigation into the potential toxicity of nanoparticles is required. Finally, additional research is needed to comprehend these treatments' enduring ramifications. Despite these challenges, the field of nanomedicine demonstrates considerable promise in enhancing the therapy of lung cancer and other respiratory diseases.

Probing the Effects of Chemical Modifications on Anticoagulant and Antiproliferative Activity of Thrombin Binding Aptamer

Thrombin binding aptamer (TBA) is one of the best-known G-quadruplex (G4)-forming aptamers that efficiently binds to thrombin, resulting in anticoagulant effects. TBA also possesses promising antiproliferative properties. As with most therapeutic oligonucleotides, chemical modifications are critical for therapeutic applications, particularly to improve thermodynamic stability, resistance in biological environment, and target affinity. To evaluate the effects of nucleobase and/or sugar moiety chemical modifications, five TBA analogues have been designed and synthesized considering that the chair-like G4 structure is crucial for biological activity. Their structural and biological properties have been investigated by Circular Dichroism (CD), Nuclear Magnetic Resonance (NMR), native polyacrylamide gel electrophoresis (PAGE) techniques, and PT and MTT assays. The analogue TBAB contains 8-bromo-2'-deoxyguanosine (B) in G-syn glycosidic positions, while TBAL and TBAM contain locked nucleic acid guanosine (L) or 2'-O-methylguanosine (M) in G-anti positions, respectively. Instead, both the two types of modifications have been introduced in TBABL and TBABM with the aim of obtaining synergistic effects. In fact, both derivatives include B in syn positions, exhibiting in turn L and M in the anti ones. The most appealing results have been obtained for TBABM, which revealed an interesting cytotoxic activity against breast and prostate cancer cell lines, while in the case of TBAB, extraordinary thermal stability (Tm approximately 30 °C higher than that of TBA) and an anticoagulant activity higher than original aptamer were observed, as expected. These data indicate TBAB as the best TBA anticoagulant analogue here investigated and TBABM as a promising antiproliferative derivative.

Recent advances in aptamer discovery, modification and improving performance

Aptamers are nucleic acid (Ribonucleic acid (RNA) and single strand deoxyribonucleic acid (ssDNA)) with a length of approximately 25-80 bases that can bind to particular target molecules, similar to monoclonal antibodies. Due to their many benefits, which include a long shelf life, minimal batch-to-batch variations, extremely low immunogenicity, the possibility of chemical modifications for improved stability, an extended serum half-life, and targeted delivery, they are receiving a lot of attention in a variety of clinical applications. The development of high-affinity modification approaches has attracted significant attention in aptamer applications. Stable three-dimensional aptamers that have undergone chemical modification can engage firmly with target proteins through improved non-covalent binding, potentially leading to hundreds of affinity improvements. This review demonstrates how cutting-edge methodologies for aptamer discovery are being developed to consistently and effectively construct high-performing aptamers that need less money and resources yet have a high chance of success. Also, High-affinity aptamer modification techniques were discussed.

Nanomaterial-enabled drug transport systems: a comprehensive exploration of current developments and future avenues in therapeutic delivery

Over the years, nanotechnology has gained popularity as a viable solution to address gene and drug delivery challenges over conventional methods. Extensive research has been conducted on nanosystems that consist of organic/inorganic materials, drugs, and its biocompatibility become the primary goal of improving drug delivery. Various surface modification methods help focus targeted and controlled drug release, further enabling multidrug delivery also. This newer technology ensures the stability of drugs that can unravel the mechanisms involved in cellular processes of disease development and its management. Tailored medication delivery provides benefits such as therapy, controlled release, and reduced adverse effects, which are especially important for controlling illnesses like cancer. However, multifunctional nanocarriers that possess high viscoelasticity, extended circulation half-life, biocompatibility, and biodegradability face some challenges and limitations too in human bodies. To produce a consistent therapeutic platform based on complex three-dimensional nanoparticles, careful design and engineering, thorough orthogonal analysis methods, and reproducible scale-up and manufacturing processes will be required in the future. Safety and effectiveness of nano-based drug delivery should be thoroughly investigated in preclinical and clinical trials, especially when considering biodistribution, targeting specific areas, and potential immunological toxicities. Overall, the current review article explores the advancements in nanotechnology, specific to nanomaterial-enabled drug delivery systems, carrier fabrication techniques and modifications, disease management, clinical research, applications, limitations, and future challenges. The work portrays how nanomedicine distribution affects healthcare with an emphasis on the developments in drug delivery techniques.

Aptamers: ushering in new hopes in targeted glioblastoma therapy

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

Crossing the Halfway Point: Aptamer-Based, Highly Multiplexed Assay for the Assessment of the Proteome

Measuring responses in the proteome to various perturbations improves our understanding of biological systems. The value of information gained from such studies is directly proportional to the number of proteins measured. To overcome technical challenges associated with highly multiplexed measurements, we developed an affinity reagent-based method that uses aptamers with protein-like side chains along with an assay that takes advantage of their unique properties. As hybrid affinity reagents, modified aptamers are fully comparable to antibodies in terms of binding characteristics toward proteins, including epitope size, shape complementarity, affinity and specificity. Our assay combines these intrinsic binding properties with serial kinetic proofreading steps to allow highly effective partitioning of stable specific complexes from unstable nonspecific complexes. The use of these orthogonal methods to enhance specificity effectively overcomes the severe limitation to multiplexing inherent to the use of sandwich-based methods. Our assay currently measures half of the unique proteins encoded in the human genome with femtomolar sensitivity, broad dynamic range and exceptionally high reproducibility. Using machine learning to identify patterns of change, we have developed tests based on measurement of multiple proteins predictive of current health states and future disease risk to guide a holistic approach to precision medicine.

A colorimetric-aptamer-based assay for the determination of enrofloxacin through triggering the aggregation of gold nanoparticles

Although enrofloxacin (ENR) is a widely used broad-spectrum antibiotic in veterinary medicine, its residues in animals can pose a risk to human health. Thus, we developed a new method for detecting ENR based on aptamers and AuNPs. In the absence of ENR, the aptamers attached to the surface of the AuNPs via electrostatic interactions to protect the AuNPs from NaCl, and the solution remained red. Conversely, the aptamer bonded with ENR, leading the aptamer to detach from the AuNP surface, and the color of the solution changed from red to blue. Based on this principle, ENR can be qualitatively detected by the naked eye and quantitatively detected by measuring the absorbance ratio at 650 nm and 530 nm. The experimental results showed a good linear relationship within the ENR concentration range of 0-400 nM, with a limit of detection (LOD) of 1.72 nM, which is satisfactory for detection in food safety. Additionally, this method has also been successfully applied to the detection of ENR in tap water, river water, milk, serum and urine, with good recovery rates and RSD values of less than 7%, indicating its great potential for ENR detection in environmental water samples. More importantly, the combination of this method with a smartphone platform provided great convenience for on-site and visual detection of ENR, offering promising applicability prospects.

Unlocking precision in aptamer engineering: a case study of the thrombin binding aptamer illustrates why modification size, quantity, and position matter

The thrombin binding aptamer (TBA) is a prototypical platform used to understand the impact of chemically-modified nucleotides on aptamer stability and target affinity. To provide structural insight into the experimentally-observed effects of modification size, location, and number on aptamer performance, long time-scale molecular dynamics (MD) simulations were performed on multiple binding orientations of TBA-thrombin complexes that contain a large, flexible tryptophan thymine derivative (T-W) or a truncated analogue (T-K). Depending on modification position, T-W alters aptamer-target binding orientations, fine-tunes aptamer-target interactions, strengthens networks of nucleic acid-protein contacts, and/or induces target conformational changes to enhance binding. The proximity and 5'-to-3' directionality of nucleic acid structural motifs also play integral roles in the behavior of the modifications. Modification size can differentially influence target binding by promoting more than one aptamer-target binding pose. Multiple modifications can synergistically strengthen aptamer-target binding by generating novel nucleic acid-protein structural motifs that are unobtainable for single modifications. By studying a diverse set of modified aptamers, our work uncovers design principles that must be considered in the future development of aptamers containing chemically-modified nucleotides for applications in medicine and biotechnology, highlighting the value of computational studies in nucleic acids research.

Recent advances in surface plasmon resonance for the detection of ovarian cancer biomarkers: a thorough review

Early detection of ovarian cancer (OC) is crucial for effective management and treatment, as well as reducing mortality rates. However, the current diagnostic methods for OC are time-consuming and have low accuracy. Surface plasmon resonance (SPR) biosensors offer a promising alternative to conventional techniques, as they enable rapid and less invasive screening of various circulating indicators. These biosensors are widely used for biomolecular interaction analysis and detecting tumor markers, and they are currently being investigated as a rapid diagnostic tool for early-stage cancer detection. Our main focus is on the fundamental concepts and performance characteristics of SPR biosensors. We also discuss the latest advancements in SPR biosensors that enhance their sensitivity and enable high-throughput quantification of OC biomarkers, including CA125, HE4, CEA, and CA19-9. Finally, we address the future challenges that need to be overcome to advance SPR biosensors from research to clinical applications. The ultimate goal is to facilitate the translation of SPR biosensors into routine clinical practice for the early detection and management of OC.

Aptamer-decorated nanocarriers for viral adsorption: A special look at COVID-19

Viral infections are one of the leading causes of death in the world. One main challenge in fighting against these diseases is the unavailability of effective eradicating drugs and specific treatments. Nanocarriers and aptamer-decorated nanocarriers are designed to attach to many targets, including viral particles. By lowering the viral infectivity and attachment capability, they add therapeutic values even without containing antiviral drugs. Nevertheless, the nanoparticles (NPs) with encapsulated antiviral drugs can display extra therapeutic effects. Furthermore, it has been shown that aptamers can bind to viral particles and nanocarriers, presenting promising approaches for the identification of viruses and treatment of viral infections. Although there is no satisfying literature revealing the strong therapeutic potential of nanotechnology against COVID-19, the following information can provide new perspectives for upcoming investigations pertaining to developing effective aptamer-nanocarrier agents against COVID-19.

In silico selection of aptamers against SARS-CoV-2

Aptamers are molecular recognition elements that have been extensively deployed in a wide array of applications ranging from diagnostics to therapeutics. Due to their unique properties as compared to antibodies, aptamers were also largely isolated during the COVID-19 pandemic for multiple purposes. Typically generated by conventional SELEX, the inherent drawbacks of the process including the time-consuming, cumbersome and resource-intensive nature catalysed the move to adopt in silico approaches to isolate aptamers. Impressive performances of these in silico-derived aptamers in their respective assays have been documented thus far, bearing testimony to the huge potential of the in silico approaches, akin to the traditional SELEX in isolating aptamers. In this study, we provide an overview of the in silico selection of aptamers against SARS-CoV-2 by providing insights into the basic steps involved, which comprise the selection of the initial single-stranded nucleic acids, determination of the secondary and tertiary structures and in silico approaches that include both rigid docking and molecular dynamics simulations. The different approaches involving aptamers against SARS-CoV-2 were illuminated and the need to verify these aptamers by experimental validation was also emphasized. Cognizant of the need to continuously improve aptamers, the strategies embraced thus far for post-in silico selection modifications were enumerated. Shedding light on the steps involved in the in silico selection can set the stage for further improvisation to augment the functionalities of the aptamers in the future.

Facile Synthesis of Aptamer-Functionalized Polydopamine-Coated Magnetic Graphene Oxide Nanocomposites for Highly Efficient Purification of His-Tagged Proteins

Recombinant proteins hold significant importance in numerous disciplines. As the demand for expressing and purifying these proteins grows, the scientific community is in dire need of a simple yet versatile methodology that can efficiently purify these proteins. Aptamers as synthetic nucleic acid-based ligands with high affinity have shown promise in this regard, as they can capture targets through molecular recognition. In this study, novel aptamer-functionalized polydopamine-coated magnetic graphene oxide nanocomposites were facilely prepared, achieving an impressive average aptamer coverage density (45 nmol/mg). These nanocomposites exhibited a uniform structure and robust magnetic responsiveness. The findings indicated that they possess several advantages, such as rapid adsorption, substantial capacity (171.4 mg/g), and excellent reusability. Notably, due to the inherent properties of nucleic acids, the immobilized aptamer-magnetic beads can be utilized repeatedly with high purification efficiency. Finally, the nanocomposites were further employed to purify His-tagged proteins from actual samples. Remarkably, they were able to selectively and efficiently isolate His-tagged retinoid X receptor alpha protein from complex Escherichia coli lysate. The purified His-tagged retinoid X receptor alpha protein was analyzed using matrix-assisted laser desorption/ionization time-of-flight mass spectrometry. This confirmed the efficacy of developed nanocomposites, reinforcing their vast potential for purification of His-tagged recombinant proteins.

Current developments of SELEX technologies and prospects in the aptamer selection with clinical applications

Aptamers are single-stranded oligonucleotide sequences capable of binding to specific ligands with high affinity. In this manner, they are like antibodies but have advantages such as lower manufacturing costs, lower immunogenicity, fewer batch-to-batch differences, a longer shelf life, high tolerance to different molecular milieus, and a greater number of potential targets. Due to their special features, they have been used in drug delivery, biosensor technology, therapy, and diagnostics. The methodology that allowed its production was the "Systematic Evolution of Ligands by Exponential enrichment" (SELEX). Unfortunately, the traditional protocol is time-consuming and laborious. Therefore, numerous variants with considerable optimization steps have been developed, nonetheless, there are still challenges to achieving real applications in the clinical field. Among them, are control of in vivo activities, fast renal filtration, degradation by nucleases and toxicity testing. This review focuses on current technologies based on SELEX, the critical factors for successful aptamer selection, and its upcoming biomedical and biotechnological applications.

Novel Aptamer Strategies in Combating Bacterial Infections: From Diagnostics to Therapeutics

Bacterial infections and antimicrobial resistance are posing substantial difficulties to the worldwide healthcare system. The constraints of conventional diagnostic and therapeutic approaches in dealing with continuously changing infections highlight the necessity for innovative solutions. Aptamers, which are synthetic oligonucleotide ligands with a high degree of specificity and affinity, have demonstrated significant promise in the field of bacterial infection management. This review examines the use of aptamers in the diagnosis and therapy of bacterial infections. The scope of this study includes the utilization of aptasensors and imaging technologies, with a particular focus on their ability to detect conditions at an early stage. Aptamers have shown exceptional effectiveness in suppressing bacterial proliferation and halting the development of biofilms in therapeutic settings. In addition, they possess the capacity to regulate immune responses and serve as carriers in nanomaterial-based techniques, including radiation and photodynamic therapy. We also explore potential solutions to the challenges faced by aptamers, such as nuclease degradation and in vivo instability, to broaden the range of applications for aptamers to combat bacterial infections.

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

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

Selection of antibody-binding covalent aptamers

Aptamers are oligonucleotides with antibody-like binding function, selected from large combinatorial libraries. In this study, we modified a DNA aptamer library with N-hydroxysuccinimide esters, enabling covalent conjugation with cognate proteins. We selected for the ability to bind to mouse monoclonal antibodies, resulting in the isolation of two distinct covalent binding motifs. The covalent aptamers are specific for the Fc region of mouse monoclonal IgG1 and are cross-reactive with mouse IgG2a and other IgGs. Investigation into the covalent conjugation of the aptamers revealed a dependence on micromolar concentrations of Cu2+ ions which can be explained by residual catalyst remaining after modification of the aptamer library. The aptamers were successfully used as adapters in the formation of antibody-oligonucleotide conjugates (AOCs) for use in detection of HIV protein p24 and super-resolution imaging of actin. This work introduces a new method for the site-specific modification of native monoclonal antibodies and may be useful in applications requiring AOCs or other antibody conjugates.

Cornea-SELEX for aptamers targeting the surface of eyes and liposomal drug delivery

Cornea is the major barrier to drug delivery to the eye, which results in low bioavailability and poor efficacy of topical eye treatment. In this work, we first select cornea-binding aptamers using tissue-SELEX on pig cornea. The top two abundant aptamers, Cornea-S1 and Cornea-S2, could bind to pig cornea, and their K d values to human corneal epithelial cells (HCECs) were 361 and 174 nм, respectively. Aptamer-functionalized liposomes loaded with cyclosporine A (CsA) were developed as a treatment for dry eye diseases. The K d of Cornea-S1- or Cornea-S2-functionalized liposomes reduces to 1.2 and 15.1 nм, respectively, due to polyvalent binding. In HCECs, Cornea-S1 or Cornea-S2 enhanced liposome uptake within 15 min and extended retention to 24 h. Aptamer CsA liposomes achieved similar anti-inflammatory and tight junction modulation effects with ten times less CsA than a free drug. In a rabbit dry eye disease model, Cornea-S1 CsA liposomes demonstrated equivalence in sustaining corneal integrity and tear break-up time when compared to commercial CsA eye drops while utilizing a lower dosage of CsA. The aptamers obtained from cornea-SELEX can serve as a general ligand for ocular drug delivery, suggesting a promising avenue for the treatment of various eye diseases and even other diseases.

Aptamer-functionalized liposomes for drug delivery

Among the various targeting ligands for drug delivery, aptamers have attracted much interest in recent years because of their smaller size compared to antibodies, ease of modification, and better batch-to-batch consistency. In addition, aptamers can be selected to target both known and even unknown cell surface biomarkers. For drug loading, liposomes are the most successful vehicle and many FDA-approved formulations are based on liposomes. In this paper, aptamer-functionalized liposomes for targeted drug delivery are reviewed. We begin with the description of related aptamers selection, followed by methods to conjugate aptamers to liposomes and the fate of such conjugates in vivo. Then a few examples of applications are reviewed. In addition to intravenous injection for systemic delivery and hoping to achieve accumulation at target sites, for certain applications, it is also possible to have aptamer/liposome conjugates applied directly at the target tissue such as intratumor injection and dropping on the surface of the eye by adhering to the cornea. While previous reviews have focused on cancer therapy, the current review mainly covers other applications in the last four years. Finally, this article discusses potential issues of aptamer targeting and some future research opportunities.

Molecular Modeling Methods in the Development of Affine and Specific Protein-Binding Agents

High-affinity and specific agents are widely applied in various areas, including diagnostics, scientific research, and disease therapy (as drugs and drug delivery systems). It takes significant time to develop them. For this reason, development of high-affinity agents extensively utilizes computer methods at various stages for the analysis and modeling of these molecules. The review describes the main affinity and specific agents, such as monoclonal antibodies and their fragments, antibody mimetics, aptamers, and molecularly imprinted polymers. The methods of their obtaining as well as their main advantages and disadvantages are briefly described, with special attention focused on the molecular modeling methods used for their analysis and development.

Nucleic acids in modern molecular therapies: A realm of opportunities for strategic drug design

RNA vaccines have made evident to society what was already known by the scientific community: nucleic acids will be the "drugs of the future." By modifying the genome, interfering in transcription or translation, and by introducing new catalysts into the cell or by mimicking antibody effects, nucleic acids can generate therapeutic activities that are not accessible by any other therapeutic agents. There are, however, challenges that need to be solved in the next few years to make nucleic acids usable in a wide range of therapeutic scenarios. This review illustrates how simulation methods can help achieve this goal.

Emerging Biohybrids of Aptamer-Based Nano-Biosensing Technologies for Effective Early Cancer Detection

Cancer is a leading global cause of mortality, which underscores the imperative of early detection for improved patient outcomes. Biorecognition molecules, especially aptamers, have emerged as highly effective tools for early and accurate cancer cell identification. Aptamers, with superior versatility in synthesis and modification, offer enhanced binding specificity and stability compared with conventional antibodies. Hence, this article reviews diagnostic strategies employing aptamer-based biohybrid nano-biosensing technologies, focusing on their utility in detecting cancer biomarkers and abnormal cells. Recent developments include the synthesis of nano-aptamers using diverse nanomaterials, such as metallic nanoparticles, metal oxide nanoparticles, carbon-derived substances, and biohybrid nanostructures. The integration of these nanomaterials with aptamers significantly enhances sensitivity and specificity, promising innovative and efficient approaches for cancer diagnosis. This convergence of nanotechnology with aptamer research holds the potential to revolutionize cancer treatment through rapid, accurate, and non-invasive diagnostic methods.

Aptamer-modified paper-based analytical devices for the detection of food hazards: Emerging applications and future perspective

Food analysis plays a critical role in assessing human health risks and monitoring food quality and safety. Currently, there is a pressing need for a reliable, portable, and quick recognition element for point-of-care testing (POCT) to better serve the demands of on-site food analysis. Aptamer-modified paper-based analytical devices (Apt-PADs) have excellent characteristics of high portability, high sensitivity, high specificity, and on-site detection, which have been widely used and concerned in the field of food safety. The article reviews the basic components and working principles of Apt-PADs, and introduces their representative applications detecting food hazards. Finally, the advantages, challenges, and future directions of Apt-PADs-based sensing performance are discussed, to provide new directions and insights for researchers to select appropriate Apt-PADs according to specific applications.

Advancements and Challenges in Aptamer-Based Therapeutics and Diagnostics Across Diverse Medical Domains: A Comprehensive Review

Aptamers, which are single-stranded DNA or RNA molecules, are increasingly recognized as important tools in diagnostics and therapeutics across various medical disciplines such as oncology, respiratory diseases, and neurological disorders. This review provides a comprehensive evaluation of the recent progress and obstacles encountered in the field of aptamer-based applications. Aptamers have shown promise in oncology for early cancer detection and targeted drug delivery, effectively reducing off-target effects. They also hold potential for significantly impacting the management of respiratory conditions such as asthma and Chronic Obstructive Pulmonary Disease (COPD) by selectively targeting cytokines and regulating the inflammatory response. In the realm of neurological disorders, aptamers offer novel methods by influencing the gut-brain axis and proposing potential approaches for early detection and specific therapy. Despite these notable benefits, persistent challenges remain in areas such as molecular stability, delivery mechanisms, and economic viability. This review offers a comprehensive overview of aptamer-based diagnostics and therapeutics while exploring potential avenues for future research.

New Insights into Aptamers: An Alternative to Antibodies in the Detection of Molecular Biomarkers

Aptamers are short oligonucleotides with single-stranded regions or peptides that recently started to transform the field of diagnostics. Their unique ability to bind to specific target molecules with high affinity and specificity is at least comparable to many traditional biorecognition elements. Aptamers are synthetically produced, with a compact size that facilitates deeper tissue penetration and improved cellular targeting. Furthermore, they can be easily modified with various labels or functional groups, tailoring them for diverse applications. Even more uniquely, aptamers can be regenerated after use, making aptasensors a cost-effective and sustainable alternative compared to disposable biosensors. This review delves into the inherent properties of aptamers that make them advantageous in established diagnostic methods. Furthermore, we will examine some of the limitations of aptamers, such as the need to engage in bioinformatics procedures in order to understand the relationship between the structure of the aptamer and its binding abilities. The objective is to develop a targeted design for specific targets. We analyse the process of aptamer selection and design by exploring the current landscape of aptamer utilisation across various industries. Here, we illuminate the potential advantages and applications of aptamers in a range of diagnostic techniques, with a specific focus on quartz crystal microbalance (QCM) aptasensors and their integration into the well-established ELISA method. This review serves as a comprehensive resource, summarising the latest knowledge and applications of aptamers, particularly highlighting their potential to revolutionise diagnostic approaches.

Recent Progress of Multifunctional Molecular Probes for Triple-Negative Breast Cancer Theranostics

Breast cancer (BC) poses a significant threat to women's health, with triple-negative breast cancer (TNBC) representing one of the most challenging and aggressive subtypes due to the lack of estrogen receptor (ER), progesterone receptor (PR), and human epidermal growth factor receptor 2 (HER2) expression. Traditional TNBC treatments often encounter issues such as low drug efficiency, limited tumor enrichment, and substantial side effects. Therefore, it is crucial to explore novel diagnostic and treatment systems for TNBC. Multifunctional molecular probes (MMPs), which integrate target recognition as well as diagnostic and therapeutic functions, introduce advanced molecular tools for TNBC theranostics. Using an MMP system, molecular drugs can be precisely delivered to the tumor site through a targeted ligand. Real-time dynamic monitoring of drug release achieved using imaging technology allows for the evaluation of drug enrichment at the tumor site. This approach enables accurate drug release, thereby improving the therapeutic effect. Therefore, this review summarizes the recent advancements in MMPs for TNBC theranostics, encompassing the design and synthesis of MMPs as well as their applications in the field of TNBC theranostics.

Multiplexed In Vivo Screening Using Barcoded Aptamer Technology to Identify Oligonucleotide-Based Targeting Reagents

Recent FDA approvals of mRNA vaccines, short-interfering RNAs, and antisense oligonucleotides highlight the success of oligonucleotides as therapeutics. Aptamers are excellent affinity reagents that can selectively label protein biomarkers, but their clinical application has lagged. When formulating a given aptamer for in vivo use, molecular design details can determine biostability and biodistribution; therefore, extensive postselection manipulation is often required for each new design to identify clinically useful reagents harboring improved pharmacokinetic properties. Few methods are available to comprehensively screen such aptamers, especially in vivo, constituting a significant bottleneck in the field. In this study, we introduce barcoded aptamer technology (BApT) for multiplexed screening of predefined aptamer formulations in vitro and in vivo. We demonstrate this technology by simultaneously investigating 20 aptamer formulations, each harboring different molecular designs, for targeting Non-Small Cell Lung Cancer cells and tumors. Screening in vitro identified a 45 kDa bispecific formulation as the best cancer cell targeting reagent, whereas screening in vivo identified a 30 kDa monomeric formulation as the best tumor-specific targeting reagent. The multiplexed analysis pipeline also identified biodistribution phenotypes shared among formulations with similar molecular architectures. The BApT approach we describe here has the potential for broad application to fields where oligonucleotide-based targeting reagents are desired.

Polyfluoroalkyl Tag Decoration Enables Significantly Enhanced Tumor Penetration Ability of a PTK7 Targeting Aptamer

Aptamers are widely used molecular recognition tools in targeted therapy, but their ability to effectively penetrate deep into solid tumors remains a significant challenge, leading to suboptimal treatment efficacy. Here, we developed a polyfluoroalkyl (PFA) decoration strategy to enhance aptamer recognition, cell internalization, and solid tumor penetration. Our results indicate that PFA with around 11 fluorine atoms significantly improves aptamer internalization both in vitro and in vivo settings. However, we also observed that the use of PFA tags containing 19 and 23 fluorine atoms on aptamers resulted in nonspecific cell anchoring in control cell lines, affecting the specificity of aptamers. Overall, we found that using a chemical modification strategy could enhance the deep tumor penetration ability of aptamers and validate their effectiveness in vivo. This approach has significant practical applications in targeted drug delivery for cancer treatment.

Catalytic hairpin self-assembly amplification fluorescence detection of chloramphenicol based on cross-shaped DNA and UiO-66

A catalytic hairpin self-assembly (CHA) amplification method was developed for CAP detection based on cross-shaped DNA and UiO-66. MOF was used to quench the fluorescent signal of FAM labeled DNA. Cross-shaped DNA with four fluorophore group (FAM) was utilized to enhance the fluorescent intensity. CAP could open hairpin structure of H-apt and induce CHA reaction. The product of CHA hybridized with cross-shaped DNA, resulting its leaving from the surface of UiO-66 and recovery of fluorescent signal. The limit of detection (LOD) was low to 0.87 pM. This method had been successfully applied for the detection of CAP in actual samples. Importantly, the high sensitivity was attributed to the great amplification efficiency of CHA, strong fluorescent intensity of cross-shaped DNA structure and great fluorescent quenched efficiency of UiO-66.

Tumor versus Tumor Cell Targeting in Metal-Based Nanoparticles for Cancer Theranostics

The application of metal-based nanoparticles (mNPs) in cancer therapy and diagnostics (theranostics) has been a hot research topic since the early days of nanotechnology, becoming even more relevant in recent years. However, the clinical translation of this technology has been notably poor, with one of the main reasons being a lack of understanding of the disease and conceptual errors in the design of mNPs. Strikingly, throughout the reported studies to date on in vivo experiments, the concepts of "tumor targeting" and "tumor cell targeting" are often intertwined, particularly in the context of active targeting. These misconceptions may lead to design flaws, resulting in failed theranostic strategies. In the context of mNPs, tumor targeting can be described as the process by which mNPs reach the tumor mass (as a tissue), while tumor cell targeting refers to the specific interaction of mNPs with tumor cells once they have reached the tumor tissue. In this review, we conduct a critical analysis of key challenges that must be addressed for the successful targeting of either tumor tissue or cancer cells within the tumor tissue. Additionally, we explore essential features necessary for the smart design of theranostic mNPs, where 'smart design' refers to the process involving advanced consideration of the physicochemical features of the mNPs, targeting motifs, and physiological barriers that must be overcome for successful tumor targeting and/or tumor cell targeting.

Research progress on the detection of foodborne pathogens based on aptamer recognition

Foodborne diseases caused by bacterial contamination are a serious threat to food safety and human health. The classical plate culture method has the problems of long detection cycle, low sensitivity and specificity, and complicated operation, which cannot meet the growing demand for rapid quantitative detection of pathogenic bacteria. The frequent outbreak of foodborne diseases has put forward higher requirements for rapid and simple detection technology of foodborne pathogens. Aptamer is a kind of oligonucleotide fragment that can recognize targets with the advantages of high affinity and good specificity. The target can be range from proteins, small molecules, cells bacteria, and even viruses. Herein, the latest advances in sensitive and rapid detection of foodborne pathogens based on aptamer recognition was reviewed. Special attention has been paid to the obtained sequences of aptamers to various foodborne pathogens, the optimization of sequences, and the mechanism of aptamer recognition. Then, the research progress of biosensors for the detection of pathogenic bacteria based on aptamer recognition were summarized. Some challenges and prospects for the detection of foodborne pathogens based on aptamer recognition were prospected. In summary, with the further deepening of aptamer research and improvement of detection technology, aptamer-based recognition can meet the needs of rapid, sensitive, and accurate detection in practical applications.

Mesophilic Argonaute-Based Single Polystyrene Sphere Aptamer Fluorescence Platform for the Multiplexed and Ultrasensitive Detection of Non-Nucleic Acid Targets

The rapid, simultaneous, and accurate identification of multiple non-nucleic acid targets in clinical or food samples at room temperature is essential for public health. Argonautes (Agos) are guided, programmable, target-activated, next-generation nucleic acid endonucleases that could realize one-pot and multiplexed detection using a single enzyme, which cannot be achieved with CRISPR/Cas. However, currently reported thermophilic Ago-based multi-detection sensors are mainly employed in the detection of nucleic acids. Herein, this work proposes a Mesophilic Argonaute Report-based single millimeter Polystyrene Sphere (MARPS) multiplex detection platform for the simultaneous analysis of non-nucleic acid targets. The aptamer is utilized as the recognition element, and a single millimeter-sized polystyrene sphere (PSmm) with a large concentration of guide DNA on the surface served as the microreactor. These are combined with precise Clostridium butyricum Ago (CbAgo) cleavage and exonuclease I (Exo I) signal amplification to achieve the efficient and sensitive recognition of non-nucleic acid targets, such as mycotoxins (<60 pg mL-1) and pathogenic bacteria (<102 cfu mL-1). The novel MARPS platform is the first to use mesophilic Agos for the multiplex detection of non-nucleic acid targets, overcoming the limitations of CRISPR/Cas in this regard and representing a major advancement in non-nucleic acid target detection using a gene-editing-based system.

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.

Multivalent Aptamer-Based Lysosome-Targeting Chimeras (LYTACs) Platform for Mono- or Dual-Targeted Proteins Degradation on Cell Surface

Selective protein degradation platforms have opened novel avenues in therapeutic development and biological inquiry. Antibody-based lysosome-targeting chimeras (LYTACs) have emerged as a promising technology that extends the scope of targeted protein degradation to extracellular targets. Aptamers offer an advantageous alternative owing to their potential for modification and manipulation toward a multivalent state. In this study, a chemically engineered platform of multivalent aptamer-based LYTACs (AptLYTACs) is established for the targeted degradation of either single or dual protein targets. Leveraging the biotin-streptavidin system as a molecular scaffold, this investigation reveals that trivalently mono-targeted AptLYTACs demonstrate optimum efficiency in degrading membrane proteins. The development of this multivalent AptLYTACs platform provides a principle of concept for mono-/dual-targets degradation, expanding the possibilities of targeted protein degradation.