Aptamers: versatile molecular recognition probes for cancer detection

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

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

Role of Exosomes in Cancer and Aptamer-Modified Exosomes as a Promising Platform for Cancer Targeted Therapy

Exosomes are increasingly recognized as important mediators of intercellular communication in cancer biology. Exosomes can be derived from cancer cells as well as cellular components in tumor microenvironment. After secretion, the exosomes carrying a wide range of bioactive cargos can be ingested by local or distant recipient cells. The released cargos act through a variety of mechanisms to elicit multiple biological effects and impact most if not all hallmarks of cancer. Moreover, owing to their excellent biocompatibility and capability of being easily engineered or modified, exosomes are currently exploited as a promising platform for cancer targeted therapy. In this review, we first summarize the current knowledge of roles of exosomes in risk and etiology, initiation and progression of cancer, as well as their underlying molecular mechanisms. The aptamer-modified exosome as a promising platform for cancer targeted therapy is then briefly introduced. We also discuss the future directions for emerging roles of exosome in tumor biology and perspective of aptamer-modified exosomes in cancer therapy.

Super-resolution imaging of folate receptor alpha on cell membranes using peptide-based probes

Folate receptor alpha (FRα) is a vital membrane protein which have great association with cancers and involved in various biological processes including folate transport and cell signaling. However, the distribution and organization pattern of FRα on cell membranes remains unclear. Previous studies relied on antibodies to recognize the proteins. However, multivalent crosslinking and large size of antibodies confuse the direct observation to some extent. Fortunately, the emergence of peptide, which are small-sized and monovalent, has supplied us an unprecedented choice. Here, we applied fluorophore-conjugated peptide probe to recognize the FRα and study the distribution pattern of FRα on cell membrane using dSTORM super-resolution imaging technique. FRα were found to organized as clusters on cell surface with different sizes. And they have a higher expression level and formed larger clusters on various cancer cells than normal cells, which hinted that its specific distribution could be utilized for cancer diagnosis. Furthermore, we revealed that the lipid raft and cortical actin as restrictive factors for the FRα clustering, suggesting a potential assembly mechanism insight into FRα clustering on cell membrane. Collectively, our work clarified the morphology distribution and clustered organization of FRα with peptide probes at the nanometer scale, which paves the way for further revealing the relationship between the spatial organization and functions of membranal proteins.

Aptamer-Protein Interactions: From Regulation to Biomolecular Detection

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

Bibliometric analysis of aptamer-conjugated nanoparticles for diagnosis in the last two decades

Objective.Aptamer-conjugated nanoparticles for diagnosis have recently gained increasing attention. Here, we performed a bibliometric analysis to provide an overview of this field over the past two decades.Methods. The terms 'aptamer, nanoparticles and diagnosis' were used to search for relevant original articles published in English from 2003 to 2022 in the Web of Science database. VOSviewer and CiteSpace software were employed to analyze the development process, knowledge structure, research hotspots, and potential trends in the field of aptamer-conjugated nanoparticles for diagnosis.Results. A total of 1076 original articles were retrieved, with a rapid increase in the annual output and citation. The journal 'Biosensors and Bioelectronics' has contributed the most in this field, and the most influential researcher, institution and country were Weihong Tan, the Chinese Academy of Sciences, China, respectively. Gold nanoparticles and quantum dots were the most used, but in the past three years, research hotspots focused on carbon dots and graphene quantum dots. Diagnostic directions primarily focused on cancer. The most used strategy was label-free electrochemical detection, but in the past two years, colorimetric analysis and fluorescence imaging emerged as hot topics.Conclusion.The bibliometric analysis reveals a rapid increase in the research on aptamer-conjugated nanoparticles for diagnosis, major contributors at the levels of journals, authors, institutions, and countries, and research preferences in diagnostic objects, nanoparticle types, and detection methods, as well as the evolution of research hotspots and future trends.

Sensitive Detection of Tumor Cells Using Protein Nanoparticles with Multiple Displays of DNA Aptamers and Bioluminescent Reporters

Simple and effective detection methods for circulating tumor cells are essential for early detection and progression monitoring of tumors. The use of DNA aptamer and bioluminescence is expected to be a key tool for the simple, effective, and sensitive detection of tumor cells. Herein, we designed multifunctional protein nanoparticles for the detection of tumor cells using DNA aptamer and bioluminescence. Fusion proteins (ELP-poly(d)-POIs), composed of elastin-like polypeptide (ELP) fused with protein of interests (POIs) via poly(aspartic acid) (poly(d)), formed the protein nanoparticles based on the temperature responsivity of ELP sequences, leading to multiply displayed POIs on the protein nanoparticles. In the present study, we focused on porcine circovirus type 2 replication initiation protein (Rep), which covalently conjugated with DNA aptamers, and NanoLuc luciferase (Nluc), which emitted a strong bioluminescence, as POIs. ELP-poly(d)-Rep and ELP-poly(d)-Nluc were constructed and formed the protein nanoparticles with multiply displayed Nluc and Rep (DNA aptamer) that amplified the bioluminescence signal and tumor recognition ability. Mucin-1 (MUC1)-overexpressing human breast tumor MCF7 cells and MUC1-recognizing aptamer (MUC1 aptamer) were selected as models. The MUC1 aptamer-conjugated protein nanoparticles exhibited a 13.7-fold higher bioluminescence signal to MCF-7 cells than to human embryonic kidney 293 (HEK293) cells, which express low levels of MUC1. Furthermore, the protein nanoparticles could detect up to 70.7 cells/mL of MCF-7 cells from a cell suspension containing HEK-293. The protein nanoparticles with multiple Rep and Nluc show a great potential as a material for detecting CTCs.

Oncogene-targeting nanoprobes for early imaging detection of tumor

Malignant tumors have been one of the major reasons for deaths worldwide. Timely and accurate diagnosis as well as effective intervention of tumors play an essential role in the survival of patients. Genomic instability is the important foundation and feature of cancer, hence, in vivo oncogene imaging based on novel probes provides a valuable tool for the diagnosis of cancer at early-stage. However, the in vivo oncogene imaging is confronted with great challenge, due to the extremely low copies of oncogene in tumor cells. By combining with various novel activatable probes, the molecular imaging technologies provide a feasible approach to visualize oncogene in situ, and realize accurate treatment of tumor. This review aims to declare the design of nanoprobes responded to tumor associated DNA or RNA, and summarize their applications in detection and bioimaging for tumors. The significant challenges and prospective of oncogene-targeting nanoprobes towards tumors diagnosis are revealed as well.

Bioengineering extracellular vesicles: smart nanomaterials for bone regeneration

In the past decade, extracellular vesicles (EVs) have emerged as key regulators of bone development, homeostasis and repair. EV-based therapies have the potential to circumnavigate key issues hindering the translation of cell-based therapies including functional tissue engraftment, uncontrolled differentiation and immunogenicity issues. Due to EVs' innate biocompatibility, low immunogenicity, and high physiochemical stability, these naturally-derived nanoparticles have garnered growing interest as potential acellular nanoscale therapeutics for a variety of diseases. Our increasing knowledge of the roles these cell-derived nanoparticles play, has made them an exciting focus in the development of novel pro-regenerative therapies for bone repair. Although these nano-sized vesicles have shown promise, their clinical translation is hindered due to several challenges in the EV supply chain, ultimately impacting therapeutic efficacy and yield. From the biochemical and biophysical stimulation of parental cells to the transition to scalable manufacture or maximising vesicles therapeutic response in vivo, a multitude of techniques have been employed to improve the clinical efficacy of EVs. This review explores state of the art bioengineering strategies to promote the therapeutic utility of vesicles beyond their native capacity, thus maximising the clinical potential of these pro-regenerative nanoscale therapeutics for bone repair.

Secondary Structure of DNA Aptamer Influences Biomimetic Mineralization of Calcium Carbonate

Calcium materials, such as calcium carbonate, are produced in natural and industrial settings that range from oceanic to biomedical. An array of biological and biomimetic template molecules have been employed in controlling and understanding the mineralization reaction but have largely focused on small molecule additives or disordered polyelectrolytes. DNA aptamers are synthetic and programmable biomolecules with polyelectrolyte characteristics but with predictable and controllable secondary structure akin to native extracellular moieties. This work demonstrates for the first time the influence of DNA aptamers with known G-quadruplex structures on calcium carbonate mineralization. Aptamers demonstrate kinetic inhibition of mineral formation, sequence and pH-dependent uptake into the mineral, and morphological control of the primarily calcite material in controlled solution conditions. In reactions initiated from the complex matrix of ocean water, DNA aptamers demonstrated enhancement of mineralization kinetics and resulting amorphous material. This work provides new biomimetic tools to employ in controlled mineralization and demonstrates the influence that template secondary structure can have in material formation.

Recent Progress in Nanotechnology-Based Approaches for Food Monitoring

Throughout the food supply chain, including production, storage, and distribution, food can be contaminated by harmful chemicals and microorganisms, resulting in a severe threat to human health. In recent years, the rapid advancement and development of nanotechnology proposed revolutionary solutions to solve several problems in scientific and industrial areas, including food monitoring. Nanotechnology can be incorporated into chemical and biological sensors to improve analytical performance, such as response time, sensitivity, selectivity, reliability, and accuracy. Based on the characteristics of the contaminants and the detection methods, nanotechnology can be applied in different ways in order to improve conventional techniques. Nanomaterials such as nanoparticles, nanorods, nanosheets, nanocomposites, nanotubes, and nanowires provide various functions for the immobilization and labeling of contaminants in electrochemical and optical detection. This review summarizes the recent advances in nanotechnology for detecting chemical and biological contaminations in the food supply chain.

A Novel ssDNA Aptamer Targeting Carcinoembryonic Antigen: Selection and Characterization

One of the major causes of a drastically shorter life expectancy and one of the most prevalent diseases in the world today is cancer. Given the data on the rise in cancer cases throughout the world, it is obvious that, despite the diagnostic techniques currently being used, there is a pressing need to develop precise and sensitive techniques for early diagnosis of the disease. A high degree of affinity and specificity towards particular targets is maintained by the short nucleic acid molecules known as aptamers. Aptamers outperform antibodies due to their unique benefits, such as their simplicity in synthesis and modification, lack of toxicity, and long-term stability. Utilizing an accurate recognition element and a robust signal transduction mechanism, molecular diagnostics can be extremely sensitive and specific. In this study, development of new single-stranded DNA aptamers against CEA for use in cancer diagnostics was accomplished using SELEX and NGS methods. As a result of 12 iterative SELEX rounds, nine aptamer candidates against CEA were developed. NGS comparative analysis revealed that round twelve had an enriched number of aptamers that were specifically bound, as opposed to round eight. Among the selected nine sequences characterized by bioinformatics analysis and ELONA, an aptamer sequence with the highest specificity and affinity for the target protein was identified and further examined. Aptamer sequence (6) was screened in a concentration-dependent assay, specificity analysis was performed, and its potential secondary and tertiary structures were predicted, which enabled us to test one of the possible putative interactions with CEA. Finally, aptamer sequence (6) labelled with a Cy5 fluorescent tag was used in confocal microscopy to observe its binding towards the CEA expressed in HT-29 human colon adenocarcinoma cell line.

Bioimaging Nucleic-Acid Aptamers with Different Specificities in Human Glioblastoma Tissues Highlights Tumoral Heterogeneity

Nucleic-acid aptamers are of strong interest for diagnosis and therapy. Compared with antibodies, they are smaller, stable upon variations in temperature, easy to modify, and have higher tissue-penetration abilities. However, they have been little described as detection probes in histology studies of human tissue sections. In this study, we performed fluorescence imaging with two aptamers targeting cell-surface receptors EGFR and integrin α5β1, both involved in the aggressiveness of glioblastoma. The aptamers’ cell-binding specificities were confirmed using confocal imaging. The affinities of aptamers for glioblastoma cells expressing these receptors were in the 100–300 nM range. The two aptamers were then used to detect EGFR and integrin α5β1 in human glioblastoma tissues and compared with antibody labeling. Our aptafluorescence assays proved to be able to very easily reveal, in a one-step process, not only inter-tumoral glioblastoma heterogeneity (differences observed at the population level) but also intra-tumoral heterogeneity (differences among cells within individual tumors) when aptamers with different specificities were used simultaneously in multiplexing labeling experiments. The discussion also addresses the strengths and limitations of nucleic-acid aptamers for biomarker detection in histology.

Extracellular vesicles and particles impact the systemic landscape of cancer

Intercellular cross talk between cancer cells and stromal and immune cells is essential for tumor progression and metastasis. Extracellular vesicles and particles (EVPs) are a heterogeneous class of secreted messengers that carry bioactive molecules and that have been shown to be crucial for this cell-cell communication. Here, we highlight the multifaceted roles of EVPs in cancer. Functionally, transfer of EVP cargo between cells influences tumor cell growth and invasion, alters immune cell composition and function, and contributes to stromal cell activation. These EVP-mediated changes impact local tumor progression, foster cultivation of pre-metastatic niches at distant organ-specific sites, and mediate systemic effects of cancer. Furthermore, we discuss how exploiting the highly selective enrichment of molecules within EVPs has profound implications for advancing diagnostic and prognostic biomarker development and for improving therapy delivery in cancer patients. Altogether, these investigations into the role of EVPs in cancer have led to discoveries that hold great promise for improving cancer patient care and outcome.

Exosome detection via surface-enhanced Raman spectroscopy for cancer diagnosis

As nanoscale extracellular vesicles, exosomes are secreted by various cell types, and they are widely distributed in multiple biological fluids. Studies have shown that tumor-derived exosomes can carry a variety of primary tumor-specific molecules, which may represent a novel tool for the early detection of cancer. However, the clinical translation of exosomes remains a challenge due to the requirement of large quantities of samples when enriching the cancer-related exosomes in biological fluids, the insufficiency of traditional techniques for exosome subpopulations, and the complex exosome isolation of the current commercially available exosome phenotype profiling approaches. The evolving surface-enhanced Raman scattering (SERS) technology, with properties of unique optoelectronics, easy functionalization, and the particular interaction between light and nanoscale metallic materials, can achieve sensitive detection of exosomes without large quantities of samples and multiplexed phenotype profiling, providing a new mode of real-time and noninvasive analysis for cancer patients. In the present review, we mainly discussed exosome detection based on SERS, especially SERS immunoassay. The basic structure and function of exosomes were firstly introduced. Then, recent studies using the SERS technique for cancer detection were critically reviewed, which mainly included various SERS substrates, biological modification of SERS substrates, SERS-based exosome detection, and the combination of SERS and other technologies for cancer diagnosis. This review systematically discussed the essential aspects, limitations, and considerations of applying SERS technology in the detection and analysis of cancer-derived exosomes, which could provide a valuable reference for the early diagnosis of cancer through SERS technology. STATEMENT OF SIGNIFICANCE: Surface-enhanced Raman scattering (SERS) has been applied to exosomes detection to obtain better diagnostic results. In past three years, several reviews have been published in exosome detection, which were narrowly focus on methods of exosome detection. Selection and surface functionalization of the substrate and the combination detection with different methods based on SERS will provide new strategies for the detection of exosomes. This review will focus on the above aspects. This emerging detection method is constantly evolving and contributing to the early discovery of diseases in the future.

Pre-miRNA-149 G-quadruplex as a molecular agent to capture nucleolin

One of the most significant challenges in capturing and detecting biomarkers is the choice of an appropriate biomolecular receptor. Recently, RNA G-quadruplexes emerged as plausible receptors due to their ability to recognize with high-affinity proteins. Herein, we have unveiled and characterized the capability of the precursor microRNA 149 to form a G-quadruplex structure and determined the role that some ligands may have in its folding and binding capacity to nucleolin. The G-quadruplex formation was induced by K+ ions and stabilized by ligands, as demonstrated by nuclear magnetic resonance and circular dichroism experiments. Surface plasmon resonance measurements showed a binding affinity of precursor microRNA 149 towards ligands in the micromolar range (10-5-10-6 M) and a strong binding affinity to nucleolin RNA-binding domains 1 and 2 (8.38 × 10-10 M). Even in the presence of the ligand PhenDC3, the binding remains almost identical and in the same order of magnitude (4.46 × 10-10 M). The molecular interactions of the RNA G-quadruplex motif found in precursor miRNA 149 (5'-GGGAGGGAGGGACGGG- 3') and nucleolin RNA-binding domains 1 and 2 were explored by means of molecular docking and molecular dynamics studies. The results showed that RNA G-quadruplex binds to a cavity between domains 1 and 2 of the protein. Then, complex formation was also evaluated through polyacrylamide gel electrophoresis. The results suggest that precursor microRNA 149/ligands and precursor microRNA 149/nucleolin RNA-binding domains 1 and 2 form stable molecular complexes. The in vitro co-localization of precursor microRNA 149 and nucleolin in PC3 cells was demonstrated using confocal microscopy. Finally, a rapid and straightforward microfluidic strategy was employed to check the ability of precursor microRNA 149 to capture nucleolin RNA-binding domains 1 and 2. The results revealed that precursor microRNA 149 can capture nucleolin RNA-binding domains 1 and 2 labeled with Fluorescein 5-isothiocyanate in a concentration-dependent manner, but PhenDC3 complexation seems to decrease the ability of precursor microRNA 149 to capture the protein. Overall, our results proved the formation of the G-quadruplex structure in the precursor microRNA 149 and the ability to recognize and detect nucleolin. This proof-of-concept study could open up a new framework for developing new strategies to design improved molecular receptors for capture and detection of nucleolin in complex biological samples.

Aptamer grafted nanoparticle as targeted therapeutic tool for the treatment of breast cancer

Breast carcinomas repeat their number and grow exponentially making it extremely frequent malignancy among women. Approximately, 70-80% of early diagnosed or non-metastatic conditions are treatable while the metastatic cases are considered ineffective to treat with current ample amount of therapy. Target based anti-cancer treatment has been in the limelight for decades and is perceived significant consideration of scientists. Aptamers are the 'coming of age' therapeutic approach, selected using an appropriate tool from the library of sequences. Aptamers are non-immunogenic, stable, and high-affinity ligand which are poised to reach the clinical benchmark. With the heed in nanoparticle application, the delivery of aptamer to the specific site could be enhanced which also protects them from nuclease degradation. Moreover, nanoparticles due to robust structure, high drug entrapment, and modifiable release of cargo could serve as a successful candidate in the treatment of breast carcinoma. This review would showcase the method and modified method of selection of aptamers, aptamers that were able to make its way towards clinical trial and their targetability and selectivity towards breast cancers. The appropriate usage of aptamer-based biosensor in breast cancer diagnosis have also been discussed.

Oligonucleotide aptamers for pathogen detection and infectious disease control

During an epidemic or pandemic, the primary task is to rapidly develop precise diagnostic approaches and effective therapeutics. Oligonucleotide aptamer-based pathogen detection assays and control therapeutics are promising, as aptamers that specifically recognize and block pathogens can be quickly developed and produced through simple chemical synthesis. This work reviews common aptamer-based diagnostic techniques for communicable diseases and summarizes currently available aptamers that target various pathogens, including the SARS-CoV-2 virus. Moreover, this review discusses how oligonucleotide aptamers might be leveraged to control pathogen propagation and improve host immune system responses. This review offers a comprehensive data source to the further develop aptamer-based diagnostics and therapeutics specific for infectious diseases.

Quantum dot biosensor combined with antibody and aptamer for tracing food-borne pathogens

Due to the increasing number of food-borne diseases, more attention is being paid to food safety. Food-borne pathogens are the main cause of food-borne diseases, which seriously endanger human health, so it is necessary to detect and control them. Traditional detection methods cannot meet the requirements of rapid detection of food due to many shortcomings, such as being time-consuming, laborious or requiring expensive instrumentation. Quantum dots have become a promising nanotechnology in pathogens tracking and detection because of their excellent optical properties. New biosensor detection methods based on quantum dots are have been gradually developed due to their high sensitivity and high specificity. In this review, we summarize the different characteristics of quantum dots synthesized by carbon, heavy metals and composite materials firstly. Then, attention is paid to the principles, advantages and limitations of the quantum dots biosensor with antibodies and aptamers as recognition elements for recognition and capture of food-borne pathogens. Finally, the great potential of quantum dots in pathogen detection is summarized.

Targeting Strategies for Enhancing Paclitaxel Specificity in Chemotherapy

Paclitaxel (PTX) has been used for cancer treatment for decades and has become one of the most successful chemotherapeutics in the clinic and financially. However, serious problems with its use still exist, owing to its poor solubility and non-selective toxicity. With respect to these issues, recent advances have addressed the water solubility and tumor specificity related to PTX application. Many measures have been proposed to remedy these limitations by enhancing tumor recognition via ligand-receptor-mediated targeting as well as other associated strategies. In this review, we investigated various kinds of ligands that have emerged as PTX tumor-targeting tools. In particular, this article highlights small molecule-, protein-, and aptamer-functionalized conjugates and nanoparticles (NPs), providing a promising approach for PTX-based individualized treatment prospects.

The Landscape of RNA-Protein Interactions in Plants: Approaches and Current Status

RNAs transmit information from DNA to encode proteins that perform all cellular processes and regulate gene expression in multiple ways. From the time of synthesis to degradation, RNA molecules are associated with proteins called RNA-binding proteins (RBPs). The RBPs play diverse roles in many aspects of gene expression including pre-mRNA processing and post-transcriptional and translational regulation. In the last decade, the application of modern techniques to identify RNA-protein interactions with individual proteins, RNAs, and the whole transcriptome has led to the discovery of a hidden landscape of these interactions in plants. Global approaches such as RNA interactome capture (RIC) to identify proteins that bind protein-coding transcripts have led to the identification of close to 2000 putative RBPs in plants. Interestingly, many of these were found to be metabolic enzymes with no known canonical RNA-binding domains. Here, we review the methods used to analyze RNA-protein interactions in plants thus far and highlight the understanding of plant RNA-protein interactions these techniques have provided us. We also review some recent protein-centric, RNA-centric, and global approaches developed with non-plant systems and discuss their potential application to plants. We also provide an overview of results from classical studies of RNA-protein interaction in plants and discuss the significance of the increasingly evident ubiquity of RNA-protein interactions for the study of gene regulation and RNA biology in plants.

Generation and characterization of aptamers against grass carp reovirus infection for the development of rapid detection assay

Grass carp reovirus (GCRV) causes devastating viral haemorrhagic disease in farmed grass carp (Ctenopharyngon idellus). As novel molecular probes, aptamers have been widely applied in rapid diagnosis and efficient therapies against virus or diseases. In this study, three single-stranded DNA (ssDNA) aptamers were selected against GCRV-infected CIK cells via SELEX (systematic evolution of ligands by exponential enrichment technology). Secondary structures predicted by MFOLD indicated that aptamers formed stem-loop structures, and GVI-11 had the lowest ΔG value of -30.84 KJ/mol. Three aptamers could specifically recognize GCRV-infected CIK cells, with calculated dissociation constants (Kd) of 220.86, 176.63 and 278.66 nM for aptamers GVI-1, GVI-7 and GVI-11, respectively, which indicated that they could serve as specific delivery system for antiviral therapies. The targets of aptamers GVI-1, GVI-7 and GVI-11 on the surface of GCRV-infected cells could be membrane proteins, which were trypsin-sensitive. Furthermore, FAM-labelled aptamer GVI-7 could be applied to detect GCRV infection in vivo. It is the first time to generate and characterize aptamers against GCRV-infected cells. These aptamers have great potentials in development of rapid diagnosis technology and antiviral agents against GCRV infection in aquaculture.

Targeting Strategies for Enhancing Paclitaxel Specificity in Chemotherapy

Paclitaxel (PTX) has been used for cancer treatment for decades and has become one of the most successful chemotherapeutics in the clinic and financially. However, serious problems with its use still exist, owing to its poor solubility and non-selective toxicity. With respect to these issues, recent advances have addressed the water solubility and tumor specificity related to PTX application. Many measures have been proposed to remedy these limitations by enhancing tumor recognition via ligand-receptor-mediated targeting as well as other associated strategies. In this review, we investigated various kinds of ligands that have emerged as PTX tumor-targeting tools. In particular, this article highlights small molecule-, protein-, and aptamer-functionalized conjugates and nanoparticles (NPs), providing a promising approach for PTX-based individualized treatment prospects.

Selective aptamer conjugation to silver-coated magnetite nanoparticles for magnetic solid-phase extraction of trace amounts of Pb2+ ions

Herein, a novel aptamer-functionalized magnetic adsorbent was developed and combined with magnetic solid-phase extraction (MSPE) for the specific enrichment of Pb²⁺ ions prior to flame atomic absorption spectrometric detection.

Modern isolation and separation techniques for extracellular vesicles

Extracellular vesicles (EVs) are heterogenous membrane-bound vesicles released from various origins. EVs play a crucial role in cellular communication and mediate several physiological and pathological processes, highlighting their potential therapeutic and diagnostic applications. Due to the rapid increase in interests and needs to elucidate EV properties and functions, numerous isolation and separation approaches for EVs have been developed to overcome limitations of conventional techniques, such as ultracentrifugation. This review focuses on recently emerging and modern EV isolation and separation techniques, including size-, charge-, and affinity-based techniques while excluding ultracentrifugation and precipitation-based techniques due to their multiple limitations. The advantages and drawbacks of each technique are discussed together with insights into their applications. Emerging approaches all share similar features in terms of being time-effective, easy-to-operate, and capable of providing EVs with suitable and desirable purity and integrity for applications of interest. Combination and hyphenation of techniques have been used for EV isolation and separation to yield EVs with the best quality. The most recent development using an automated on-line system including selective affinity-based trapping unit and asymmetrical flow field-flow fractionation allows reliable isolation and fractionation of EV subpopulations from human plasma.

In vivo Targeting of Liver Cancer with Tissue- and Nuclei-Specific Mesoporous Silica Nanoparticle-Based Nanocarriers in mice

Purpose

Cancer tissue-specific and nuclei-targeted drug delivery is ideal for the delivery of chemotherapy. However, it has only been achieved in in vitro studies mainly due to low efficiency in vivo. In this study, we aimed to establish an efficient dual-targeted system that targets liver cancer tissue as well as the nuclei of cancer cells in vivo.

Methods

We first synthesized TAT peptide (TATp)-mesoporous silica nanoparticle (MSN) complex (TATp-MSN) and generated liposomes that carried liver cancer-specific aptamer TLS11a (TLS11a-LB). We then generated the drug TLS11a-LB@TATp-MSN/doxorubicin (DOX) by mixing TLS11a-LB and DOX-loaded TATp-MSN. After physical and chemical characterization of the nanoparticles, DOX release from these formulations was evaluated at pH 5.0 and 7.4. Furthermore, we also evaluated nuclear localization and cytotoxicity of the drug in H22 cells in vitro and investigated the liver cancer targeting and antitumor activities of the nano-drug in vivo using a H22 tumor-bearing mice model.

Results

TLS11a-LB@TATp-MSN/DOX and its controls were confirmed as nano-drugs (<100 nm) using transmission electron microscopy (TEM). The DOX release rate of TLS11a-LB@TATp-MSN/DOX was significantly faster at pH 5.0 than at pH 7.4. TLS11a-LB@TATp-MSN/DOX effectively targeted the nuclei of H22 cells and released DOX with a higher efficiency than that of the control groups. In addition, TLS11a-LB@TATp-MSN/DOX exhibited slight cytotoxicity, but not significantly more than controls. In vivo studies showed that TLS11a-LB@TATp-MSN accumulated in subcutaneous H22 tumors in the right axilla of BALB/c mice, reaching peak levels at 48 h after intravenous injection, respectively, and demonstrated that TLS11a-LB@TATp-MSN/DOX group enhanced tumor treatment efficacy while reducing systemic side effects.

Conclusion

TLS11a-LB@TATp-MSN/DOX can efficiently deliver DOX to the nuclei of liver cancer cells by dual targeting liver cancer tissue and the nuclei of the cancer cells in mice. Thus, it is a promising nano-drug for the treatment of liver cancer.

Machine Learning Aided Photonic Diagnostic System for Minimally Invasive Optically Guided Surgery in the Hepatoduodenal Area

Abdominal cancer is a widely prevalent group of tumours with a high level of mortality if diagnosed at a late stage. Although the cancer death rates have in general declined over the past few decades, the mortality from tumours in the hepatoduodenal area has significantly increased in recent years. The broader use of minimal access surgery (MAS) for diagnostics and treatment can significantly improve the survival rate and quality of life of patients after surgery. This work aims to develop and characterise an appropriate technical implementation for tissue endogenous fluorescence (TEF) and assess the efficiency of machine learning methods for the real-time diagnosis of tumours in the hepatoduodenal area. In this paper, we present the results of the machine learning approach applied to the optically guided MAS. We have elaborated tissue fluorescence approach with a fibre-optic probe to record the TEF and blood perfusion parameters during MAS in patients with cancers in the hepatoduodenal area. The measurements from the laser Doppler flowmetry (LDF) channel were used as a sensor of the tissue vitality to reduce variability in TEF data. Also, we evaluated how the blood perfusion oscillations are changed in the tumour tissue. The evaluated amplitudes of the cardiac (0.6-1.6 Hz) and respiratory (0.2-0.6 Hz) oscillations was significantly higher in intact tissues (p < 0.001) compared to the cancerous ones, while the myogenic (0.2-0.06 Hz) oscillation did not demonstrate any statistically significant difference. Our results demonstrate that a fibre-optic TEF probe accompanied with ML algorithms such as k-Nearest Neighbours or AdaBoost is highly promising for the real-time in situ differentiation between cancerous and healthy tissues by detecting the information about the tissue type that is encoded in the fluorescence spectrum. Also, we show that the detection can be supplemented and enhanced by parallel collection and classification of blood perfusion oscillations.

Advances in Exosomes-Based Drug Delivery Systems

Exosomes, a subgroup of extracellular vesicles, are important mediators of long-distance intercellular communication and are involved in a diverse range of biological processes such as the transport of lipids, proteins, and nucleic acids. Researchers, seeing the problems caused by the toxic effects and clearance of synthetic nanoparticles, consider exosomes as an interesting alternative to such nanoparticles in the specific and controlled transport of drugs. In recent years, there have been remarkable advances in the use of exosomes in cancer therapeutics or for treating neurological diseases, among other applications. The objective of this work is to analyze studies focused on exosomes used in drug delivery system, present and future applications in this field of research are discussed based on the results obtained.

An ssDNA aptamer specific for detection and purification of hexahistidine-tagged proteins

Aptamers are small-sized RNA or ssDNA ligands with a unique structure, which have high specificity and affinity to their cognate targets. Thus, in addition to the extensive values in various bio-medical fields, aptamers can also be alternatively used as affinity ligands in the bioprocess, such as for protein purification. In the present study, a hexahistidine specific aptamer named AptHis-C, was developed through the SELEX methodology, which has high affinity to hexahistidine, and its dissociation constant was as low as 20.8 nM. The structural prediction revealed that AptHis-C contains two connected stem-loop conformations. AptHis-C can only specifically recognize recombinant proteins with the hexahistidine-tag in simple or complex situations, and not to those with other tags. When immobilized on magnetic beads, AptHis-C can be used as a tool for hexahistidine-tagged recombinant protein purification. Its effectiveness is as good as traditional Ni-based beads. Besides, due to the intrinsic characteristics of nucleic acids, such as high thermal/chemical stability, immobilized aptamer-magnetic beads can be reused many times without an obvious decrease of purification effectiveness. This aptamer may represent a novel method for the detection and purification of hexahistidine-tagged recombinant proteins.

Electrochemical aptasensors for cancer diagnosis in biological fluids - A review

The tunability of SELEX procedure is an essential feature to supply bioaffinity receptors (aptamers) almost on demand for analytical and therapeutic purposes. This longstanding ambition is, however, not straightforward. Non-invasive cancer diagnosis, so called liquid biopsy, requires collection of body fluids with minimal or no sample pretreatment. In those raw matrices, aptamers must recognize minute amounts of biomarkers that are not unique entities but large sets of variants evolving with the disease stage. The susceptibility of aptasensors to assay conditions has driven the selection of aptamers to natural environments to ensure their optimum performance in clinical samples. We present herein a compilation of the SELEX procedures in natural milieus. By revising the electrochemical aptasensors applied to clinical samples for cancer diagnosis and tracing back to the original SELEX we analyze whether aptamers raised using these SELEX strategies are being incorporated to the diagnostic devices and how aptasensors are finding their way to a market dominated by antibody-based assays.

Aptamer-Equipped Protamine Nanomedicine for Precision Lymphoma Therapy

Anaplastic large cell lymphoma (ALCL) is the most common T-cell lymphoma in children. ALCL cells characteristically express surface CD30 molecules and carry the pathogenic ALK oncogene, both of which are diagnostic biomarkers and are also potential therapeutic targets. For precision therapy, we report herein a protamine nanomedicine incorporated with oligonucleotide aptamers to selectively target lymphoma cells, a dsDNA/drug payload to efficiently kill targeted cells, and an siRNA to specifically silence ALK oncogenes. The aptamer-equipped protamine nanomedicine was simply fabricated through a non-covalent charge-force reaction. The products had uniform structure morphology under an electron microscope and a peak diameter of 103 nm by dynamic light scattering measurement. Additionally, flow cytometry analysis demonstrated that under CD30 aptamer guidance, the protamine nanomedicine specifically bound to lymphoma cells, but did not react to off-target cells in control experiments. Moreover, specific cell targeting and intracellular delivery of the nanomedicine were also validated by electron and confocal microscopy. Finally, functional studies demonstrated that, through combined cell-selective chemotherapy using a drug payload and oncogene-specific gene therapy using an siRNA, the protamine nanomedicine effectively killed lymphoma cells with little toxicity to off-target cells, indicating its potential for precision therapy.

Selected DNA aptamers as hydroxyapatite affinity reagents

DNA aptamers were selected for their ability to bind specifically and quickly to crystalline hydroxyapatite (Ca₁₀(PO₄)₆(OH)₂; HAP), the primary mineral component of enamel and bone. Aptamers were found to have an enhanced percent of G-nucleotides and a propensity for forming a G-quadruplex secondary structure. One aptamer was studied in comparison to control sequences and was found to bind with high affinity and at high loading capacity, with enhanced binding kinetics, and with specificity for crystalline HAP material over amorphous calcium phosphate (ACP) and β-tricalcium phosphate (TCP). The fluorescently-functionalized aptamer was demonstrated to specifically label HAP in a surface binding experiment and suggests the usefulness of this selected aptamer in biomedical or biotechnology fields where the labeling of specific calcium phosphate materials is required.

Extracellular pH-manipulated in situ reconfiguration of aptamer functionalized DNA monomer enables specifically improved affinity, detection and drug delivery

Aptamers are promising in cancer diagnosis and therapy, but their poor affinity under physiological conditions is a challenge. In view of the acidic microenvironment of solid tumors, we herein developed an extracellular pH-manipulated multivalent approach to exclusively improve the affinity to target cells at physiological temperature. Specifically, an aptamer based DNA monomer (AptDM) with split i-motif fragments overhanging was rationally designed, it possessed pH-responsiveness and doxorubicin loading capacity. At neutral pH, AptDMs existed as well dispersed small units, showing weakly undesired binding and internalization. In acidic extracellular conditions, AptDMs tended to crosslink of each other into multivalent DNA assemblies (MDAs) via formation of an intermolecular i-motif structure. Due to the multivalent effect, the resulting MDAs showed greatly enhanced affinity (K_d = 9.96 ± 1.06 nM) and stable binding ability at 37 °C, thus allowing highly sensitive diagnosis, efficient drug delivery, and improved inhibition to target tumor cells, but decreased cytotoxicity to nontarget cells. It is believed that this multivalent approach may boost the development of novel aptamer functionalized nanodevices for clinical validation.

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.

Aptamer technology: a new approach to treat lymphoma?

Oligonucleotide aptamers are a class of small-molecule ligands. Functionally similar to protein antibodies, aptamers can specifically bind to their targets with high affinity. Biomedical studies have revealed the potential clinical value of aptamer technology for disease diagnosis and targeted therapy. Lymphoma is a group of cancers originating from the lymphatic system. Currently, chemotherapy is the primary treatment for lymphoma, although it may cause serious side effects in patients due to lack of target specificity. Here, we selectively discuss the recent development of potential applications of aptamer technology for precision lymphoma therapy, which are able to not only achieve high therapeutic efficacy but also do not cause off-target side effects.

A dichromatic label-free aptasensor for sulfadimethoxine detection in fish and water based on AuNPs color and fluorescent dyeing of double-stranded DNA with SYBR Green I

A dichromatic label-free aptasensor was described for sulfadimethoxine (SDM) detection. Compared with the binding of SDM-aptamer to SDM, the higher affinity of aptamer to cDNA may result in the hybridization of dsDNA. In the presence of SDM, the aptamer specifically binds to SDM, leading to a blue color of AuNPs in deposit and fluorescence at 530 nm in supernatant after adding cDNA and SGI. With no target of SDM, AuNPs protected with the aptamer re-disperse in PBS with a red color, and no fluorescence occurs in supernatant. Based on the principle, SDM can be quantitatively detected through both fluorescent emission and AuNPs color changes with recoveries ranging from 99.2% to 102.0% for fish and from 99.5% to 100.5% for water samples. An analytical linear range of 2-300 ng mL^-1 was achieved with the detection limits of 3.41 ng mL^-1 for water and 4.41 ng g^-1 for fish samples (3σ, n = 9).

RNA Aptamers Targeting Integrin α5β1 as Probes for Cyto- and Histofluorescence in Glioblastoma

Nucleic acid aptamers are often referred to as chemical antibodies. Because they possess several advantages, like their smaller size, temperature stability, ease of chemical modification, lack of immunogenicity and toxicity, and lower cost of production, aptamers are promising tools for clinical applications. Aptamers against cell surface protein biomarkers are of particular interest for cancer diagnosis and targeted therapy. In this study, we identified and characterized RNA aptamers targeting cells expressing integrin α5β1. This αβ heterodimeric cell surface receptor is implicated in tumor angiogenesis and solid tumor aggressiveness. In glioblastoma, integrin α5β1 expression is associated with an aggressive phenotype and a decrease in patient survival. We used a complex and original hybrid SELEX (selective evolution of ligands by exponential enrichment) strategy combining protein-SELEX cycles on the recombinant α5β1 protein, surrounded by cell-SELEX cycles using two different cell lines. We identified aptamer H02, able to differentiate, in cyto- and histofluorescence assays, glioblastoma cell lines, and tissues from patient-derived tumor xenografts according to their α5 expression levels. Aptamer H02 is therefore an interesting tool for glioblastoma tumor characterization.

Electrochemical biosensors for the detection of lung cancer biomarkers: A review

Cancer is one of the most widespread challenges and important diseases, which has the highest mortality rate. Lung cancer is the most common type of cancer, so that about 25% of all cancer deaths are related to the lung cancer. The lung cancer is classified as two different types with different treatment methodology: the small cell lung carcinoma and nonsmall cell lung carcinoma are two categories of the lung cancer. Since the lung cancer is often in the latent period in its early stages, therefore, early diagnosis of lung cancer has many challenges. Hence, there is a need for sensitive and reliable tools for preclinical diagnosis of lung cancer. Therefore, many detection methods have been employed for early detection of lung cancer. As lung cancer tumors growth in the body, the cancerous cells release numerous DNA, proteins, and metabolites as special biomarkers of the lung cancer. The levels of these biomarkers show the stages of the lung cancer. Therefore, detection of the biomarkers can be used for screening and clinical diagnosis of the lung cancer. There are numerous biomarkers for the lung cancer such as EGFR, CEA, CYFRA 21-1, ENO1, NSE, CA 19-9, CA 125 and VEGF. Nowadays, electrochemical methods are very attractive and useful in the lung cancer detections. So, in this paper, the recent advances and improvements (2010-2018) in the electrochemical detection of the lung cancer biomarkers have been reviewed.

Detection of sulfadimethoxine using optical images of liquid crystals

A label-free method for sulfadimethoxine (SDM) detection using an aptamer-based liquid crystal biosensor is developed. The sensor probe is fabricated by immobilizing amine-functionalized aptamers onto the glass slide decorating mixed self-assembled layers of triethoxysilylbutyraldehyde (TEA) and N,N-dimethyl-n-octadecyl-3-aminopropyltrimethoxysilylchloride (DMOAP). Liquid crystals (LCs) are supported on the surface and serve as response elements, which assume the homeotropic alignment and cause a dark optical appearance under crossed polarizers. In the presence of SDM, the formation of SDM-aptamer compounds induces a notable change in the topographical structure of the surface, which disturbs the original homeotropic orientation of LCs and results in a bright optical appearance. A detection limit of 10 μg L-1 is obtained, which is far lower than the maximum residue limit (100 μg L-1 in China). This facile method shows good specificity for SDM detection and may have great potential for detecting other small molecules.

Current approaches for RNA-labelling to identify RNA-binding proteins

RNA is involved in all domains of life, playing critical roles in a host of gene expression processes, host-defense mechanisms, cell proliferation, and diseases. A critical component in many of these events is the ability for RNA to interact with proteins. Over the past few decades, our understanding of such RNA-protein interactions and their importance has driven the search and development of new techniques for the identification of RNA-binding proteins. In determining which proteins bind to the RNA of interest, it is often useful to use the approach where the RNA molecule is the "bait" and allow it to capture proteins from a lysate or other relevant solution. Here, we review a collection of methods for modifying RNA to capture RNA-binding proteins. These include small-molecule modification, the addition of aptamers, DNA-anchoring, and nucleotide substitution. With each, we provide examples of their application, as well as highlight their advantages and potential challenges.

Evaluation of the binding of natural products with thrombin binding aptamer G-quadruplex using electrospray ionization mass spectrometry and spectroscopic methods

A 15-mer thrombin-binding aptamer (TBA) was discovered with specificity for thrombin. It forms a unique G-quadruplex (G4), which is postulated to be the molecular basis for its binding specificity. Many analytical methods make use of affinity binding between the thrombin and TBA as they form a very stable complex. We develop a strategy to stabilize TBA/G4's structure by introducing G4-interactive molecules, which may enhance its ability to recognize the target. Herein, a fast screening ESI-MS assay was employed to determine potential binding of natural products molecules with the TBA/G4 complex. The experimental results showed that four investigated natural alkaloids had apparent binding affinities. One of them, jatrorrhizine (L1), has been shown to bind strongly to the TBA/G4 mainly in 1:2 M ratio. Once the working conditions were established, the interaction of the jatrorrhizine with the TBA/G4 was explored using a combination of ESI-MS and spectroscopic techniques. Ligand-induced effects on TBA/G4 structure and its stability were examined by means of circular dichroism (CD). Jatrorrhizine inducing the G4 formation seems also to be the more effective in terms of thermal stabilization under the experimental conditions used. Both results of UV and fluorescence experiments undoubtedly showed a good binding affinity with the binding constant around 10⁵ L mol^-1. The stacking interactions of jatrorrhizine with the G-tetrads in TBA/G4 were further confirmed by competition experiment. ESI-MS was carried out to determine the coexistence of 1:1 and 1:2 complexes in TBA/G4-L1 system, and showed a dynamical shift from 1:1 to 1:2 complex in minutes.

Selective Detection of Human Lung Adenocarcinoma Cells Based on the Aptamer-Conjugated Self-Assembled Monolayer of Gold Nanoparticles

This study established a microfluidic chip for the capture of A549 human lung circulating tumor cells via the aptamer-conjugated self-assembled monolayer (SAM) of gold nanoparticles (AuNPs) in the channel. AuNPs are among the most attractive nanomaterials for the signal enhancement of biosensors owing to their unique chemical, physical, and mechanical properties. The microchip was fabricated using soft photolithography and casting and molding techniques. A self-assembly method was designed to attach AuNPs, cell-specific aptamers, and target cells onto the desired area (i.e., SAM area). In this study, the gold microelectrode configuration was characterized by fluorescence microscopy and impedance measurements to confirm the important modification steps. Subsequently, several investigations with the proposed assay were conducted with different cell samples to determine the specific binding ability of the device for A549 adenocarcinoma cancer cells. This work has ensured a simple, convenient, selective, and sensitive approach for the development of biosensors for lung cancer detection during the early stages.

Recent Advances in Aptamer Discovery and Applications

Aptamers are short, single-stranded DNA, RNA, or synthetic XNA molecules that can be developed with high affinity and specificity to interact with any desired targets. They have been widely used in facilitating discoveries in basic research, ensuring food safety and monitoring the environment. Furthermore, aptamers play promising roles as clinical diagnostics and therapeutic agents. This review provides update on the recent advances in this rapidly progressing field of research with particular emphasis on generation of aptamers and their applications in biosensing, biotechnology and medicine. The limitations and future directions of aptamers in target specific delivery and real-time detection are also discussed.