Proteomics comparison of exosomes from serum and plasma between ultracentrifugation and polymer‐based precipitation kit methods

Exosomes are vesicles with sizes ranging from 30 to 150 nm. The analysis and detection of blood exosomes offers an effective route for cancer diagnosis, prognosis assessment, and therapeutic evaluation of diseases. Due to the difference in separation procedure, collection method and the usage of anticoagulants, serum and plasma samples show diversity test results. In order to evaluate the isolation effect of exosomes in serum and plasma samples, two commonly used exosomal isolation methods, ultracentrifugation and polymer‐based precipitation kit, were used, respectively. And the isolation effects were evaluated by comparing the composition and abundant of proteins from isolated exosomes based on MS‐based proteomics analysis. The results showed that the plasma exosomes extracted by ultracentrifugation identified more exosome biomarkers, and the concentrations of these biomarkers were higher than others. And plasma exosomes could be a better sample for blood‐based proteomics research of exosomes. It would be more useful for future targeted biomarker discovery.     

Rapid Detection of Exosomal MicroRNAs Using Virus‐Mimicking Fusogenic Vesicles

Exosomal microRNAs (miRNAs) are important biomarkers for clinical diagnosis and disease treatment monitoring. However, most approaches for exosomal miRNA detection are time‐consuming, laborious, and expensive. Herein, we report a virus‐mimicking fusogenic vesicle (Vir‐FV) that enables rapid, efficient, and high‐throughput detection of exosomal miRNAs within 2 h. Fusogenic proteins on Vir‐FVs can specifically target the sialic‐acid‐containing receptors on exosomes, inducing efficient fusion of Vir‐FVs and exosomes. Upon vesicle content mixing, the molecular beacons encapsulated in Vir‐FVs specifically hybridize with the target miRNAs in the exosomes, generating fluorescence. Combined with flow cytometry, the Vir‐FVs can not only detect exosomal miRNAs but also distinguish tumor exosomes from normal exosomes by sensing the tumor‐related miRNAs, paving the way towards the rapid and efficient detection of exosomal miRNAs for diagnosis and prognosis prediction of diseases.     

Ultrasensitive Detection and Binding Mechanism of Cocaine in an Aptamer‐based Single‐molecule Device

Aptamer serves as a potential candidate for the micro‐detection of cocaine due to its high specificity, high affinity and good stability. Although cocaine aptasensors have been extensively studied, the binding mechanism of cocaine‐aptamer interactions is still unknown, which limits the structural refinement in the design of an aptamer to improve the performance of cocaine aptasensors. Herein, we report a label‐free, ultrasensitive detection of single‐molecule cocaine‐aptamer interaction by using an electrical nanocircuit based on graphene‐molecule‐ graphene single‐molecule junctions (GMG‐SMJs). Real‐time recordings of cocaine‐aptamer interactions have exhibited distinct current oscillations before and after cocaine treatment, revealing the dynamic mechanism of the conformational changes of aptamer upon binding with cocaine. Further concentration‐dependent experiments have proved that these devices can act as a single‐molecule biosensor with at least a limit of detection as low as 1 nmol?L^–1. The method demonstrated in this work provides a novel strategy for shedding light on the interaction mechanism of biomolecules as well as constructing new types of aptasensors toward practical applications.     

Aptamer‐based Biosensor Developed to Monitor MUC1 Released by Prostate Cancer Cells

Electrochemical aptasensors can detect cancer biomarkers such as mucin 1 (MUC1) to provide point‐of‐care diagnosis that is low‐cost, specific and sensitive. Herein, a DNA hairpin containing MUC1 aptamer was thiolated, conjugated with methylene blue (MB) redox tag, and immobilized on a gold electrode by self‐assembly. The fabrication process was characterized by scanning electron microscopy, X‐ray spectroscopy analysis and electrochemistry techniques. The results evidenced a stable and sensitivity sensor presenting wide linear detection range (0.65–110 ng/mL). Therefore, it was able to precisely detect MUC1 production patterns in normal (RWPE‐1) and prostate cancer cells (LNCaP and PC3). The biosensor has ability to detect MUC1 in complex samples being an efficient and useful platform for cancer diagnosing in early stages and for physiological applications such as cancer treatment monitoring.      

An Aptamer‐Nanotrain Assembled from Six‐Letter DNA Delivers Doxorubicin Selectively to Liver Cancer Cells

Expanding the number of nucleotides in DNA increases the information density of functional DNA molecules, creating nanoassemblies that cannot be invaded by natural DNA/RNA in complex biological systems. Here, we show how six‐letter GACTZP DNA contributes this property in two parts of a nanoassembly: 1) in an aptamer evolved from a six‐letter DNA library to selectively bind liver cancer cells; and 2) in a six‐letter self‐assembling GACTZP nanotrain that carries the drug doxorubicin. The aptamer‐nanotrain assembly, charged with doxorubicin, selectively kills liver cancer cells in culture, as the selectivity of the aptamer binding directs doxorubicin into the aptamer‐targeted cells. The assembly does not kill untransformed cells that the aptamer does not bind. This architecture, built with an expanded genetic alphabet, is reminiscent of antibodies conjugated to drugs, which presumably act by this mechanism as well, but with the antibody replaced by an aptamer.     

Cross‐Linked Aptamer–Lipid Micelles for Excellent Stability and Specificity in Target‐Cell Recognition

The specific binding ability of DNA–lipid micelles (DLMs) can be increased by the introduction of an aptamer. However, supramolecular micellar structures based on self‐assemblies of amphiphilic DLMs are expected to demonstrate low stability when interacting with cell membranes under certain conditions, which could lead to a reduction in selectivity for targeting cancer cells. We herein report a straightforward cross‐linking strategy that relies on a methacrylamide branch to link aptamer and lipid segments. By an efficient photoinduced polymerization process, covalently linked aptamer–lipid units help stabilize the micelle structure and enhance aptamer probe stability, further improving the targeting ability of the resulting nanoassembly. Besides the development of a facile cross‐linking method, this study clarifies the relationship between aptamer–lipid concentration and the corresponding binding ability.     

Aptamer/AuNP Biosensor for Colorimetric Profiling of Exosomal Proteins

Exosomes constitute an emerging biomarker for cancer diagnosis because they carry multiple proteins that reflect the origins of parent cells. Assessing exosome surface proteins provides a powerful means of identifying a combination of biomarkers for cancer diagnosis. We report a sensor platform that profiles exosome surface proteins in minutes by the naked eye. The sensor consists of a gold nanoparticle (AuNP) complexed with a panel of aptamers. The complexation of aptamers with AuNPs protects the nanoparticles from aggregating in a high‐salt solution. In the presence of exosomes, the non‐specific and weaker binding between aptamers and the AuNP is broken, and the specific and stronger binding between exosome surface protein and the aptamer displaces aptamers from the AuNP surface and results in AuNP aggregation. This aggregation results in a color change and generates patterns for the identification of multiple proteins on the exosome surface.     

Self‐Assembled Aptamer‐Based Drug Carriers for Bispecific Cytotoxicity to Cancer Cells

Monovalent aptamers can deliver drugs to target cells by specific recognition. However, different cancer subtypes are distinguished by heterogeneous biomarkers and one single aptamer is unable to recognize all clinical samples from different patients with even the same type of cancers. To address heterogeneity among cancer subtypes for targeted drug delivery, as a model, we developed a drug carrier with a broader recognition range of cancer subtypes. This carrier, sgc8c‐sgd5a (SD), was self‐assembled from two modified monovalent aptamers. It showed bispecific recognition abilities to target cells in cell mixtures; thus broadening the recognition capabilities of its parent aptamers. The self‐assembly of SD simultaneously formed multiple drug loading sites for the anticancer drug doxorubicin (Dox). The Dox‐loaded SD (SD–Dox) also showed bispecific abilities for target cell binding and drug delivery. Most importantly, SD–Dox induced bispecific cytotoxicity in target cells in cell mixtures. Therefore, by broadening the otherwise limited recognition capabilities of monovalent aptamers, bispecific aptamer‐based drug carriers would facilitate aptamer applications for clinically heterogeneous cancer subtypes that respond to the same cancer therapy.     

Room‐Temperature Phosphorescence‐active Boronate Particles: Characterization and Ratiometric Afterglow‐sensing Behavior by Surface Grafting of Rhodamine B

We found that boronate particles ( BP ), as a self‐assembled system prepared by sequential dehydration of benzene‐1,4‐diboronic acid with pentaerythritol, showed greenish room‐temperature phosphorescence (RTP). This emission was observed in both solid and dispersion state in water. To understand the RTP properties, X‐ray crystallographic analysis, and density functional theory (DFT) and time‐dependent DFT at M06‐2X/6‐31G(d,p) level were performed using 3,9‐dibenzo‐2,4,8,10‐tetraoxa‐3,9‐diboraspiro[5.5]undecane ( 1 ) as a model compound. Our interest in functionalizing the RTP‐active particles led us to graft Rhodamine B onto their surface. The resulting system emitted a dual afterglow via a Förster‐type resonance energy transfer process from the BP in the excited triplet state to Rhodamine B acting as an acceptor fluorophore. This emission behavior was used for ratiometric afterglow sensing of water content in THF with a detection limit of 0.28 %, indicating that this study could pave the way for a new strategy for developing color‐variable afterglow chemosensors for various analytes.     

A Pretreatment‐Free,Polymer‐Based Platform Prepared by Molecular Imprinting and Post‐Imprinting Modifications for Sensing Intact Exosomes

Exosomes are small (30–100 nm) membrane vesicles that serve as regulatory agents for intercellular communication in cancers. Currently, exosomes are detected by immuno‐based assays with appropriate pretreatments like ultracentrifugation and are time consuming (>12 h). We present a novel pretreatment‐free fluorescence‐based sensing platform for intact exosomes, wherein exchangeable antibodies and fluorescent reporter molecules were aligned inside exosome‐binding cavities. Such antibody‐containing fluorescent reporter‐grafted nanocavities were prepared on a substrate by well‐designed molecular imprinting and post‐imprinting modifications to introduce antibodies and fluorescent reporter molecules only inside the binding nanocavities, enabling sufficiently high sensitivity to detect intact exosomes without pretreatment. The effectiveness of the system was demonstrated by using it to discriminate between normal exosomes and those originating from prostate cancer and analyze exosomes in tear drops.     

A Pretreatment‐Free,Polymer‐Based Platform Prepared by Molecular Imprinting and Post‐Imprinting Modifications for Sensing Intact Exosomes

Exosomes are small (30–100 nm) membrane vesicles that serve as regulatory agents for intercellular communication in cancers. Currently, exosomes are detected by immuno‐based assays with appropriate pretreatments like ultracentrifugation and are time consuming (>12 h). We present a novel pretreatment‐free fluorescence‐based sensing platform for intact exosomes, wherein exchangeable antibodies and fluorescent reporter molecules were aligned inside exosome‐binding cavities. Such antibody‐containing fluorescent reporter‐grafted nanocavities were prepared on a substrate by well‐designed molecular imprinting and post‐imprinting modifications to introduce antibodies and fluorescent reporter molecules only inside the binding nanocavities, enabling sufficiently high sensitivity to detect intact exosomes without pretreatment. The effectiveness of the system was demonstrated by using it to discriminate between normal exosomes and those originating from prostate cancer and analyze exosomes in tear drops.     

Temperature‐Correlated Afterglow of a Semiconducting Polymer Nanococktail for Imaging‐Guided Photothermal Therapy

Nanoparticles for photothermal therapy: Real‐time temperature monitoring is critical to reduce the nonspecific damage during photothermal therapy (PTT); however, PTT agents that can emit temperature‐related signals are rare and limited to few inorganic nanoparticles. We herein synthesize a semiconducting polymer nanococktail (SPN_CT) that can not only convert photo‐energy to heat but also emit temperature‐correlated luminescence after cessation of light excitation. Such an afterglow luminescence of the SPN_CT detects tumors more sensitively than fluorescence as a result of the elimination of tissue autofluorescence, while its temperature‐dependent nature allows tumor temperature to be optically monitored under near‐infrared (NIR) laser irradiation. Thus, SPN_CT represents the first organic optical nanosystem that enables optical‐imaging guided PTT without real‐time light excitation.     

Aptamer‐based detection and quantitative analysis of human immunoglobulin E in capillary electrophoresis with chemiluminescence detection

A novel aptamer‐based CE with chemiluminescence (CL) assay was developed for highly sensitive detection of human immunoglobulin E (IgE). The IgE aptamer was conjugated with gold nanoparticles (AuNPs) to form AuNPs‐aptamer that could specifically recognize the IgE to produce an AuNPs‐aptamer‐IgE complex. The mixture of the AuNPs‐aptamer‐IgE complex and the unbounded AuNPs‐aptamer could be effectively separated by CE and sensitively detected with luminol‐H₂O₂ CL system. By taking the advantage of the excellent catalytic behavior of AuNPs on luminol‐H₂O₂ CL system, the ultrasensitive detection of IgE was achieved. The detection limit of IgE is 7.6 fM (S/N = 3) with a linear range from 0.025 to 250 pM. Successful detection of IgE in human serum samples was demonstrated and the recoveries of 94.9–103.2% were obtained. The excellent assay features of the developed approach are its specificity, sensitivity, adaptability, and very small sample consumption. Our design provides a methodology model for determination of rare proteins in biological samples.     

Bioinspired Engineering of a Multivalent Aptamer‐Functionalized Nanointerface to Enhance the Capture and Release of Circulating Tumor Cells

Circulating tumor cell (CTC)‐enrichment by using aptamers has a number of advantages, but the issue of compromised binding affinities and stabilities in real samples hinders its wide applications. Inspired by the high efficiency of the prey mechanism of the octopus, we engineered a deterministic lateral displacement (DLD)‐patterned microfluidic chip modified with multivalent aptamer‐functionalized nanospheres (AP‐Octopus‐Chip) to enhance capture efficiency. The multivalent aptamer–antigen binding efficiency improves 100‐fold and the capture efficiency is enhanced more than 300 % compared with a monovalent aptamer‐modified chip. Moreover, the captured cancer cells can be released through a thiol exchange reaction with up to 80 % efficiency and 96 % viability, which is fully compatible with downstream mutation detection and CTC culture. Using the chip, we were able to find CTCs in all cancer samples analyzed.     

Aptamers as Recognition Elements for Electrochemical Detection of Exosomes

Exosome analysis is emerging as an attractive noninvasive approach for disease diagnosis and treatment monitoring in the field of liquid biopsy. Aptamer is considered as a promising molecular probe for exosomes detection because of the high binding affinity, remarkable specificity, and low cost. Recently, many approaches have been developed to further improve the performance of electrochemical aptamer based(E-AB) sensors with a lower limit of detection. In this review, we focus on the development of using aptamer as a specific recognition element for exosomes detection in electrochemical sensors. We first introduce recent advances in evolving aptamers against exosomes. Then, we review methods of immobilization aptamers on electrode surfaces, followed by a summary of the main strategies of signal amplification. Finally, we present the insights of the challenges and future directions of E-AB sensors for exosomes analysis.     

Multianalyte Electrochemical Biosensor Based on Aptamer‐ and Nanoparticle‐Integrated Bio‐Barcode Amplification

In the present work, a signal‐on electrochemical sensing strategy for the simultaneous detection of adenosine and thrombin is developed based on switching structures of aptamers. An Au electrode as the sensing surface is modified with two kinds of thiolated capture probes complementary to the linker DNA that contains either an adenosine aptamer or thrombin aptamer. The capture probes hybridize with their corresponding linker DNA, which has prehybridized with the reporter DNA loaded onto the gold nanoparticles (AuNPs). The AuNP contained two kinds of bio‐barcode DNA: one is complementary to the linker DNA (reporter), whereas the other is not (signal) and is tagged with different metal sulfide nanoparticles. Thus a “sandwich‐type” sensing interface is fabricated for adenosine and thrombin. With the introduction of adenosine and thrombin, the aptamer parts bind with their targets and fold to form the complex structures. As a result, the bio‐barcoded AuNPs are released into solution. The metal sulfide nanoparticles are measured by anodic stripping voltammetry (ASV), and the concentrations of adenosine and thrombin are proportional to the signal of either metal ion. With the dual amplification of the bio‐barcoded AuNP and the preconcentration of metal ions through ASV technology, detection limits as low as 6.6×10^?12 M for adenosine and 1.0×10^?12 M for thrombin are achieved. The sensor exhibits excellent selectivity and detectability in biological samples.     

Label‐ and modification‐free‐based in situ selection of bovine serum albumin specific aptamer

Systematic evolution of ligands by exponential enrichment is a traditional approach to select aptamer, which has a great potential in biosensing field. However, chemical modifications of DNA library or targets before selection might block the real recognition and binding sites between aptamers and their targets. In this study, a label‐ and modification‐free‐based in situ selection strategy was developed to overcome this limitation. The strategy is an attempt to screen bovine serum albumin aptamers according to the principle of electrophoretic mobility shift assay, and allowed single‐stranded DNA sequence to be fully exposed to interact with bovine serum albumin which was mixed with the agarose gel beforehand. After eight rounds of selection, specific aptamer with low dissociation constant (K_d) value of 69.44 ± 7.60 nM was selected and used for subsequent establishment of fluorescence biosensor. After optimization, the optimal aptasensor exhibited a high sensitivity toward bovine serum albumin with a limit of detection of 0.24 ng/mL (linear range from 1 to 120 ng/mL). These results indicated that the label‐ and modification‐free‐based in situ selection strategy proposed in this work could effectively select specific aptamer to develop aptasensor for sensitive detection of bovine serum albumin or other targets in actual complicated samples.     

Studies on the Affinity‐based Biosensors for Electrochemical Detection of HER2 Cancer Biomarker

As cancer diseases are the second main cause of death it is necessary to elaborate fast and efficient early diagnosis methods for their detection. One of the possibilities is the analysis of protein biomarkers, which abnormal concentration in physiological fluids might be an indication of cancer disease progression. Herein, we present the studies on the development of affinity‐based biosensors for electrochemical detection of HER2 protein, which is a common biomarker of breast cancer. The main objective was to verify the possibility of fabrication of HER2‐specific hybrid aptamer‐polyclonal antibody and antibody‐based sandwich sensing layer on gold electrode surface. The effectiveness of each electrode modification step was confirmed using voltammetric and impedimetric techniques in the presence of ferri/ferrocyanide redox couple. It was observed that hybrid construct was unlikely to be formed on the gold electrode due to a higher affinity of secondary polyclonal antibody towards target protein, which resulted in the separation of HER2‐antibody complex from the electrode surface. On the contrary, an antibody‐based sandwich receptor layer allowed for protein discrimination in the range from 1 to 100 ng mL^?1 by the application of TMB/H₂O₂ system and chronoamperometry detection technique. Though, the occurrence of interactions between interfering proteins and antibody‐based layer was noted, it led to at least two times smaller current responses than for HER2 protein.     

Ultrasensitive and Signal‐on Electrochemiluminescence Aptasensor Using the Multi‐tris(bipyridine)ruthenium(II)‐β‐cyclodextrin Complexes

An ultrasensitive and signal‐on electrochemiluminescence (ECL) aptasensor to detect target protein (thrombin or lysozyme) was developed using the host‐guest recognition between a metallocyclodextrin complex and single‐stranded DNA (ss‐DNA). The aptasensor uses both the photoactive properties of the metallocyclodextrins named multi‐tris(bipyridine)ruthenium(II)‐β‐cyclodextrin complexes and their specific recognition with ss‐DNA, which amplified the ECL signal without luminophore labeling. After investigating the ECL performance of different multi‐tris(bipyridine)ruthenium(II)‐β‐cyclodextrin (multi‐Ru‐β‐CD) complexes, tris‐tris(bipyridine)‐ruthenium(II)‐β‐cyclodextrin (tris(bpyRu)‐β‐CD) was selected as a suitable host molecule to construct an atasensor. First, double‐stranded DNA (ds‐DNA) formed by hybridization of the aptamer and its target DNA was attached to a glassy carbon electrode via coupling interaction, which showed low ECL intensity with 2‐(dibutylamino) ethanol (DBAE) as coreactant, because of the weak recognition between ds‐DNA and tris(bpyRu)‐β‐CD. Upon addition of the corresponding protein, the ECL intensity increased when target ss‐DNA was released because of the higher stability of the aptamer‐protein complex than the aptamer‐DNA one. A linear relationship was observed in the range of 0.01 pmol/L to 100 pmol/L between ECL intensity and the logarithm of thrombin concentrations with a limited detection of 8.5 fmol/L (S/N=3). Meanwhile, the measured concentration of lysozyme was from 0.05 pmol/L to 500 pmol/L and the detection limit was 33 fmol/L (S/N=3). The investigations of proteins in human serum samples were also performed to demonstrate the validity of detection in real clinical samples. The simplicity, high sensitivity and specificity of this aptasensor show great promise for practical applications in protein monitoring and disease diagnosis.     

Multi‐Level Logic Gate Operation Based on Amplified Aptasensor Performance

Conventional electronic circuits can perform multi‐level logic operations; however, this capability is rarely realized by biological logic gates. In addition, the question of how to close the gap between biomolecular computation and silicon‐based electrical circuitry is still a key issue in the bioelectronics field. Here we explore a novel split aptamer‐based multi‐level logic gate built from INHIBIT and AND gates that performs a net XOR analysis, with electrochemical signal as output. Based on the aptamer–target interaction and a novel concept of electrochemical rectification, a relayed charge transfer occurs upon target binding between aptamer‐linked redox probes and solution‐phase probes, which amplifies the sensor signal and facilitates a straightforward and reliable diagnosis. This work reveals a new route for the design of bioelectronic logic circuits that can realize multi‐level logic operation, which has the potential to simplify an otherwise complex diagnosis to a “yes” or “no” decision.