Construction of a DNA-AuNP-based satellite network for exosome analysis

Exosomes as Powerful Biomarkers in Cancer: Recent Advances in Isolation and Detection Techniques

Exosomes, small extracellular vesicles derived from cells, are known to carry important bioactive molecules such as proteins, nucleic acids, and lipids. These bioactive components play crucial roles in cell signaling, immune response, and tumor metastasis, making exosomes potential diagnostic biomarkers for various diseases. However, current methods for detecting tumor exosomes face scientific challenges including low sensitivity, poor specificity, complicated procedures, and high costs. It is essential to surmount these obstacles to enhance the precision and dependability of diagnostics that rely on exosomes. Merging DNA signal amplification techniques with the signal boosting capabilities of nanomaterials presents an encouraging strategy to overcome these constraints and improve exosome detection. This article highlights the use of DNA signal amplification technology and nanomaterials' signal enhancement effect to improve the detection of exosomes. This review seeks to offer valuable perspectives for the enhancement of amplification methods applied in practical cancer diagnosis and prognosis by providing an overview of how these novel technologies are utilized in exosome-based diagnostic procedures.

A fuel-initiated DNA molecular machine for microRNA detection in serum via poly-adenine-mediated spherical nucleic acids

MicroRNAs (miRNAs) have been identified as promising disease diagnostic biomarkers. However, it is challenging to sensitively detect miRNAs, especially in complex biological environments, due to their low abundance and small size. Herein, we have developed a DNA-fueled molecular machine for sensitive detection of miRNA-22 (miR-22) in undiluted serum by combining poly-adenine-mediated spherical nucleic acids (polyA-SNAs) with a toehold mediated strand displacement reaction (TMSDR). The polyA-SNAs are constructed by the assembly of diblock DNA probes on a AuNP surface through the high binding affinity of polyA to AuNPs. The surface density of the diblock DNA probe can be controlled by tuning the length of the polyA block, and the orientation of the diblock DNA probe can adopt an upright conformation, which is beneficial to target hybridization and TMSDRs. TMSDR is an enzyme-free target recycling amplification approach. Taking advantage of polyA-mediated SNAs and TMSDR, the operation of the molecular machine based on two successive TMSDRs on polyA20-SNAs is rapid and efficient, which can significantly amplify the fluorescence response for detection of miR-22 in an undiluted complex matrix. The developed sensor can detect as low as 10 pM of target miRNA/DNA in undiluted fetal bovine serum within 30 min. The synergetic effect of polyA-mediated SNAs and TMSDR presents a potential alternative tool for the detection of biomarkers in real biological samples.

Improving aptamer performance: key factors and strategies

Aptamers are functional single-stranded oligonucleotide fragments isolated from randomized libraries by Systematic Evolution of Ligands by Exponential Enrichment (SELEX), exhibiting excellent affinity and specificity toward targets. Compared with traditional antibody reagents, aptamers display many desirable properties, such as low variation and high flexibility, and they are suitable for artificial and large-scale synthesis. These advantages make aptamers have a broad application potential ranging from biosensors, bioimaging to therapeutics and other areas of application. However, the overall performance of aptamer pre-selected by SELEX screening is far from being satisfactory. To improve aptamer performance and applicability, various post-SELEX optimization methods have been developed in the last decade. In this review, we first discuss the key factors that influence the performance or properties of aptamers, and then we summarize the key strategies of post-SELEX optimization which have been successfully used to improve aptamer performance, such as truncation, extension, mutagenesis and modification, splitting, and multivalent integration. This review shall provide a comprehensive summary and discussion of post-SELEX optimization methods developed in recent years. Moreover, by discussing the mechanism of each approach, we highlight the importance of choosing the proper method to perform post-SELEX optimization.

Functional DNA sensors integrated with nucleic acid signal amplification strategies for non-nucleic acid targets detection

In addition to carrying and transmitting genetic material, some DNA molecules have specific binding ability or catalytic function. DNA with this special function is collectively referred to as functional DNA (fDNA), such as aptamer, DNAzyme and so on. fDNA has the advantages of simple synthetic process, low cost and low toxicity. It also has high chemical stability, recognition specificity and biocompatibility. In recent years, fDNA biosensors have been widely investigated as signal recognition elements and signal transduction elements for the detection of non-nucleic acid targets. However, the main problem of fDNA sensors is their limited sensitivity to trace targets, especially when the affinity of fDNA to the targets is low. To further improve the sensitivity, various nucleic acid signal amplification strategies (NASAS) are explored to improve the limit of detection of fDNA. In this review, we will introduce four NASAS (hybridization chain reaction, entropy-driven catalysis, rolling circle amplification, CRISPR/Cas system) and the corresponding design principles. The principle and application of these fDNA sensors integrated with signal amplification strategies for detection of non-nucleic acid targets are summarized. Finally, the main challenges and application prospects of NASAS integrated fDNA biosensing system are discussed.

Nanomaterials for Molecular Detection and Analysis of Extracellular Vesicles

Extracellular vesicles (EVs) have emerged as a novel resource of biomarkers for cancer and certain other diseases. Probing EVs in body fluids has become of major interest in the past decade in the development of a new-generation liquid biopsy for cancer diagnosis and monitoring. However, sensitive and specific molecular detection and analysis are challenging, due to the small size of EVs, low amount of antigens on individual EVs, and the complex biofluid matrix. Nanomaterials have been widely used in the technological development of protein and nucleic acid-based EV detection and analysis, owing to the unique structure and functional properties of materials at the nanometer scale. In this review, we summarize various nanomaterial-based analytical technologies for molecular EV detection and analysis. We discuss these technologies based on the major types of nanomaterials, including plasmonic, fluorescent, magnetic, organic, carbon-based, and certain other nanostructures. For each type of nanomaterial, functional properties are briefly described, followed by the applications of the nanomaterials for EV biomarker detection, profiling, and analysis in terms of detection mechanisms.

Label-Free Analysis of Exosomes with Hairpin Structure-Mediated Multiple Signal Amplification Strategy

Considering the crucial role of exosomes in various biological processes and disease diagnosis, development of label-free and sensitive exosome detection methods is in urgent demand. Herein, we develop an exponential amplification-based method pining the hope on sensitive exosomes detection in a label-free manner. In this method, a designed SMB (Streptavidin magnetic bead)-capture probe is utilized to specially recognize CD63 protein on the surface of exosome. The recognition of CD63 protein by SMB-capture probe induces the subsequent hairpin structure probe-mediated multiple signal amplifications. Eventually, the proposed approach can detect exosomes at a concentration as low as 1.2 × 10² particles/μl and can be potentially applied for clinical practices.

Dumbbell structure probe-triggered rolling circle amplification (RCA)-based detection scaffold for sensitive and specific neonatal infection-related small extracellular vesicle (sEV) detection

Small extracellular vesicles (sEVs) have been reported to play important roles in cell-to-cell communication and are promising biomarkers for the early diagnosis of infections. Therefore, it is in high demand to develop a method that can integrate easy-to-operate sEV isolation and sensitive quantification. We herein propose a novel detection scaffold for sEV isolation via low-speed centrifugation and the quantification of sEVs through DNAzyme-based signal amplification. The detection scaffold is established through dumbbell probe-based RCA (rolling circle amplification), containing repeated CD63 aptamer sections and DNAzyme sections. The original state of the DNAzyme section is locked in a hairpin structure in the detection scaffold. In the presence of sEVs, the CD63 aptamer recognizes and binds with sEVs, leading to the aggregation of sEVs, which can be isolated by low-speed centrifugation and the exposure of the DNAzyme section. After the catalytic fluorescence signal generation from the DNAzyme-based molecular beacon (MB) cleavage, the method exhibited a detection range of 10² to 10⁶ particles per μL. Considering the high sensitivity and wash-free and easy-to-operate features, the strategy reported herein paves a new avenue for the effective determination of sEVs and other membrane biomolecules in fundamental and applied research.

Allosteric Probe Recognition Initiated Cascade Transcription Amplification for Sensitive Analysis of Exosomes

Sensitive and accurate analysis of exosome plays considerable roles in multifarious biological processes and being deemed to be important biomarkers for cerebral venous thrombosis (CVT) diagnosis and therapy. Herein, we established a sensitive and specific exosomes detection approach based on target recognition initiated cascade signal amplification. In this method, allosteric probe is designed with hairpin structure for specific recognition of exosome and inducing the following signal amplification. Eventually, generated spinach RNA sequences after the cascade signal amplification process bind to DFHBI ((Z)-4-(3,5-difluoro-4-hydroxybenzylidene)-1,2-dimethyl-1H-imidazol-5(4H)-one) to produce enhanced fluorescence signal (approximate 2000 fold than that of inactive DFHBI). Compared with former proposed exosomes detection methods, the method exhibited a comparable detection range, but with an easy-to-design toolbox. Therefore, we believe that the proposed approach holds great potential for exosome based early diagnosis and prognosis of disease.

Multivalent Aptamer Approach: Designs, Strategies, and Applications

Aptamers are short and single-stranded DNA or RNA molecules with highly programmable structures that give them the ability to interact specifically with a large variety of targets, including proteins, cells, and small molecules. Multivalent aptamers refer to molecular constructs that combine two or more identical or different types of aptamers. Multivalency increases the avidity of aptamers, a particularly advantageous feature that allows for significantly increased binding affinities in comparison with aptamer monomers. Another advantage of multivalency is increased aptamer stabilities that confer improved performances under physiological conditions for various applications in clinical settings. The current study aims to review the most recent developments in multivalent aptamer research. The review will first discuss structures of multivalent aptamers. This is followed by detailed discussions on design strategies of multivalent aptamer approaches. Finally, recent developments of the multivalent aptamer approach in biosensing and biomedical applications are highlighted.

Aptasensors for Cancerous Exosome Detection

Cancerous exosomes that carry multiple biomarkers are attractive targets for the early diagnosis and therapy of cancer. As one of the powerful molecular recognition tools, aptamers with excellent binding affinity and specificity toward biomarkers have been exploited to construct various aptamer-based biosensors (aptasensors) for exosome detection. Here, we review recent advances in aptasensors for the detection of cancerous exosomes. We first discuss the importance and potential of cancerous exosomes in cancer diagnosis and then summarize some conventional aptasensors from the perspective of biomarker recognition and signal collection strategies. Finally, we comment on the outlook for aptasensor research and new directions for cancerous exosome detection.

Rolling Circle Amplification as a Universal Method for the Analysis of a Wide Range of Biological Targets

Detection and quantification of biotargets are important analytical tasks, which are solved using a wide range of various methods. In recent years, methods based on the isothermal amplification of nucleic acids (NAs) have been extensively developed. Among them, a special place is occupied by rolling circle amplification (RCA), which is used not only for the detection of a specific NA but also for the analysis of other biomolecules, and is also a versatile platform for the development of highly sensitive methods and convenient diagnostic devices. The present review reveals a number of methodical aspects of RCA-mediated analysis; in particular, the data on its key molecular participants are presented, the methods for increasing the efficiency and productivity of RCA are described, and different variants of reporter systems are briefly characterized. Differences in the techniques of RCA-mediated analysis of biotargets of various types are shown. Some examples of using different RCA variants for the solution of specific diagnostic problems are given.

Recent advances in nanomaterial-based biosensors for the detection of exosomes

Exosomes are a type of extracellular vesicle actively secreted by almost all eukaryotic cells. They are ideal candidates for reliable next-generation biomarkers in the early diagnosis and therapeutic response evaluation of cancer. Thus, the quantification of exosomes is crucial in facilitating clinical research and application. Compared with traditional materials, nanomaterials have better optical, magnetic, electrical, and catalytic properties due to their small size, high specific surface area, and variable structure. The incorporation of nanomaterials into sensing systems is an attractive approach towards improving sensitivity and can provide improved sensor selectivity and stability. In this paper, we summarize the progress in nanomaterial-based exosome detection methods, including electrochemical biosensors, photoelectrochemical biosensors, colorimetric biosensors, fluorescence biosensors, chemiluminescence biosensors, electrochemiluminescence biosensors, surface plasmon resonance biosensors, and surface-enhanced Raman spectroscopy biosensors. Moreover, future research directions and challenges in exosome detection methods are discussed. We hope that this article will offer an overview of nanomaterial-based exosome detection techniques and open new avenues in disease research.Graphical abstract.

Recent advances of aptasensors for exosomes detection

Exosomes are nanoscale phospholipid bilayer membrane-enclosed vesicles released from cells with diameters of 30-150 nm. Their contents reflect significant information regarding the cancer microenvironment from their parent cells, which attracts increasing attention as potential biomarkers for noninvasive early diagnosis. Among their detection methods, aptasensor has been becoming an attractive star with its properties of affordability, easy to use, fast response, high sensitivity, remarkable specificity, and multiplexing capability. This review mainly summarizes the recent advances of single-stranded DNA (ssDNA) aptamer-based sensors for cancer and tumor-derived exosomes detection. Firstly, we present a brief overview of aptamers and exosomes. Then, we introduce the exosomal proteins used as potential biomarkers of various cancers, and their specific ssDNA aptamers used in aptasensors. We emphasize eight major types of aptasensors: fluorescent, electrochemical, colorimetric, luminescence, lateral flow strips, surface-enhanced Raman scattering, surface plasmon resonance, and giant magnetoresistance sensors, based on fabrication methods, bio-recognition mechanism, as well as detection evaluation. The future directions and challenges are finally proposed for aptamers and their more applications in exosomes research.

de la Fuente J, Moros M. Nanoparticle-based biosensors for detection of extracellular vesicles in liquid biopsies

Selecting the appropriate nanoparticle, functionalization chemistry and sensing methodology can speed up the translation of liquid biopsies into the clinic.

Probing exosome internalization pathways through confocal microscopy imaging

We developed a novel fluorescence labelling method to track exosome internalization pathways in cells by confocal microscopy. The proposed method allows evaluation and comparison of the uptake pathways of exosomes originating from different cells, which would offer the potential for understanding the functions of exosomes in intercellular communication and their applications in drug delivery.