A strategy for electrochemical biosensing based on dendritic HCR amplification for detection of RNA m5C and m6A methylation

Sensitive and efficient detection of RNA methylation sites is considered an integral part of epigenetic assessment. Contrary to previous studies on the detection of RNA m5C or m6A methylation alone, this study innovatively designed a biosensor capable of detecting RNA m5C or m6A methylation at the same time. Substances with specific electrochemical reactions such as ferrocene (FC) or methylene blue (MB) were modified onto the hairpin probe. When the hairpin probe was activated under specific conditions, it triggered a dendritic nonlinear hybridization chain reaction (HCR), which resulted in signal amplification. Gold (Au) and iron tetraoxide (Fe3O4) composite nanomaterials were employed as the linking materials: the carboxylated ends of Fe3O4 were connected to an antibody that specifically recognizes the m5C and m6A methylation sites, while Au nanoparticle ends adhering to the carboxylated Fe3O4 surface are connected to the HCR enhanced signal amplifier. The m5C antibody was linked to Fc-containing HCR amplification products by this material, and similarly, the m6A antibody was linked to MB-containing amplifiers. Thus, the dandelion complex, a multifunctional body with methyl recognition and signal amplification, was formed. The capture probe immobilized on the surface of the gold electrode by Au-S recognized the target RNA sequence by base complementary pairing. Upon addition of the dandelion complex, due to its multi-functionality, the amplified signals were carried to the electrode by the antigen-antibody recognition mechanism, generating a current signal. The positions and heights of the current signal peaks enabled rapid determination of target RNA methyl modification sites and their abundance. The detection limits of this biosensor for RNA m5C and m6A were 4.68 × 10-16 M and 1.10 × 10-15 M, respectively, and the linear range was from 10-15 mol/L to 10-8 mol/L. The sensor developed in this study has the advantages of cost-effectiveness, ease of fabrication, and fast response time, and has the potential to be promoted for RNA methylation detection.

Characterization of extracellular vesicles by capillary zone electrophoresis: A novel concept for characterization of a next-generation drug delivery platform

Extracellular vesicles (EVs) are a part of a cell-to-cell communication system of prokaryotic and eukaryotic organisms. Their ability to penetrate biological barriers and to transfer molecules between cells shows their potential as a novel class of drug delivery platform. However, because of the great heterogeneity of EVs and the complexity of biological matrices from which they are typically isolated, reliable quality control procedures need to be established to ensure their safety for medical use. According to current recommendations, quantification of EVs, confirmation of their identity, and purity assessment require the use of several analytical techniques, including particle-size distribution analysis, proteomics, and electron microscopy, making the characterization process demanding. Capillary electrophoresis (CE) has recently emerged as an alternative tool for EV characterization. In this study, the available literature on this novel concept for EV characterization was reviewed. Its performance was critically evaluated and compared with currently used methods. The utility of CE in the quality control of EV-based medicines was discussed.

Recent Advances in Wash-Free Detection Methods of Extracellular Vesicles: A Mini Review

Extracellular vesicles (EVs) are emerging biomarkers in liquid biopsy that have gained increasing attention in disease diagnosis and prognosis monitoring. Most reported detection methods require the isolation of EVs from complex body liquids, often involving multiple washing steps to remove excess reagents and eliminate background interference. Nonetheless, these methods not only cause the loss of EVs but also result in poor repeatability and prolonged detection duration. The focus on wash-free detection methods is increasing due to the specific ability to avoid the removal of surplus reagents and, in some cases, even the isolation and purification of EVs. Viewing from different methodological perspectives, this review summarizes the recent advances in wash-free detection of EVs, containing aggregation induction, proximity sensing, allosteric probes, phase separation, Roman spectroscopy, field-effect transistor and microcantilever. The pros and cons of each detection strategy are impartially evaluated and this review concludes the prospects for future developments in this field.

A new di-recognition and di-functional nanosurface aptamer molecularly imprinted polymer probe for trace glyphosate with SERS/RRS/Abs trimode technique

A new di-recognition nitrogen-doped carbon dot nanosurface aptamer molecularly imprinted polymer (CDNAg@MIPApt) nanocatalytic di-functional probe was prepared by microwave irradiation. The probe was utilized nitrogen-doped silver carbon dots (CDNAg) as the matrix, glyphosate (Gly) as the template molecule, α-methyl acrylate as the monomer, ethylene glycol dimethacrylate as the cross-linker, and aptamer as the biorecognition element. It could not only recognize Gly but also exhibits catalytic amplification function. It was found that CDNAg@MIPApt catalyzed the redox reaction of polyethylene glycol 400 (PEG400)-AgNO3 to generate silver nanoparticles (AgNPs). The AgNPs indicator component exhibit the effects of surface-enhanced Raman scattering (SERS), resonance Rayleigh scattering (RRS) and surface plasmon resonance absorption (Abs). In the presence of Gly, it binds to the surface imprinted site of CDNAg@MIPApt, to reduce AgNPs generation due to the catalytic activity of CDNAg@MIPApt decreasing. Thus, the SERS/RRS/Abs signal values decreased linearly. The linear ranges of SERS/RRS/Abs assay were 0.1-2.5 nM, 0.25-2.75 nM and 0.5-5 nM respectively. The detection limits were 0.034 nM, 0.071 nM and 0.18 nM Gly.

Cell Membrane-Anchored AND Logic Gate Aptasensor for Tumor Cell-Specific Imaging with Improved Accuracy

Accurate and rapid imaging of tumor cells is of vital importance for early cancer diagnosis and intervention. Aptamer-based fluorescence sensors have become a potent instrument for bioimaging, while false positives and on-target off-tumors linked to single-biomarker aptasensors compromise the specificity and sensitivity of cancer imaging. In this paper, we describe a sequential response aptasensor for precise cancer cell identification that is based on a DNA "AND" logic gate. Specifically, the sensor consists of three single-stranded DNA, including the P-strand that can sensitively respond to an acid environment, the L-strand containing the ATP aptamer sequence, and the R-strand for target cell anchoring. These DNA strands hybridize with one another to create a Y-shaped structure (named Y-ALGN). The aptamer in the R-strand is utilized to anchor the sensor to the target cell membrane primarily. Responding to the extracellular acidic environment of the tumor (input 1), the I-motif sequence forms a tetramer structure so that the P-strand is released from the Y-shaped structure and exposes the ATP binding sites in the L-strand. Extracellular ATP, as input 2, continuously operates the DNA aptasensor to complete the logic computation. Upon the sequential response of both protons and ATP molecules, the aptasensor is activated with restored fluorescence on a particular cancer cell membrane. Benefiting from the precise computation capacity of the "AND" logic gate, the Y-ALGN aptasensor can distinguish between MCF-7 cells and normal cells with high accuracy. As a simple and dual-stimuli-responsive strategy, this nanodevice would offer a fresh approach for accurately diagnosing tumor cells.

Target-induced DNA nanomachine operation for the detection of proteins

Accurate and sensitive detection of disease-associated proteins in early stage of patients plays an important role in timely treatment and successfully extending patients' lives. To meet this demand, we herein rationally designed a flexible target-induced DNA nanomachine operation (TIDNMO) sensor for the detection of proteins. The TIDNMO system was composed of DNA nanoswitch and DNA walker. Triplex DNA nanoswitch was triggered by specific target, followed by the release of the walking strand, which initiated the DNA walker amplification as signal output. In addition, the Exo III could drive walking strand autonomously move on gold nanoparticle surface to realize 2 orders of magnitude signal amplification. What's more, this sensor could transform its suitable functional recognition element of DNA nanoswitch to recognize other specific molecule and realize different targets sensing based on identical walking tracks. Considering the facile reporter elements and efficient amplification performance, the present DNA nanomachine as a sensor could achieve a detection limit of 68 pM for anti-Dig antibody, 0.95 pM for mucin-1 respectively, along with a superb specificity. Furthermore, the method reported here opened a new chapter in disease-related protein sensing for the development of clinical early diagnosis.

Ratiometric fluorometric assay triggered by alkaline phosphatase: Proof-of-concept toward a split-type biosensing strategy for DNA detection

Herein, a sensitive ratiometric and split-type fluorescent sensing platform has been constructed for DNA detection based on one signal precursor and two fluorescent signal indicators. In this assay, o-phenylenediamine (OPD) was selected as the signal precursor. On one hand, Cu2+ can oxidize OPD to produce 2, 3-diaminophenazine (DAP), which with an emission peak at 555 nm. On the other hand, ascorbic acid (AA) could react with Cu2+ to generate dehydroascorbic acid (DHAA), which could further react with OPD to form 3-(1, 2-dihydroxy ethyl)furo[3, 4-b]quinoxalin-1 (3H)-on (DFQ) with a strong emission peak at 420 nm. As a result, the formation of DAP was inhibited, and leading to the decrease of fluorescence intensity at 555 nm. Alkaline phosphatase (ALP) could catalyze the substrate l-ascorbic acid-2-phosphate (AA2P) to produce AA in situ. Inspired by the successful use of ALP as a biocatalytic marker in bioassay, a split-type ratiometric fluorescent assay has been designed for DNA detection by using H1N1 DNA as the target model. It was realized for ratiometric fluorescent determination of H1N1 in a linear ranging from 50 pM to 1.5 nM with a limit of detection of 10 pM. The novel strategy could reduce the mutual interferences between the biomolecular recognition system and the fluorescence signal conversion system, which improving the accuracy of detection and effectively reducing the background signal. Furthermore, the strategy provided a promising platform for biomarkers detection in the fields of ratiometric fluorescent biosensors and bioanalysis.

Self-Assembled DNA Machine and Selective Complexation Recognition Enable Rapid Homogeneous Portable Quantification of Lung Cancer CTCs

In this study, we systematically investigated the interactions between Cu2+ and various biomolecules, including double-stranded DNA, Y-shaped DNA nanospheres, the double strand of the hybridization chain reaction (HCR), the network structure of cross-linked HCR (cHCR), and small molecules (PPi and His), using Cu2+ as an illustrative example. Our research demonstrated that the coordination between Cu2+ and these biomolecules not only is suitable for modulating luminescent material signals through complexation reactions with Cu2+ but also enhances signal intensities in materials based on chemical reactions by increasing spatial site resistance and local concentration. Building upon these findings, we harnessed the potential for signal amplification in self-assembled DNA nanospheres and the selective complexation modulation of calcein in conjunction with the aptamer targeting mucin 1 as a recognition probe. We applied this approach to the analysis of circulating tumor cells, with the lung cancer cell line A549 serving as a representative model. Our assay, utilizing both a fluorometer and a handheld detector, achieved impressive detection limits of ag/ml and single-cell levels for mucin 1 and A549 cells, and this approach was successfully validated using 46 clinical samples, yielding 100% specificity and 86.5% sensitivity. Consequently, our strategy has paved the way for more portable and precise disease diagnosis.

DNA Logical Device Combining an Entropy-Driven Catalytic Amplification Strategy for the Simultaneous Detection of Exosomal Multiplex miRNAs In Situ

Exosomal miRNAs are considered promising biomarkers for cancer diagnosis, but their accuracy is severely compromised by the low content of miRNAs and the large amount of exosomal miRNAs released from normal cells. Here, we presented a dual-specific miRNA's logical recognition triggered by an entropy-driven catalysis (EDC)-enhanced system in exosomes for accurate detection of liver cancer-cell-derived exosomal miR-21 and miR-122. Taking advantage of the accurate analytical performance of the logic device, the excellent membrane penetration of gold nanoparticles, and the outstanding amplification ability of the EDC reaction, this method exhibits high sensitivity and selectivity for the detection of tumor-derived exosomal miRNAs in situ. Moreover, due to its excellent performance, this logic device can effectively distinguish liver cancer patients from healthy donors by determining the amount of cancer-cell-derived exosomal miRNAs. Overall, this strategy has great potential for analyzing various types of exosomes and provides a viable tool to improve the accuracy of cancer diagnosis.

Split aptamer-based sandwich-type ratiometric biosensor for dual-modal photoelectrochemical and electrochemical detection of 17β-estradiol

BACKGROUND

As one of the most potent environmental estrogens, 17β-estradiol (E2), which can be enriched into organisms through the food chain and cause harmful biological effects in humans, has been frequently detected in the water environment of the world. High performance liquid chromatography (HPLC) and gas chromatograohy-mass spectrometry (GC/MS) have been widely used for quantification of E2. Despite excellent accuracy, tedious pretreatment and expensive instruments result in their limited application. It is clear that there is an urgent need to establish simple, sensitive and accurate methods for the determination of E2.

RESULTS

A split aptamer-based sandwich-type ratiometric biosensor based on split aptamer was developed by coupling photoelectrochemical and electrochemical assays for E2 detection. For analysis, the two fragments of split aptamer recognized E2 by forming sandwich structure, which triggered hybridization chain reaction (HCR) to produce double-stranded DNA (dsDNA) with CdTe quantum dots (QDs) labeled hairpin DNA. The resultant dsDNA can further absorb methylene blue (MB) to sensitize CdTe QDs for an enlarged photocurrent (IPEC) and output a redox current of IMB, and both of them acted as response signals for detection; [Fe(CN)6]3-/4- probe produced redox current of I[Fe(CN)6]3-/4- as reference signal. Using IMB/I[Fe(CN)6]3-/4- and IPEC/I[Fe(CN)6]3-/4- as yardsticks, the developed split aptamer-based sandwich-type ratiometric biosensor provides two linear ranges of 0.1-5000 pg mL-1 for IMB/I[Fe(CN)6]3-/4- and 0.1-10000 pg mL-1 for IPEC/I[Fe(CN)6]3-/4- with detection limits of 0.06 pg mL-1 and 0.02 pg mL-1, respectively.

SIGNIFICANCE

These results of the biosensor are benefiting from the coupling of photoelectrochemical (PEC) and electrochemical (EC) assays as well as the unique cooperative recognition mechanism of split aptamer. This method not only enabled the biosensor to be successfully applied to the determination of E2 in lake water, but also broadens the prospects for the realization of sensitive and accurate detection of E2.

The Amplified DNA Logic Gates Based on Aptamer-Receptor Recognition for Cell Detection and Bioimaging

A powerful and accurate method for identifying and isolating cells would be of great importance due to its sensitivity, gentleness and effectiveness. Here, we designed a receptor-based DNA logic device that allows Boolean logic analysis of multiple cells. For ease of expression, the molecules on the cell surface that can bind to the aptamer are referred to as "receptors". This DNA logic device sends signals based on cell surface sgc8c and sgc4f receptor expression by performing NOT, NOR, AND and OR logic operations, and amplifies and evaluates the signals using HCR. Meanwhile, the release of ICG from the endopore of HMSNs is controlled by affecting structural changes in the DNA logic device. This approach can accurately identify and treat multiple cells on demand based on the presence or absence of cell-specific receptors, facilitating the development of personalized medicine.

Designing Multimodal Informative Sensing with an Exosome-Mediated Signal Coupling Transduction Strategy Based on a Single-Stimulus Multiresponse Recognition Interface

Given that exosomes released from cancer cells carry various tumor-specific proteins on their surface, they have emerged as a source of biomarkers for cancer diagnosis. However, developing accurate and reliable assays to detect exosomes in the early stages of disease with low abundance and complex systems remains challenging. Here, the prepared PDIG film has the ability to sense multiple signals from a single stimulus, in which the presence of cobalt(II) chloride and deep eutectic solvents (DES) endows PDIG with thermochromic and thermosensitive properties. Concretely, the PDIG served as the recognition interface in series with a bipolar electrode (BPE) that exhibits a highly sensitive color and conductivity response to temperature stimuli triggered by the light-harvesting probe TiO2@CNOs introduced via proximity hybridization assay triggering a rolling circle amplification strategy, resulting in the output of colorimetric, photoacoustic, and electrochemiluminescent signals for the detection of colorectal cancer exosomes. This work is expected to provide a new direction for exploring the multisignal amplification strategy of BPE, broaden the application of BPE in biological analysis, and provide new insights for developing highly information-sensing elements to ensure the multimodal coupling for cancer-specific exosome detection.

"One suction and one extrusion" mode-based wash-free platform for determination of breast cancer cell-derived exosomes

A simple and wash-free POCT platform based on microcapillary was developed, using breast cancer cell-derived exosomes as a model. This method adopted the "one suction and one extrusion" mode. The hybridized complex of epithelial cell adhesion molecule (EpCAM) aptamer and complementary DNA-horseradish peroxidase conjugate (CDNA-HRP) was pre-modified on the microcapillary's inner surface. "One suction" meant inhaling the sample into the functionalized microcapillary. The exosomes could specifically bind with the EpCAM aptamer on the microcapillary's inner wall, and then the CDNA-HRP complex was released. "One extrusion" referred to squeezing the shedding CDNA-HRP into the 3,3',5,5'-tetramethylbenzidine (TMB)/H₂O₂ solution, and then the enzyme-catalyzed reaction would occur to make the solution yellow using sulfuric acid as the terminator. Therefore, exosome detection could be realized. The limit of detection was 2.69 × 10⁴ particles mL^-1 and the signal value had excellent linearity in the concentration range from 2.75 × 10⁴ to 2.75 × 10⁸ particles⋅mL^-1 exosomes. In addition, the wash-free POCT platform also displayed a favorable reproducibility (RSD = 2.9%) in exosome detection. This method could effectively differentiate breast cancer patients from healthy donors. This work provided an easy-to-operate method for detecting cancer-derived exosomes without complex cleaning steps, which is expected to be applied to breast cancer screening.

A non-invasive wearable stress patch for real-time cortisol monitoring using a pseudoknot-assisted aptamer

Stress is part of everyone's life and is exacerbated by traumatic events such as pandemics, disasters, violence, lifestyle changes, and health disorders. Chronic stress has many detrimental health effects and can even be life-threatening. Long-term stress monitoring outside of a hospital is often accomplished by measuring heart rate variability. While easy to measure, this digital biomarker has low specificity, greatly limiting its utility. To address this shortcoming, we report a non-invasive, wearable biomolecular sensor to monitor cortisol levels in sweat. Cortisol is a neuroendocrine hormone that regulates homeostasis as part of the stress pathway. Cortisol is detected using an electrochemical sensor functionalized with a pseudoknot-assisted aptamer and a flexible microfluidic sweat sampling system. The skin-worn microfluidic sampler provides rapid sweat collection while separating old and new sweat. The conformation-switching aptamer provides high specificity towards cortisol while being regenerable, allowing it to monitor temporal changes continuously. The aptamer was engineered to add a pseudoknot, restricting it to only two states, thus minimizing the background signal and enabling high sensitivity. An electrochemical pH sensor allows pH-corrected amperometric measurements. Device operation was demonstrated invitro with a broad linear dynamic range (1 pM - 1 μM) covering the physiological range and a sub-picomolar (0.2 pM) limit of detection in sweat. Real-time, on-body measurements were collected from human subjects using an induced stress protocol, demonstrating in-situ signal regeneration and the ability to detect dynamic cortisol fluctuations continuously for up to 90 min. The reported device has the potential to improve prognosis and enable personalized treatments.

β-Cyclodextrin Polymer-Based Fluorescence Enhancement Strategy via Host-Guest Interaction for Sensitive Assay of SARS-CoV-2

Nucleocapsid protein (N protein) is an appropriate target for early determination of viral antigen-based severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). We have found that β-cyclodextrin polymer (β-CDP) has shown a significant fluorescence enhancement effect for fluorophore pyrene via host-guest interaction. Herein, we developed a sensitive and selective N protein-sensing method that combined the host-guest interaction fluorescence enhancement strategy with high recognition of aptamer. The DNA aptamer of N protein modified with pyrene at its 3' terminal was designed as the sensing probe. The added exonuclease I (Exo I) could digest the probe, and the obtained free pyrene as a guest could easily enter into the hydrophobic cavity of host β-CDP, thus inducing outstanding luminescent enhancement. While in the presence of N protein, the probe could combine with it to form a complex owing to the high affinity between the aptamer and the target, which prevented the digestion of Exo I. The steric hindrance of the complex prevented pyrene from entering the cavity of β-CDP, resulting in a tiny fluorescence change. N protein has been selectively analyzed with a low detection limit (11.27 nM) through the detection of the fluorescence intensity. Moreover, the sensing of spiked N protein from human serum and throat swabs samples of three volunteers has been achieved. These results indicated that our proposed method has broad application prospects for early diagnosis of coronavirus disease 2019.

Self-Assembly and Disassembly of Membrane Curvature-Sensing Peptide-Based Deep-Red Fluorescent Probe for Highly Sensitive Sensing of Exosomes

With increasing knowledge of the diverse roles of exosomes in biological processes, much attention has been paid to the development of analytical methods for exosome analysis. Here, we developed a new class of amphipathic helical (AH) peptide-based fluorescent probes for highly sensitive detection of exosomes in a mix and read manner. Membrane curvature-sensing AH peptide (ApoC) was coupled with lipophilic tail (C12)-carrying thiazole red (TR) for construction of a self-assembly/disassembly based fluorescence "off-on" sensing system for target exosomes. ApoC-TR_C12 has extremely weak emission due to the formation of the aggregates, whereas it becomes emissive in response to the target exosomes through the binding-induced disassembly of ApoC-TR_C12. We demonstrated that the C12 unit attached to the TR unit had a favorable effect on both fluorescence response (signal-to-background: S/B) and binding affinity. ApoC-TR_C12 was applicable to rapid and simple detection of exosomes with high detection sensitivity (limit of detection ≈ 10³ particles/μL).

Sensitive electrochemical detection of A549 exosomes based on DNA/ferrocene-modified single-walled carbon nanotube complex

Exosome is an emerging tumor marker, whose concentration level can reflect the occurrence and development of tumors. The development of rapid and sensitive exosome detection platform is of great significance for early warning of cancer occurrence. Here, a strategy for electrochemical detection of A549-cell-derived exosomes was established based on DNA/ferrocene-modified single-walled carbon nanotube complex (DNA/SWCNT-Fc). DNA/SWCNT-Fc complexes function as a signal amplification platform to promote electron transfer between electrochemical signal molecules and electrodes, thereby improving sensitivity. At the same time, the exosomes can be attached to DNA/SWCNT-Fc nanocomposites via the established PO₄^3--Ti⁴⁺-PO₄^3- method. Moreover, the application of EGFR antibody, which can specifically capture A549 exosomes, could improve the accuracy of this sensing system. Under optimal experimental conditions, the biosensor showed good linear relationship between the peak current and the logarithm of exosomes concentration from 4.66 × 10⁶ to 9.32 × 10⁹ exosomes/mL with a detection limit of 9.38 × 10⁴ exosomes/mL. Furthermore, this strategy provides high selectivity for exosomes of different cancer cells, which can be applied to the detection of exosomes in serum samples. Thus, owing to its advantages of high sensitivity and good selectivity, this method provides a diversified platform for exosomes identification and has great potential in early diagnosis and biomedical applications.

A Self-Serviced-Track 3D DNA Walker for Ultrasensitive Detection of Tumor Exosomes by Glycoprotein Profiling

Sensitive and accurate analysis of low-concentration of tumor-derived exosomes (Exos) in biofluids is essential for noninvasive cancer diagnosis but is still challenging due to the lack of high-sensitive methods with low-cost and easy-operation. Herein, exploiting target Exos as a three-dimensional (3D) track for the first time, we developed a self-serviced-track DNA walker (STDW) for wash-free detection of tumor Exos using exosomal glycoprotein, which was enabled by split aptamer-recognition-initiated autonomous running powered by a catalytic hairpin assembly (CHA). Benefiting from high selectivity and sensitivity of the STDW assay, direct detection of tumor Exos in cell culture medium and serum could also be realized. Furthermore, this method exhibited high accuracy in clinical sample analysis, offering the potential for early cancer diagnosis and postoperative response prediction.

Recent advances in the selection of cancer-specific aptamers for the development of biosensors

An early diagnosis has the potential to greatly decrease cancer mortality. For that purpose, specific cancer biomarkers have been molecularly targeted by aptamer sequences to enable an accurate and rapid detection. Aptamer-based biosensors for cancer diagnostics are a promising alternative to those using antibodies, due to their high affinity and specificity to the target molecules and advantageous production. Synthetic nucleic acid aptamers are generated by in vitro Systematic Evolution of Ligands by Exponential enrichment (SELEX) methodologies that have been improved over the years to enhance the efficacy and to shorten the selection process. Aptamers have been successfully applied in electrochemical, optical, photoelectrochemical and piezoelectrical-based detection strategies. These aptasensors comprise a sensitive, accurate and inexpensive option for cancer detection being used as point-of-care devices. This review highlights the recent advances in cancer biomarkers, achievements and optimizations made in aptamer selection, as well as the different aptasensors developed for the detection of several cancer biomarkers.

Nucleic Acid Substrate-Independent DNA Polymerization on the Exosome Membrane: A Mechanism Study and Application in Exosome Analysis

As generally acknowledged, terminal deoxynucleotidyl transferase (TdT) can only elongate DNA substrates from their 3'-OH ends. Herein, for the first time, we report that TdT-catalyzed DNA polymerization can directly proceed on the exosome membrane without the mediation of any nucleic acids. We prove that both the glycosyl and phenolic hydroxyl groups on the membrane proteins can initiate the DNA polymerization. Accordingly, we have developed powerful strategies for high-sensitive exosome profiling based on a conventional flow cytometer and an emerging CRISPR/Cas system. By using our strategy, the featured membrane protein distributions of different cancer cell-derived exosomes can be figured out, which can clearly distinguish plasma samples of breast cancer patients from those of healthy people. This work paves new ways for exosome profiling and liquid biopsy and expands the understanding of TdT, holding great significance in developing TdT-based sensing systems as well as establishing protein/nucleic acid hybrid biomaterials.

Spatial Confinement-Derived Double-Accelerated DNA Cascade Reaction for Ultrafast and Highly Sensitive In Situ Monitoring of Exosomal miRNA and Exosome Tracing

Exosomal microRNAs (miRNAs) are reliable biomarkers of disease progression, allowing for non-invasive detection. However, detection of exosomal miRNAs in situ remains a challenge due to low abundance, poor permeability of the lipid bilayers, and slow kinetics of previous methods. Herein, an accelerated DNA nanoprobe was implemented for fast, in situ monitoring of miRNA in exosomes by employing a spatial confinement strategy. This nanoprobe not only detects miRNA in exosomes but also distinguishes tumor exosomes from those derived from normal cells with high accuracy, paving the way toward exosomal miRNA bioimaging and disease diagnosis. Furthermore, the fast response allows for this nanoprobe to be successfully utilized to monitor the process of exosomes endocytosis, making it also a tool to explore exosome biological functions.

A label-free and signal-amplifiable assay method for colorimetric detection of carcinoembryonic antigen

In this work, an innovative colorimetric assay method for the determination of carcinoembryonic antigen is developed with aptamer probes utilized as recognition element. DNA hybridization chain reaction is used as signal amplification technique, and peroxidase-mimicking hemin/G-quadruplex-assisted catalytic oxidation of 2,2'-azino-bis-3-ethylbenzothiazoline-6-sulfonic acid (ABTS) is deployed as signal reporting mechanism. The detection principle was firstly verified by using gel electrophoresis analysis and absorbance measurements. After condition optimization, a detection limit was theoretically determined as 24.8 ng/ml. Furthermore, the method exhibited good selectivity and satisfactory recovery rates (92.2%-108.6%) in serum samples. Moreover, the sensing scheme is easily extended for the detection of other analytes via similar target-aptamer recognition principle. To sum up, this is an enzyme- and label-free, cost-effective yet signal-amplifiable assay scheme for the determination of tumor markers with promising simplicity and selectivity, practical utility, and potential universality.

Programmable DNAzyme Computing for Specific In Vivo Imaging: Intracellular Stimulus-Unlocked Target Sensing and Signal Amplification

Molecular probe that enables in vivo imaging is the cornerstone of accurate disease diagnosis, prognostic estimation, and therapies. Although several nucleic acid-based probes have been reported for tumor detection, it is still a challenge to develop programmable methodology for accurately identifying tumors in vivo. Herein, a reconfigurable DNA hybridization-based reaction was constructed to assemble DNAzyme computing that contains an intracellular miRNA-unlocked entropy-driven catalysis module and an endogenous metal ion-responsive DNAzyme module for specific in vivo imaging. By reasonable design, the programmable DNAzyme computing can not only successfully distinguish tumor cells from normal cells but also enable tumor imaging in living mice. Due to its excellent operation with high specificity and sensitivity, this design may be broadly applied in the biological study and personalized medicine.

ICP-MS and Photothermal Dual-Readout Assay for Ultrasensitive and Point-of-Care Detection of Pancreatic Cancer Exosomes

Pancreatic cancer is known to have a high mortality rate, and its early diagnosis remains challenging due to the occult location of the pancreas. Exosomes derived from pancreatic cancer cells specifically express glypican-1, which may provide a liquid biopsy opportunity for the early diagnosis of pancreatic cancer. Herein, an inductively coupled plasma mass spectrometry (ICP-MS) and photothermal dual-readout platform was proposed for the ultrasensitive and point-of-care analysis of pancreatic cancer exosomes. In our design, exosomes were specifically captured by the sandwich immunoassay, and simultaneously, alkaline phosphatase was introduced in a low-background manner. The alkaline phosphatase triggered the hydrolysis of l-ascorbic acid 2-phosphate to produce ascorbic acid, followed by the etching of Fe₃O₄@MnO₂ nanoflowers. As a result, the Mn²⁺ generated by etching stripped off the Fe₃O₄ and was quantified using ICP-MS. Meanwhile, the reduced Fe₃O₄@MnO₂ was applied for the photothermal assay by oxidizing dopamine with MnO₂. The protocol exhibits a detection limit down to 19.1 particles mL^-1, which is the most sensitive protocol reported so far. To our knowledge, this is the first endeavor for exosome quantification using ICP-MS and photothermal methods. The developed dual-readout platform not only is capable of distinguishing pancreatic cancer patients from healthy people, but also shows excellent discernibility of individual differences at low concentrations of exosomes. This dual-readout assay is a promising platform for the ultrasensitive and point-of-care detection of exosomes in liquid biopsy-based early cancer diagnosis.

Designed Co-DNA-Locker and Ratiometric SERS Sensing for Accurate Detection of Exosomes Based on Gold Nanorod Arrays

Exosomes, which can transfer and deliver information about the original cell, are considered to be ideal candidates for early cancer diagnosis and evaluation of therapeutic efficacy due to their high abundance and stability. However, the highly expressed proteins on the surface of exosomes are usually associated with a variety of cancers; it is difficult to distinguish them by a single marker. Herein, a controlled self-assembly of gold nanorod (AuNR) arrays was prepared to construct a surface-enhanced Raman spectroscopy (SERS) sensor for the specific detection of exosomes secreted by SK-Br-3 cells based on a designed colocalization-dependent system (Co-DNA-Locker) and ratiometric strategy. After the exosomes are captured in the sensing array by the EpCAM aptamer modified on the surface of AuNRs, the DNA logic process occurs because the other two proteins, CD63 and HER2, are expressed simultaneously on the surface of exosomes secreted by SK-Br-3 cells, and the SERS signal intensity of the Rhodamine 6G (R6G) tagged on the terminal of DNA T_E increased with an increase in the concentration of the exosomes, while the SERS signal intensity of Cy5 linked on the terminal of the EpCAM aptamer, which acts as an internal standard, remains stable. The AuNRs are uniformly arranged in a hexagonal shape, and the dense "hot spots" produce "hot surfaces," which greatly improve the sensitivity and uniformity of detection. In the presence of target exosomes, the DNA colocalization three-signal input switch and the ratiometric strategy realize the specific and accurate detection of exosomes. This sensing strategy achieves a wide detection range (1.0 × 10⁴-5.0 × 10⁶ particles/mL) and a lower detection limit (5.3 × 10³ particles/mL), without using any signal amplification mechanism, demonstrating promising applications in health care monitoring and clinical diagnostics.

The mechanism and improvements to the isothermal amplification of nucleic acids, at a glance

A comparative review of the most common isothermal methods is provided. In the last two decades, the challenge of using isothermal amplification systems as an alternate to the most extensive and long-standing nucleic acids-amplifying method-the polymerase chain reaction-has arisen. The main advantage of isothermal amplification is no requirement for expensive laboratory equipment for thermal cycling. Considerable efforts have been made to improve the current techniques of nucleic acid amplification and the development of new approaches based on the main drawbacks of each method. The most important and challenging goal was to achieve a low-cost, straightforward system that is rapid, specific, accurate, and sensitive.

Precise Capture and Direct Quantification of Tumor Exosomes via a Highly Efficient Dual-Aptamer Recognition-Assisted Ratiometric Immobilization-Free Electrochemical Strategy

Tumor exosomes are promising biomarkers for early cancer diagnosis in a noninvasive manner. However, precise capture and direct analysis of tumor-specific exosomes in complex biological samples are still challenging. Herein, we present a highly efficient dual-aptamer recognition system for precisely isolating and quantifying tumor exosomes from the complex biological environment based on hyperbranched DNA superstructure-facilitated signal amplification and ratiometric dual-signal strategies. When tumor exosomes were captured by the dual-aptamer recognition system, the cholesterol-modified DNA probe was anchored on the surface of the exosomes, activating DNA tetrahedron-based hyperbranched hybridization chain reaction to generate a sandwich complex. Then, the sandwich complex could bind a large number of Ru(NH₃)₆³⁺ (Ru(III)), leading to a small amount of unbound Ru(III) left in the supernatant after magnetic separation. Hence, the redox reaction between Ru(II) and [Fe(CN)₆]^3- (Fe(III)) was significantly prevented, causing an obviously enhanced I_Fe(III)/I_Ru(III) value. Consequently, highly sensitive detection of tumor exosomes was achieved. The developed approach successfully realized direct isolation and analysis of tumor exosomes in complex sample media and human serum samples as well. More significantly, this ratiometric dual-signal mode and immobilization-free strategy effectively circumvented the systematic errors caused by external factors and the tedious probe immobilization processes, thus displaying the excellent performances of high reliability, improved accuracy, and easy manipulation. Overall, this approach is expected to offer novel ways for nondestructive early cancer diagnosis.