Target-Triggered Catalytic Hairpin Assembly-Induced Core–Satellite Nanostructures for High-Sensitive “Off-to-On” SERS Detection of Intracellular MicroRNA

Catalytic Hairpin Self-Assembly-Based SERS Sensor Array for the Simultaneous Measurement of Multiple Cancer-Associated miRNAs

The abnormal expression of some miRNAs is often closely related to the development of tumors. Available detection methods or biosensors that can simultaneously quantify multiple miRNAs in a single sample have rarely been reported. Herein, a novel catalytic hairpin self-assembly (CHA)-based surface-enhanced Raman scattering (SERS) sensor array was developed to simultaneously measure multiple miRNAs associated with cancer in one sample. The sensor array with four different sensing units was constructed by immobilizing one of four different hairpin-structured DNA sequence 1 (hp1) onto one of four Au/Ag alloy nanoparticle (AuAgNP)-coated detection wells. When target miRNA is present, the SERS tags, which were prepared by modifying AuAgNPs with a Raman reporter molecule of 4-mercaptobenzonitrile (MPBN) and the related hairpin-structured DNA sequence 2 (hp2), were captured onto the corresponding sensor unit through a repeated specific CHA reaction. This generated many "hot spots" because of interactions between the SERS tags and the AuAgNP layer-coated surface of the sensor, which ultimately produced a strong SERS signal that allowed the detection of target miRNAs with the detection limit of 0.15 pM. Using this SERS sensor array, multiple cancer-associated miRNAs (miR-1246, miR-221, miR-133a, and miR-21) were successfully determined in buffer, serum, and cellular RNA extracts.

High-Fidelity Determination and Tracing of Small Extracellular Vesicle Cargoes

Direct tracing of small extracellular vesicle (sEV) cargoes holds unprecedented importance for elucidating the mechanisms involved in intercellular communication. However, high-fidelity determination of sEVs' molecular cargoes in situ has yet to be achieved due to the difficulty in transporting molecular probes into intact sEVs. Herein, a fLuorescent Intracellular-Guided Hairpin-Tetrahedron (fLIGHT) nanoprobe is described for direct visualization of sEV microRNAs in situ. Integrating the advantages of nondestructive sEV penetration via DNA origami and single-nucleotide discrimination as well as wash-free fluorescence readout using a hairpin probe, the proposed approach enables high-fidelity fluorescence visualization of sEVs' microRNA without RNA extraction or leakage, demonstrating the potential of on-site tracing of sEV cargoes. This strategy opens an avenue to establishing universal molecular detection and labeling platforms that can facilitate both sEV-derived fundamental biological studies and molecular diagnostics.

Droplet array for open-channel high-throughput SERS biosensing

Open-channel and high throughput are two important aspects of clinical diagnosis, correlation biochemical analysis, cell culture techniques and food safety. Here, we propose the mini-pillar based array for open-channel and high-throughput SERS detection of miRNA. The polydimethylsiloxane (PDMS) mini-pillars are used as a high-throughput platform, which have good anchoring and aggregation effects on microdroplets, greatly reducing the amount of analytical solution and facilitate the homogeneous sample distribution after evaporation. The deposited gold nanorods (Au NRs) on the pillars with optimized diameter served as SERS-active substrate, can greatly improve the sensitivity of SERS signal compared to other planar substrates. On the open-channel biological chip, sensitive, simultaneous, and specific detection of breast cancer marker miRNA-1246 can be performed. In this mini-pillar array SERS system, the limit of detection (LOD) is 10^-12 M. The mini-pillar array shows enormous potential for open channel, high-throughput biomolecular detection, providing an opportunity for biomedical point-of-care testing (POCT) and drug screening.

DNA-Based Plasmonic Heterogeneous Nanostructures: Building, Optical Responses, and Bioapplications

The integration of multiple functional nanoparticles into a specific architecture allows the precise manipulation of light for coherent electron oscillations. Plasmonic metals-based heterogeneous nanostructures are fabricated by using DNA as templates. This comprehensive review provides an overview of the controllable synthesis and self-assembly of heterogeneous nanostructures, and analyzes the effects of structural parameters on the regulation of optical responses. The potential applications and challenges of heterogeneous nanostructures in the fields of biosensors and bioanalysis, in vivo monitoring, and phototheranostics are discussed.

Aptamer-Braked Multi-hairpin Cascade Circuits for Logic-Controlled Label-Free In Situ Bioimaging

As a common hairpin-based amplification strategy, catalytic-hairpin assembly (CHA) has been widely used to construct various DNA circuits for biosensing and imaging. However, the hairpin substrates can potentially react without catalysts and result in circuit leakage, which may be quite severe in a CHA reaction consisting of three or four hairpins due to the formation of stable three-/four-way junction product. To circumvent this problem, here we introduce a well-designed ATP aptamer as a DNA brake into a four-hairpin cascade circuit, where the triggering toehold is blocked by the aptamer brake and thus the circuit leakage decreases dramatically. Such an aptamer-braked DNA circuit is then employed to build an AND logic gate in response to multiple external stimuli in acidic cell membrane microenvironments. Induced by a bimolecular i-motif that binds thioflavin T (ThT), the dimerization of a four-way junction in situ assembled on the cell surface is accomplished, enabling the logic-controlled cell membrane imaging in a label-free manner. Our design would be applicable to other hairpin-based amplification strategies and may find more applications in the construction of multiresponsive DNA cascade circuits in complex living systems.

Integrated Ultrasonic Aggregation-Induced Enrichment with Raman Enhancement for Ultrasensitive and Rapid Biosensing

Enrichment and enhancement are two important aspects of ultratrace biomolecule recognition in complex biological samples. Here we integrate acoustic aggregation of modified Au nanorods with Raman enhancement for all-in-one ultratrace rapid biomolecule detection in one microliter solution. Arising from the interaction between individual nanoparticles and the acoustic field, the aggregation of Au nanorods results in rapid migration of specifically modified Au nanorods toward pressure node in a few seconds and accompanies the enrichment of specific biomolecular. As a proof concept, rapid and sensitive surface-enhanced Raman scattering (SERS) detection of nucleic acids (10^-13 M) in microliter-scale (10^-6 L) sample is achieved. Such an approach integrates ultrasonic aggregation-induced enrichment (uAIE) with Raman enhancement, holding considerable promise for efficient, sensitive, and rapid on-chip detection of ultratrace biomarkers in a clinical sample solution.

Target-fueled catalytic hairpin assembly for sensitive and multiplex microRNA detection

As a typical strand displacement-based DNA circuit, the catalytic hairpin assembly (CHA) has the potential to transduce and amplify signals for analytical applications, but little practice has been fulfilled in Luminex-based multiple microRNAs (miRNAs) detection. Here, we proposed a target-fueled CHA-based platform for sensitive and multiple miRNAs detection, by virtue of the multiplex characteristic of the Luminex xMAP platform. The cyclic use of target miRNA, which forms a substantial amount of H1-H2 duplexes, has amplified the fluorescent response to achieve sensitive sensing. Key experimental conditions including hairpin probe concentrations, reaction temperature, and concentration of SA-PE were optimized. Liver tumor-related miRNA-21, miRNA-122, and miRNA-222 could be simultaneously detected with LOD of 2 pM. Overall, the proposed method first combined CHA with the Luminex xMAP system to construct a sensitive sensing platform suitable for multiple miRNAs detection in real sample analysis, which could potentially be applied in biomedical research and clinical diagnosis. Graphical abstract.

Gold nanocage-based surface-enhanced Raman scattering probes for long-term monitoring of intracellular microRNA during bone marrow stem cell differentiation

The ability to monitor the differentiation of living stem cells is essential for understanding stem cell biology and the practical application of stem cell therapies. However, conventional methods of analyzing biomarkers related to differentiation still require a large number of cells or cell lysates. This requirement leads to the unavoidable loss of cell sources and hinders the real-time monitoring of cellular processes. In this study, we report an ultrasensitive surface-enhanced Raman scattering (SERS) method for the long-term detection and imaging of miR-144-3p in osteogenic differentiation of BMSCs, by using target miRNA-induced gold nanocage (GNC)-hairpin DNA1 (hpDNA1)-hpDNA2-GNC assembly in living cells. The finite-difference time domain method demonstrated that the electromagnetic intensities of the dimer and polymer of the GNCs were significantly enhanced compared to that of GNCs only, which theoretically confirmed the rational design of the SERS strategy. The hpDNA-conjugated GNC probes were prepared and used to recognize the target and distinguish from other miRNAs. This method enabled excellent sensitivity and high selectivity toward miR-144-3p with a limit of detection of 13.6 aM and a broad range from 100 aM to 100 pM in cell lysates. Then, we used transmission electron microscopy images, fluorescence microscopy images, and dark-field microscopy images to study the internalization of the probes in BMSCs. A Cell Counting Kit-8 experiment indicated that the probes were not cytotoxic in a certain concentration range. BMSCs were treated with an osteogenic inductor so that they would subsequently differentiate into osteocytes. Upon cellular uptake of these nanoprobes, we observed intense and time-dependent SERS responses from the important osteogenic biomarker miR-144-3p, only in BMSCs undergoing osteogenic differentiation and living undifferentiated BMSCs but not in osteoblasts. Finally, the accuracy of SERS has been proved by a quantitative real-time polymerase chain reaction experiment. The above results demonstrated that our nanoprobes are capable of long-term tracking of the dynamic expression of miR-144-3p (21 days) in the differentiating BMSCs. SERS has broad application prospects in the long-term detection of stem cell differentiation, and identification and isolation of specific cell types as well as in biomedical diagnosis.

From single cells to complex tissues in applications of surface-enhanced Raman scattering

This tutorial review explores how three of the most common methods for introducing nanoparticles to single cells for surface-enhanced Raman scattering measurements can be adapted for experiments with complex tissues.

DNA nanotechnology approaches for microRNA detection and diagnosis

MicroRNAs are involved in the crucial processes of development and diseases and have emerged as a new class of biomarkers. The field of DNA nanotechnology has shown great promise in the creation of novel microRNA biosensors that have utility in lab-based biosensing and potential for disease diagnostics. In this Survey and Summary, we explore and review DNA nanotechnology approaches for microRNA detection, surveying the literature for microRNA detection in three main areas of DNA nanostructures: DNA tetrahedra, DNA origami, and DNA devices and motifs. We take a critical look at the reviewed approaches, advantages and disadvantages of these methods in general, and a critical comparison of specific approaches. We conclude with a brief outlook on the future of DNA nanotechnology in biosensing for microRNA and beyond.

Fluorometric determination of ssDNA based on functionalized magnetic microparticles and DNA supersandwich self-assemblies

A method is described for the determination of DNA via nucleic acid amplification by using nucleic acid concatemers that result from DNA supersandwich self-assemblies (SSAs). The method employs two auxiliary probes to form self-assembled biotin SSAs. These exhibit strong fluorescence if labeled with intercalator SYBR Green I. In the presence of the target (as exemplified for a 30-mer), streptavidin is released from the surface of the functionalized magnetic microparticles (FMMPs) by competitive hybridization on the surface. However, the SSA products do not conjugate to the FMMPs. This leads to a large amount of SYBR Green I intercalated into the concatemers and eventually results in amplified fluorescence in the supernate. The SSA products can be prepared beforehand, and amplification therefore can be completed within 50 min. The method is more efficient than any other conventional amplification. The detection limit for the 30-mer is 26.4 fM which is better by a factor of 10 compared to other amplification methods. Conceivably, the method can be further extended to the determination of a wide variety of targets simply by replacing the sequences of the probes. Finally, this rapid and highly sensitive method was employed for detection of Ebola virus gene (≈30-mer) and ATP in spiked serum with satisfactory results. Graphical abstract A high sensitivity and efficiency bioassay is described based on functionalized magnetic microparticles and DNA supersandwich self-assemblies.

Applications of Catalytic Hairpin Assembly Reaction in Biosensing

Nucleic acids are considered as perfect programmable materials for cascade signal amplification and not merely as genetic information carriers. Among them, catalytic hairpin assembly (CHA), an enzyme-free, high-efficiency, and isothermal amplification method, is a typical example. A typical CHA reaction is initiated by single-stranded analytes, and substrate hairpins are successively opened, resulting in thermodynamically stable duplexes. CHA circuits, which were first proposed in 2008, present dozens of systems today. Through in-depth research on mechanisms, the CHA circuits have been continuously enriched with diverse reaction systems and improved analytical performance. After a short time, the CHA reaction can realize exponential amplification under isothermal conditions. Under certain conditions, the CHA reaction can even achieve 600 000-fold signal amplification. Owing to its promising versatility, CHA is able to be applied for analysis of various markers in vitro and in living cells. Also, CHA is integrated with nanomaterials and other molecular biotechnologies to produce diverse readouts. Herein, the varied CHA mechanisms, hairpin designs, and reaction conditions are introduced in detail. Additionally, biosensors based on CHA are presented. Finally, challenges and the outlook of CHA development are considered.

Plasmon Coupling-Enhanced Raman Sensing Platform Integrated with Exonuclease-Assisted Target Recycling Amplification for Ultrasensitive and Selective Detection of microRNA-21

A "signal-off" surface-enhanced Raman scattering (SERS) platform has been constructed for ultrasensitive detection of miRNA-21 by integrating exonuclease-assisted target recycling amplification with a plasmon coupling enhancement effect. On this platform, Raman-labeled Au nanostar (AuNS) probes can be covalently linked with the thiolated aptamer (Apt) on the Au-decorated silicon nanowire arrays (SiNWAs/Au) substrate, creating a coupled electromagnetic field between the substrate and the probes to enhance Raman signal. In the presence of miRNA-21, T7 exonuclease specifically hydrolyzed Apt on Apt/miRNA duplex to release miRNA-21. The regenerated element could then initiate another cycle of Apt/miRNA duplex formation and Apt cleavage. Correspondingly, the capture ability of substrate toward probes and the plasmon coupling effect between them were both diminished, giving a prominent attenuation of Raman intensity that can work as the detection signal. Due to the cascading integration between the target cycle process and the plasmon coupling effect, the present platform displayed a very low detection limit (0.34 fM, 3σ) for miRNA-21 detection. Furthermore, it was proven to be effective for analyzing miRNA-21 in biological samples and distinguishing the expression levels of miRNA-21 in MCF-7 cells and NIH3T3 cells, which became a promising tool to monitor miRNA-21 in cancer auxiliary diagnosis and drug screening.

Manganese dioxide nanosheets: from preparation to biomedical applications

Advancements in nanotechnology and molecular biology have promoted the development of a diverse range of models to intervene in various disorders (from diagnosis to treatment and even theranostics). Manganese dioxide nanosheets (MnO₂ NSs), a typical two-dimensional (2D) transition metal oxide of nanomaterial that possesses unique structure and distinct properties have been employed in multiple disciplines in recent decades, especially in the field of biomedicine, including biocatalysis, fluorescence sensing, magnetic resonance imaging and cargo-loading functionality. A brief overview of the different synthetic methodologies for MnO₂ NSs and their state-of-the-art biomedical applications is presented below, as well as the challenges and future perspectives of MnO₂ NSs.

Electrochemical-based biosensors for microRNA detection: Nanotechnology comes into view

Nanotechnology plays an undeniable significant role in medical sciences, particularly in the field of biomedicine. Development of several diagnostic procedures in medicine has been possible through the beneficial application of nano-materials, among which electrochemical nano-biosensors can be mentioned. They can be employed to quantify various clinical biomarkers in detection, evaluation, and follow up stages of the illnesses. MicroRNAs, a group of regulatory short RNA fragments, added a new dimension to the management and diagnosis of several diseases. Mature miRNAs are single-stranded RNA molecules approximately 22 nucleotides in length, which regulate a vast range of biological functions from cellular proliferation and death to cancer development and progression. Recently, diagnostic value of miRNAs in various diseases has been demonstrated. There are many traditional methods for detection of miRNAs including northern blotting, quantitative real time PCR (qRT-PCR), microarray technology, nanotechnology-based approaches, and molecular biology tools including miRNA biosensors. In comparison with other techniques, electrochemical nucleic acid biosensor methods exhibit many interesting features, and could play an important role in the future nucleic acid analysis. This review paper provides an overview of some different types of nanotechnology-based biosensors for detection of miRNAs.

Avenues Toward microRNA Detection In Vitro: A Review of Technical Advances and Challenges

Over the decades, the biological role of microRNAs (miRNAs) in the post-transcriptional regulation of gene expression has been discovered in many cancer types, thus initiating the tremendous expectation of their application as biomarkers in the diagnosis, prognosis, and treatment of cancer. Hence, the development of efficient miRNA detection methods in vitro is in high demand. Extensive efforts have been made based on the intrinsic properties of miRNAs, such as low expression levels, high sequence homology, and short length, to develop novel in vitro miRNA detection methods with high accuracy, low cost, practicality, and multiplexity at point-of-care settings. In this review, we mainly summarized the newly developed in vitro miRNA detection methods classified by three key elements, including biological recognition elements, additional micro-/nano-materials and signal transduction/readout elements, their current challenges and further applications are also discussed.