Synergy of Peptide-Nucleic Acid and Spherical Nucleic Acid Enabled Quantitative and Specific Detection of Tumor Exosomal MicroRNA

Smart Stimuli-Responsive Spherical Nucleic Acids: Cutting-Edge Platforms for Biosensing, Bioimaging, and Therapeutics

Spherical nucleic acids (SNAs) with exceptional colloidal stability, multiple modularity, and programmability are excellent candidates to address common molecular delivery-related issues. Based on this, the higher targeting accuracy and enhanced controllability of stimuli-responsive SNAs render them precise nanoplatforms with inestimable prospects for diverse biomedical applications. Therefore, tailored diagnosis and treatment with stimuli-responsive SNAs may be a robust strategy to break through the bottlenecks associated with traditional nanocarriers. Various stimuli-responsive SNAs are engineered through the incorporation of multifunctional modifications to meet biomedical demands with the development of nucleic acid functionalization. This review provides a comprehensive overview of prominent research in this area and recent advancements in the utilization of stimuli-responsive SNAs in biosensing, bioimaging, and therapeutics. For each aspect, SNA nanoplatforms that exhibit responsive behavior to both internal stimuli (including sequence, enzyme, redox reactions, and pH) and external stimuli (such as light and temperature) are highlighted. This review is expected to offer inspiration and guidance strategies for the rational design and development of stimuli-responsive SNAs in the field of biomedicine.

MOF-mediated dual energy transfer nanoprobe integrated with exonuclease III amplification strategy for highly sensitive detection of DNA

Accurate quantitative detection of DNA is an advanced strategy in various fields (such as disease diagnosis and environmental monitoring), but the classical DNA detection method usually suffers from low sensitivity, expensive thermal cyclers, or strict annealing conditions. Herein, a MOF-ERA platform for ultrasensitive HBV-DNA detection is constructed by integrating metal-organic framework (MOF)-mediated double energy transfer nanoprobe with exonuclease III (Exo III)-assisted target recycling amplification. The proposed double energy transfer containing a donor and two receptors is simply composed of MOFs (UiO-66-NH2, a well-studied MOF) modified with a signal probe formed by the hybridization of carboxyuorescein (FAM)-labeled DNA (FDNA) and black hole quencher (BHQ1)-terminated DNA (QDNA), resulting in low fluorescence signal. After the addition of HBV-DNA, Exo III degradation to FDNA is activated, leading to the liberation of the numerous FAM molecules, followed by the generation of a significant fluorescence signal owing to the negligible binding of MOFs with free FAM molecules. The results certify that the MOF-ERA platform can be successfully used to assay HBV-DNA in the range of 1.0-25.0 nM with a detection limit of 97.2 pM, which is lower than that without BHQ1 or Exo III. The proposed method with the superiorities of low background signal and high selectivity holds promise for early disease diagnosis and clinical biomedicine applications.

Chemically Modified Platforms for Better RNA Therapeutics

RNA-based therapies have catalyzed a revolutionary transformation in the biomedical landscape, offering unprecedented potential in disease prevention and treatment. However, despite their remarkable achievements, these therapies encounter substantial challenges including low stability, susceptibility to degradation by nucleases, and a prominent negative charge, thereby hindering further development. Chemically modified platforms have emerged as a strategic innovation, focusing on precise alterations either on the RNA moieties or their associated delivery vectors. This comprehensive review delves into these platforms, underscoring their significance in augmenting the performance and translational prospects of RNA-based therapeutics. It encompasses an in-depth analysis of various chemically modified delivery platforms that have been instrumental in propelling RNA therapeutics toward clinical utility. Moreover, the review scrutinizes the rationale behind diverse chemical modification techniques aiming at optimizing the therapeutic efficacy of RNA molecules, thereby facilitating robust disease management. Recent empirical studies corroborating the efficacy enhancement of RNA therapeutics through chemical modifications are highlighted. Conclusively, we offer profound insights into the transformative impact of chemical modifications on RNA drugs and delineates prospective trajectories for their future development and clinical integration.

Integrated FET sensing microsystem for specific detection of pancreatic cancer exosomal miRNA10b

Tumor-derived exosome (TD-Ex) serves as a crucial early diagnostic biomarker of pancreatic cancer (PC). However, accurate identification of TD-Ex from PC is still a challenging work. In this paper, a detection microsystem that integrates magnetic separation and FET biosensor is developed, which is capable of selectively separating TD-Ex of PC from the plasma and detecting exosomal miRNA10b in a sensitive and specific manner. The magnetic beads were functionalized with dual antibody (GPC-1 antibody and EpCAM antibody), enabling selective recognition and capture of PC-derived exosomes. On the other hand, a peptide nucleic acid (PNA)- functionalized reduced graphene oxide field-effect transistor (RGO FET) biosensor was subsequently utilized to detect the exosomal miRNA10b, which is highly expressed in PC- derived exosomes. This system could achieve a low detection limit down to 78 fM, and selectively identify miRNA10b from single-base mismatched miRNA. In addition, 40 clinical plasma samples were tested with this microsystem, and the results indicate that it could effectively distinguish PC patients from healthy individuals. The assay combines specific capture and enrichment of PC-derived exosomes with sensitive and selective detection of exosomal miRNA, showing its potential to be used as an effective scheme for PC early diagnosis.

Proximity-Enhanced Electrochemiluminescence Sensing Platform for Effective Capturing of Exosomes and Probing Internal MicroRNAs Involved in Cancer Cell Apoptosis

Exosomal microRNAs (miRNAs) play critical regulatory roles in many cellular processes, and so how to probe them has attracted increasing interest. Here we propose an aptamer-functionalized dimeric framework nucleic acid (FNA) nanoplatform for effective capture of exosomes and directly probing internal miRNAs with electrochemiluminescence (ECL) detection, not requiring RNA extraction in conventional counterparts. A CD63 protein-binding aptamer is tethered to one of the FNA structures, allowing exosomes to be immobilized there and release internal miRNAs after lysis. The target miRNA induces the formation of a Y-shaped junction on another FNA structure in a close proximity state, which benefits the loading of covalently hemin-modified spherical nucleic acid enzymes for enhanced ECL readout in the luminol-H2O2 system. In this facile way, the ultrasensitive detection of exosomal miR-21 from cancer cells is accomplished and then used for cell apoptosis analysis, indicating that the oncogene miR-21 negatively participates in the regulation of the apoptotic process; namely, downregulating the miR-21 level is unbeneficial for cancer cell growth.

Integrating Reliable Pt-S Bond-Mediated 3D DNA Nanomachine with Magnetic Separation in a Homogeneous Electrochemical Strategy for Exosomal MicroRNA Detection with Low Background and High Sensitivity

Precise and sensitive analysis of exosomal microRNA (miRNA) is of great importance for noninvasive early disease diagnosis, but it remains a great challenge to detect exosomal miRNA in human blood samples because of their small size, high sequence homology, and low abundance. Herein, we integrated reliable Pt-S bond-mediated three-dimensional (3D) DNA nanomachine and magnetic separation in a homogeneous electrochemical strategy for the detection of exosomal miRNA with low background and high sensitivity. The 3D DNA nanomachine was easily prepared via a facile and rapid freezing method, and it was capable of resisting the influence of biothiols, thus endowing it with high stability. Notably, the as-developed magnetic 3D DNA nanomachine not only enabled the detection system to have a low background but also coupled with liposome nanocarriers to synergistically amplify the current signal. Consequently, by ingeniously combining the low background and multiple signal-amplification strategies in homogeneous electrochemical biosensing, highly sensitive detection of exosomal miRNA was successfully achieved. More significantly, with good anti-interference ability, the as-proposed method could effectively discriminate plasma samples from cancer patients and healthy subjects, thus showing a high potential for application in the nondestructive early clinical diagnosis of disease.

Electrochemical Biosensors for Whole Blood Analysis: Recent Progress, Challenges, and Future Perspectives

Whole blood, as one of the most significant biological fluids, provides critical information for health management and disease monitoring. Over the past 10 years, advances in nanotechnology, microfluidics, and biomarker research have spurred the development of powerful miniaturized diagnostic systems for whole blood testing toward the goal of disease monitoring and treatment. Among the techniques employed for whole-blood diagnostics, electrochemical biosensors, as known to be rapid, sensitive, capable of miniaturization, reagentless and washing free, become a class of emerging technology to achieve the target detection specifically and directly in complex media, e.g., whole blood or even in the living body. Here we are aiming to provide a comprehensive review to summarize advances over the past decade in the development of electrochemical sensors for whole blood analysis. Further, we address the remaining challenges and opportunities to integrate electrochemical sensing platforms.

Primer exchange reaction-amplified protein-nucleic acid interactions for ultrasensitive and specific microRNA detection

Protein-nucleic acid interactions are not only fundamental to genetic regulation and cellular metabolism, but molecular basis to artificial biosensors. However, such interactions are generally weak and dynamic, making their specific and sensitive quantitative detection challenging. By using primer exchange reaction (PER)-amplified protein-nucleic acid interactions, we here design a universal and ultrasensitive electrochemical sensor to quantify microRNAs (miRNAs) in blood. This PER-miR sensor leverages specific recognition between S9.6 antibodies and miRNA/DNA hybrids to couple with PER-derived multi-enzyme catalysis for ultrasensitive miRNA detection. Surface binding kinetic analysis shows a rational K_d (8.9 nM) between the miRNA/DNA heteroduplex and electrode-attached S9.6 antibody. Based on such a favorable affinity, the programmable PER amplification enables the sensor to detect target miRNAs with sensitivity up to 90.5 aM, three orders of magnitude higher than that without PER in routine design, and with specificity of single-base resolution. Furthermore, the PER-miR sensor allows detecting multiple miRNAs in parallel, measuring target miRNA in lysates across four types of cell lines, and differentiating tumor patients from healthy individuals by directly analyzing the human blood samples (n = 40). These advantages make the sensor a promising tool to enable quantitative sensing of biomolecular interactions and precision diagnostics.

Progress of Endogenous and Exogenous Nanoparticles for Cancer Therapy and Diagnostics

The focus of this brief review is to describe the application of nanoparticles, including endogenous nanoparticles (e.g., extracellular vesicles, EVs, and virus capsids) and exogenous nanoparticles (e.g., organic and inorganic materials) in cancer therapy and diagnostics. In this review, we mainly focused on EVs, where a recent study demonstrated that EVs secreted from cancer cells are associated with malignant alterations in cancer. EVs are expected to be used for cancer diagnostics by analyzing their informative cargo. Exogenous nanoparticles are also used in cancer diagnostics as imaging probes because they can be easily functionalized. Nanoparticles are promising targets for drug delivery system (DDS) development and have recently been actively studied. In this review, we introduce nanoparticles as a powerful tool in the field of cancer therapy and diagnostics and discuss issues and future prospects.

Nanomechanical assay for ultrasensitive and rapid detection of SARS-CoV-2 based on peptide nucleic acid

The massive global spread of the COVID-19 pandemic makes the development of more effective and easily popularized assays critical. Here, we developed an ultrasensitive nanomechanical method based on microcantilever array and peptide nucleic acid (PNA) for the detection of severe acute respiratory syndrome-coronavirus-2 (SARS-CoV-2) RNA. The method has an extremely low detection limit of 0.1 fM (10⁵ copies/mL) for N-gene specific sequence (20 bp). Interestingly, it was further found that the detection limit of N gene (pharyngeal swab sample) was even lower, reaching 50 copies/mL. The large size of the N gene dramatically enhances the sensitivity of the nanomechanical sensor by up to three orders of magnitude. The detection limit of this amplification-free assay method is an order of magnitude lower than RT-PCR (500 copies/mL) that requires amplification. The non-specific signal in the assay is eliminated by the in-situ comparison of the array, reducing the false-positive misdiagnosis rate. The method is amplification-free and label-free, allowing for accurate diagnosis within 1 h. The strong specificity and ultra-sensitivity allow single base mutations in viruses to be distinguished even at very low concentrations. Also, the method remains sensitive to fM magnitude lung cancer marker (miRNA-155). Therefore, this ultrasensitive, amplification-free and inexpensive assay is expected to be used for the early diagnosis of COVID-19 patients and to be extended as a broad detection tool.

ELECTRONIC SUPPLEMENTARY MATERIAL

Supplementary material (experimental section, N gene sequences and all nucleic acid sequences used in the study, Figs. S1-S6, and Tables S1-S3) is available in the online version of this article at 10.1007/s12274-022-4333-3.

Practical tips and new trends in electrochemical biosensing of cancer-related extracellular vesicles

To tackle cancer and provide prompt diagnoses and prognoses, the constantly evolving biosensing field is continuously on the lookout for novel markers that can be non-invasively analysed. Extracellular vesicles (EVs) may represent a promising biomarker that also works as a source of biomarkers. The augmented cellular activity of cancerous cells leads to the production of higher numbers of EVs, which can give direct information on the disease due to the presence of general and cancer-specific surface-tethered molecules. Moreover, the intravesicular space is enriched with other molecules that can considerably help in the early detection of neoplasia. Even though EV-targeted research has indubitably received broad attention lately, there still is a wide lack of practical and effective quantitative procedures due to difficulties in pre-analytical and analytical phases. This review aims at providing an exhaustive outline of the recent progress in EV detection using electrochemical and photoelectrochemical biosensors, with a focus on handling approaches and trends in the selection of bioreceptors and molecular targets related to EVs that might guide researchers that are approaching such an unstandardised field.

Exosomal MicroRNA Profiling

Exosomes are extracellular vesicles, which have the ability to convey various types of cargo between cells. Lately, a great amount of interest has been paid to exosomal microRNAs (miRNAs), since much evidence has suggested that the sorting of miRNAs into exosomes is not an accidental process. It has been shown that exosomal miRNAs (exo-miRNAs) are implicated in a variety of cellular processes including (but not limited to) cell migration, apoptosis, proliferation, and autophagy. Exosomes can play a role in cardiovascular diseases and can be used as diagnostic biomarkers for several diseases, especially cancer. Tremendous advances in technology have led to the development of various platforms for miRNA profiling. Each platform has its own limitations and strengths that need to be understood in order to use them properly. In the current review, we summarize some exo-miRNAs that are relevant to exo-miRNA profiling studies and describe new methods used for the measurement of miRNA profiles in different human bodily fluids.

Analysis and Biomedical Applications of Functional Cargo in Extracellular Vesicles

Extracellular vesicles (EVs) can facilitate essential communication among cells in a range of pathophysiological conditions including cancer metastasis and progression, immune regulation, and neuronal communication. EVs are membrane-enclosed vesicles generated through endocytic origin and contain many cellular components, including proteins, lipids, nucleic acids, and metabolites. Over the past few years, the intravesicular content of EVs has proven to be a valuable biomarker for disease diagnostics, involving cancer, cardiovascular diseases, and central nervous system diseases. This review aims to provide insight into EV biogenesis, composition, function, and isolation, present a comprehensive overview of emerging techniques for EV cargo analysis, highlighting their major technical features and limitations, and summarize the potential role of EV cargos as biomarkers in disease diagnostics. Further, progress and remaining challenges will be discussed for clinical diagnostic outlooks.

Recent Advances in Exosomal miRNA Biosensing for Liquid Biopsy

As a noninvasive detection technique, liquid biopsy plays a valuable role in cancer diagnosis, disease monitoring, and prognostic assessment. In liquid biopsies, exosomes are considered among the potential biomarkers because they are important bioinformation carriers for intercellular communication. Exosomes transport miRNAs and, thus, play an important role in the regulation of cell growth and function; therefore, detection of cancer cell-derived exosomal miRNAs (exo-miRNAs) gives effective information in liquid biopsy. The development of sensitive, convenient, and reliable exo-miRNA assays will provide new perspectives for medical diagnosis. This review presents different designs and detection strategies of recent exo-miRNA assays in terms of signal transduction and amplification, as well as signal detection. In addition, this review outlines the current attempts at bioassay methods in liquid biopsies. Lastly, the challenges and prospects of exosome bioassays are also considered.

Nucleic acid nanoassembly-enhanced RNA therapeutics and diagnosis

RNAs are involved in the crucial processes of disease progression and have emerged as powerful therapeutic targets and diagnostic biomarkers. However, efficient delivery of therapeutic RNA to the targeted location and precise detection of RNA markers remains challenging. Recently, more and more attention has been paid to applying nucleic acid nanoassemblies in diagnosing and treating. Due to the flexibility and deformability of nucleic acids, the nanoassemblies could be fabricated with different shapes and structures. With hybridization, nucleic acid nanoassemblies, including DNA and RNA nanostructures, can be applied to enhance RNA therapeutics and diagnosis. This review briefly introduces the construction and properties of different nucleic acid nanoassemblies and their applications for RNA therapy and diagnosis and makes further prospects for their development.

Simultaneous detection of cancerous exosomal miRNA-21 and PD-L1 with a sensitive dual-cycling nanoprobe

Simultaneous detection of specific exosomal surface proteins and inner microRNAs are hampered by their heterogeneity, low abundance and spatial segregation in nanovesicles. Here, we design a dual-cycling nanoprobe (DCNP) to enable single-step simultaneous quantitation of cancerous exosomal surface programmed death-ligand 1 (PD-L1) (ExoPD-L1) and miRNA-21 (ExomiR-21) directly in exosome lysates, without resorting to either RNA extraction or time-consuming transmembrane penetration. In this design, DNA molecular machine-based dual-recognition probes co-assemble onto gold nanoparticle surface for engineering 'silent' DCNPs, which enable signal-amplified synchronous response to dual-targets as activated by ExomiR-21 and ExoPD-L1 within 20 min. Benefiting from cycling amplification of the molecular machine, DCNPs sensor achieves detection limits of tumor exosomes, ExoPD-L1 and ExomiR-21 down to 10 particles/μL, 0.17 pg/mL and 66 fM, respectively. Such a sensitive dual-response strategy allows simultaneous tracking the dynamic changes of ExoPD-L1 and ExomiR-21 expression regulated by signaling molecules or therapeutics. This approach further detects circulating ExoPD-L1 and ExomiR-21 in human plasma to differentiate breast cancer patients from healthy individuals with high accuracy, showing great potential of DCNPs for simultaneous profiling exosomal surface and inside biomarkers, and for clinical precision diagnosis.

Carbon Electrodes with Gold Nanoparticles for the Electrochemical Detection of miRNA 21-5p

Extracellular vesicles are involved in many physiological and pathological activities. They transport miRNAs to recipient cells during their role in intercellular communication, making them emerging biomarkers of many diseases. Interest in exosomal miRNAs has grown after they have shown numerous advantages as biomarkers for diagnosis, prognosis, and evaluation of cancer treatment. This work describes the development of a biosensor for the detection of 21-5p miRNA in human serum using screen-printed carbon electrodes modified with gold nanoparticles fabricated in situ, an innovative approach to avoid the use of more expensive gold substrates that provide better analytical outputs. The several variables involved in the assembly of the biosensor were optimized by univariant mode. Under the best conditions, the biosensor showed a linear response from 0.010 fM to 10 pM, with a limit of detection (LOD) of 4.31 aM. The sensitivity was 0.3718 relative Ω per decade concentration in buffered saline solutions, and the standard deviation of the blank is 2.94 Ω. A linear response was also obtained when human serum samples were tested with miRNA 21-5p. Interference from similar miRNA and miss-match miRNA sequences was evaluated and good selectivity for miRNA 21-5p was observed. Overall, the device proposed is an alternative approach to gold substrates, which typically result in more sensitive systems and lower LODs, which compares favorably to current gold-based biosensors for the targeted miRNA. This design may be further extended to other nucleic acids.

Quantitative and Multiplex Detection of Extracellular Vesicle-Derived MicroRNA via Rolling Circle Amplification within Encoded Hydrogel Microparticles

Extracellular vesicle-derived microRNA (EV-miRNA) represent a promising cancer biomarker for disease diagnosis and monitoring. However, existing techniques to detect EV-miRNA rely on complex, bias-prone strategies, and preprocessing steps, making absolute quantification highly challenging. This work demonstrates the development and application of a method for quantitative and multiplex detection of EV-miRNA, via rolling circle amplification within encoded hydrogel particles. By a one-pot extracellular vesicle lysis and microRNA capture step, the bias and losses associated with standard RNA extraction techniques is avoided. The system offers a large dynamic range (3 orders of magnitude), ease of multiplexing, and a limit of detection down to 2.3 zmol (46 × 10^-18 m), demonstrating its utility in clinical applications based on liquid biopsy tests. Furthermore, orthogonal measurements of EV concentrations coupled with the direct, absolute quantification of miRNA in biological samples results in quantitative measurements of miRNA copy numbers per volume sample, and per extracellular vesicle.

Interfacial DNA Framework-Enhanced Background-to-Signal Transition for Ultrasensitive and Specific Micro-RNA Detection

Interfacial DNA self-assembly is fundamental to solid nucleic acid biosensors, whereas how to improve the signal-to-noise ratio has always been a challenge, especially in the charge-based electrochemical DNA sensors because of the large noise from the negatively charged DNA capture probes. Here, we report a DNA framework-reversed signal-gain strategy through background-to-signal transition for ultrasensitive and highly specific electrical detection of microRNAs (miRNAs) in blood. By using a model of enzyme-catalyzed deposition of conductive molecules (polyaniline) targeting to DNA, we observed the highest signal contribution per unit area by the highly charged three-dimensional (3D) tetrahedral DNA framework probe, relative to the modest of two-dimensional (2D) polyA probe and the lowest of one-dimensional (1D) single-stranded (ss)DNA probe, suggesting the positive correlation of background DNA charge with signal enhancement. Using such an effective signal-transition design, the DNA framework-based electrochemical sensor achieves ultrasensitive miRNAs detection with sensitivity up to 0.29 fM (at least 10-fold higher than that with 1D ssDNA or 2D polyA probes) and high specificity with single-base resolution. More importantly, this high-performance sensor allows for a generalized sandwich detection of tumor-associated miRNAs in the complex matrices (multiple cell lysates and blood serum) and further distinguishes the tumor patients (e.g., breast, lung, and liver cancer) from the normal individuals. These advantages signify the promise of this miRNA sensor as a versatile tool in precision diagnosis.

Self-Propelled Janus Mesoporous Micromotor for Enhanced MicroRNA Capture and Amplified Detection in Complex Biological Samples

The slow mass transport of the target molecule essentially limits the biosensing performance. Here, we report a Janus mesoporous microsphere/Pt-based (meso-MS/Pt) nanostructure with greatly enhanced target transport and accelerated recognition process for microRNA (miRNA) amplified detection in complex biological samples. The mesoporous MS was synthesized via double emulsion interfacial polymerization, and Pt nanoparticles (PtNPs) were deposited on the half-MS surface to construct Janus meso-MS/Pt micromotor. The heterogeneous meso-MS/Pt with a large surface available was attached to an entropy-driven DNA recognition system, termed meso-MS/Pt/DNA, and the tremendous pores network was beneficial to enhanced receptor-target interaction. It enabled moving around complex biological samples to greatly enhance target miRNA mass transport and accelerate recognition procedure due to the self-diffusiophoretic propulsion. Coupling with the entropy-driven signal amplification, extremely sensitive miRNA detection in Dulbecco's modified Eagle medium (DMEM), and cell lysate without preparatory and washing steps was realized. Given the free preparatory and washing steps, fast mass transport, and amplified capability, the meso-MS/Pt/DNA micromotor provides a promising method for miRNAs analysis in real biological samples.

Photoelectrochemical Detection of Exosomal miRNAs by Combining Target-Programmed Controllable Signal Quenching Engineering

MicroRNAs extracted from exosomes (exosomal miRNAs) have recently emerged as promising biomarkers for early prognosis and diagnosis. Thus, the development of an effective approach for exosomal miRNA monitoring has triggered extensive attention. Herein, a sensitive photoelectrochemical (PEC) biosensing platform is demonstrated for exosomal miRNA assay via the target miRNA-powered λ-exonuclease for the amplification strategy. The metal-organic framework (MOF)-decorated WO₃ nanoflakes heterostructure is constructed and implemented as the photoelectrode. Also, a target exosomal miRNA-activatable programmed release nanocarrier was fabricated, which is responsible for signal control. Hemin that acted as the electron acceptor was prior entrapped into the programmed control release nanocarriers. Once the target exosomal miRNAs-21 was introduced, the as-prepared programmed release nanocarriers were initiated to trigger the release of hemin, which enabled the quenching of the photocurrent. Under the optimized conditions, the level of exosomal miRNAs-21 could be accurately tracked ranging from 1 fM to 0.1 μM with a low detection limit of 0.5 fM. The discoveries illustrate the possibility for the rapid and efficient diagnosis and prognosis prediction of diseases based on the detection of exosomal miRNAs-21 and would provide feasible approaches for the fabrication of an efficient platform for clinical applications.

Spherical nucleic acids: Organized nucleotide aggregates as versatile nanomedicine

Spherical nucleic acids (SNAs) are composed of a nanoparticle core and a layer of densely arranged oligonucleotide shells. After the first report of SNA by Mirkin and coworkers in 1996, it has created a significant interest by offering new possibilities in the field of gene and drug delivery. The controlled aggregation of oligonucleotides on the surface of organic/inorganic nanoparticles improves the delivery of genes and nucleic acid-based drugs and alters and regulates the biological profiles of the nanoparticle core within living organisms. Here in this review, we present an overview of the recent progress of SNAs that has speeded up their biomedical application and their potential transition to clinical use. We start with introducing the concept and characteristics of SNAs as drug/gene delivery systems and highlight recent efforts of bioengineering SNA by imaging and treatmenting various diseases. Finally, we discuss potential challenges and opportunities of SNAs, their ongoing clinical trials, and future translation, and how they may affect the current landscape of clinical practices. We hope that this review will update our current understanding of SNA, organized oligonucleotide aggregates, for disease diagnosis and treatment.

Exosomes as Powerful Engines in Cancer: Isolation, Characterization and Detection Techniques

Exosomes, powerful extracellular nanovesicles released from almost all types of living cells, are considered the communication engines (messengers) that control and reprogram physiological pathways inside target cells within a community or between different communities. The cell-like structure of these extracellular vesicles provides a protective environment for their proteins and DNA/RNA cargos, which serve as biomarkers for many malicious diseases, including infectious diseases and cancers. Cancer-derived exosomes control cancer metastasis, prognosis, and development. In addition to the unique structure of exosomes, their nanometer size and tendency of interacting with cells makes them a viable novel drug delivery solution. In recent years, numerous research efforts have been made to quantify and characterize disease-derived exosomes for diagnosis, monitoring, and therapeutic purposes. This review aims to (1) relate exosome biomarkers to their origins, (2) focus on current isolation and detection methods, (3) discuss and evaluate the proposed technologies deriving from exosome research for cancer treatment, and (4) form a conclusion about the prospects of the current exosome research.

An electrochemical biosensor based on ARGET ATRP with DSN-assisted target recycling for sensitive detection of tobacco mosaic virus RNA

Herein, an electrochemical biosensor for detecting tobacco mosaic virus (TMV) RNA is constructed by activator regenerated by electron transfer atom transfer radical polymerization (ARGET ATRP) combined with duplex-specific nuclease (DSN)-assisted target recycling. First, the captured DNA (cDNA) is self-assembled on the electrode surface and hybridizes with the TMV RNA (tRNA) to form cDNA/tRNA hybrids. And then the initiator of ARGET ATRP (α-bromoisobutyric acid, BMP) is attached to the cDNA via an amide bond and later triggers ARGET ATRP. Many electroactive monomers (ferrocenylmethyl methacrylate, FMMA) are polymerized and a remarkable electrical signal response of ferrocene (Fc) is obtained. However, with the present of DSN, DSN cleaves the cDNA/tRNA hybrid and releases tRNA to hybridize with another cDNA, thereby causing significant shortening of the length of the cDNA. The number of polymer chains on the electrode surface is drastically reduced, which is followed by a noticeable reduction in the signal of Fc. The method shows high sensitivity, superior selectivity, excellent stability and good reproducibility under optimal conditions with the limit of detection (LOD) of 2.9 fM. Furthermore, the biosensor showed satisfactory applicability in detecting tRNA in real samples, thereby demonstrating the potential of the method for practical TMV RNA detection.

DNase I-assisted 2'-O-methyl molecular beacon for amplified detection of tumor exosomal microRNA-21

An end-modified 2'-O-methyl molecular beacon (eMB) with unique nuclease resistance was designed and prepared. The eMB can resist the enzymatic digestion by DNase I, which would otherwise occur upon the hybridization of the eMB with a complementary sequence. As a result, the coupling use of eMBs and DNase I allows highly sensitive detection of miRNA with a limit of detection (LOD) of 2.5 pM. The analytical strategy was further used for detection of tumor exosomal microRNA-21, and down to 0.86 μg mL^-1 A375 exosomes were detected. Overall, the present method can effectively quantify tumor-derived exosomes for cancer diagnosis.

Peptide Nucleic Acid-Functionalized Nanochannel Biosensor for the Highly Sensitive Detection of Tumor Exosomal MicroRNA

Compared with free miRNAs in blood, miRNAs in exosomes have higher abundance and stability. Therefore, miRNAs in exosomes can be regarded as an ideal tumor marker for early cancer diagnosis. Here, a peptide nucleic acid (PNA)-functionalized nanochannel biosensor for the ultrasensitive and specific detection of tumor exosomal miRNAs is proposed. After PNA was covalently bound to the inner surface of the nanochannels, the detection of tumor exosomal miRNAs was achieved by the charge changes on the surface of nanochannels before and after hybridization (PNA-miRNA). Due to the neutral characteristics of PNA, the efficiency of PNA-miRNA hybridization was improved by significantly reducing the background signal. This biosensor could not only specifically distinguish target miRNA-10b from single-base mismatched miRNA but also achieve a detection limit as low as 75 aM. Moreover, the biosensor was further used to detect exosomal miRNA-10b derived from pancreatic cancer cells and normal pancreatic cells. The results indicate that this biosensor could effectively distinguish pancreatic cancer tumor-derived exosomes from the normal control group, and the detection results show good consistency with those of the quantitative reverse-transcription polymerase chain reaction method. In addition, the biosensor was used to detect exosomal miRNA-10b in clinical plasma samples, and it was found that the content of exosomal miRNA-10b in cancer patients was generally higher than that of healthy individuals, proving that the method is expected to be applied for the early diagnosis of cancer.

Nucleic Acid Tests for Clinical Translation

Nucleic acids, including deoxyribonucleic acid (DNA) and ribonucleic acid (RNA), are natural biopolymers composed of nucleotides that store, transmit, and express genetic information. Overexpressed or underexpressed as well as mutated nucleic acids have been implicated in many diseases. Therefore, nucleic acid tests (NATs) are extremely important. Inspired by intracellular DNA replication and RNA transcription, in vitro NATs have been extensively developed to improve the detection specificity, sensitivity, and simplicity. The principles of NATs can be in general classified into three categories: nucleic acid hybridization, thermal-cycle or isothermal amplification, and signal amplification. Driven by pressing needs in clinical diagnosis and prevention of infectious diseases, NATs have evolved to be a rapidly advancing field. During the past ten years, an explosive increase of research interest in both basic research and clinical translation has been witnessed. In this review, we aim to provide comprehensive coverage of the progress to analyze nucleic acids, use nucleic acids as recognition probes, construct detection devices based on nucleic acids, and utilize nucleic acids in clinical diagnosis and other important fields. We also discuss the new frontiers in the field and the challenges to be addressed.

Dual-Mode SERS and Electrochemical Detection of miRNA Based on Popcorn-like Gold Nanofilms and Toehold-Mediated Strand Displacement Amplification Reaction

MicroRNA (miRNA) has emerged as one of the ideal target biomarker analytes for cancer detection because its abnormal expression is closely related to the occurrence of many cancers. In this work, we combined three-dimensional (3D) popcorn-like gold nanofilms as novel surface-enhanced Raman scattering (SERS)-electrochemistry active substrates with toehold-mediated strand displacement reactions (TSDRs) to construct a DNA molecular machine for SERS-electrochemistry dual-mode detection of miRNA. 3D popcorn-like spatial structures generated more active "hot spots" and thus enhanced the sensitivity of SERS and electrochemical signals. Besides, the TSDRs showed high sequence-dependence and high specificity. The addition of target miRNA will trigger the molecular machine to perform two TSDRs in the presence of signal DNA strands modified by R6G (R6G-DNA), thus achieving an enzyme-free amplification detection of miRNA with a low limit of detection of 0.12 fM (for the SERS method) and 2.2 fM (for the electrochemical method). This biosensor can also serve as a universally amplified and sensitive detection platform for monitoring different biomarkers, such as cancer-related DNA, messenger RNA, or miRNA molecules, with high selectivity by changing the corresponding probe sequence.

Dual cascade isothermal amplification reaction based glucometer sensors for point-of-care diagnostics of cancer-related microRNAs

The practical use of a point-of-care (POC) device is of particular interest in performing liquid biopsies related to cancer. Herein, taking advantage of the practical convenience of a commercially available personal glucose meter (PGM), we report a convenient, low-cost and sensitive detection strategy for circulating microRNA-155 (miRNA155) in human serum. First, miRNA155 in serum triggers the catalyzed hairpin assembly (CHA) reaction, and then the CHA product is specifically captured by the peptide nucleic acid (PNA) probes attached to the surface of a 96-well plate, which in turn triggers the hybridization chain reaction (HCR), resulting in the local enrichment of invertase. Next, introduction of a substrate (sucrose) for the invertase results in the generation of glucose, which can be detected by a PGM. In this sensor, neutrally charged PNA (12 nt) is more likely to hybridize with the CHA products than with the negatively charged DNA in kinetics, which improves the detection sensitivity and specificity. Due to the synergistic isothermal amplification reaction between CHA and HCR, the sensor is able to achieve a broad dynamic range (from 1 fM to 10 nM) with a detection limit down to 0.36 fM (3 orders of magnitude lower than that without HCR) and is capable of distinguishing single-base mismatched sequences. Thus the convenient, sensitive, robust and low-cost PGM sensor makes on-site nucleic acids detection possible, suggesting its great application prospect as a promising POC device in cancer diagnostics.

Electrochemical prostate-specific antigen biosensors based on electroconductive nanomaterials and polymers

Prostate cancer (PCa), the second most malignant neoplasm in men, is also the fifth leading cause of cancer-related deaths in men globally. Unfortunately, this malignancy remains largely asymptomatic until late-stage emergence when treatment is limited due to the lack of effective metastatic PCa therapeutics. Due to these limitations, early PCa detection through prostate-specific antigen (PSA) screening has become increasingly important, resulting in a more than 50% decrease in mortality. Conventional assays for PSA detection, such as enzyme-linked immunosorbent assay (ELISA), are labor intensive, relatively expensive, operator-dependent and do not provide adequate sensitivity. Electrochemical biosensors overcome these limitations because they are rapid, cost-effective, simple to use and ultrasensitive. This article reviews electrochemical PSA biosensors using electroconductive nanomaterials such as carbon-, metal-, metal oxide- and peptide-based nanostructures, as well as polymers to significantly improve conductivity and enhance sensitivity. Challenges associated with the development of these devices are discussed thus providing additional insight into their analytic strength as well as their potential use in early PCa detection.

A simple, one-pot and ultrasensitive DNA sensor via Exo III-Assisted target recycling and 3D DNA walker cascade amplification

Rapid, sensitive, and user-friendly nucleic acid detection is of growing importance in early clinical diagnosis. Here, we construct a simple, one-pot and ultrasensitive DNA sensor via exonuclease III (Exo III)-assisted target recycling amplification (ERA) combined with 3D DNA walker cascade amplification. In the presence of single-stranded DNA target, the ERA process is activated to generate numerous walker strands (WS). Thereafter, Exo III-powered WSs autonomously move along magnetic bead (MB)-based 3D track to release numerous AgNCs into the supernatant as an amplified signal output. This biosensor had a low detection limit of 18 fM and an analytical range of 40 fM to 1 pM. Furthermore, the practical application potential of this biosensor was also confirmed by the spiking experiments of p53 into human serum and urine samples.

Surface plasmon resonance imaging-based biosensor for multiplex and ultrasensitive detection of NSCLC-associated exosomal miRNAs using DNA programmed heterostructure of Au-on-Ag

Exosomal miRNAs are potential tumor biomarkers for early diagnosis of non-small cell lung cancer (NSCLC). Herein, a surface plasmon resonance imaging (SPRi)-based biosensor was developed for simultaneous detection of multiplex NSCLC-associated exosomal miRNAs in a clinical sample using Au-on-Ag heterostructure and DNA tetrahedral framework (DTF). Exosomal miRNAs are captured by various DTF probes immobilized on the gold array chip. Subsequently, single-stranded DNA (ssDNA) functionalized silver nanocube (AgNC) hybridizes with the captured exosomal miRNAs and then the ssDNA-coated Au nanoparticles assembled on the surface of AgNC, forming Au-on-Ag heterostructures as essential labels to realize amplified SPR response. With the aid of DNA programmed Au-on-Ag heterostructure and DTF, the SPRi-based biosensor exhibits wide detection range from 2 fM to 20 nM, ultralow limit of detection of 1.68 fM, enhanced capture efficiency, and improved antifouling capability. Furthermore, the biosensor enables accurate discrimination of NSCLC patients based on detection results of exosomal miRNAs. Overall, this developed biosensor is a promising tool for multiplex exosomal miRNAs detection, providing a new possibility for early diagnosis of NSCLC.