Near-infrared triggered strand displacement amplification for MicroRNA quantitative detection in single living cells

A DNA octahedral amplifier for endogenous circRNA detection and bioimaging in living cells and its biomarker study

The discovery of reliable biomarkers is essential for early diagnosis, treatment, and prognosis assessment of diseases. Many research studies have shown that circRNA is a potential biomarker for diagnosis and prognosis of diseases. However, in situ monitoring circRNA in live cells is still a challenge at present, which brings a major limitation to the development and verification of circRNA as a disease biomarker. In this study, a catalytic hairpin assembly (CHA) reaction-based DNA octahedral amplifier (DOA) was developed for fluorescence resonance energy transfer (FRET) detection and bioimaging of circRNA in living cells. The DOA was first produced by self-assembling a DNA octahedron with six customized single-stranded DNAs, and two hairpins H1 (Cy3) and H2 (Cy5) were then hybridized to four vertices of the DNA octahedron. Idiopathic pulmonary fibrosis (IPF)-related circHIPK3 was used as the target. Once the CHA reaction from H1 and H2 on DOA was activated by a sequence-specific back-splice junction (BSJ) of circHIPK3, a significant FRET signal can be obtained from Cy3 to Cy5. The circHIPK3 was subsequently released to cause the next CHA reaction. Because the DOA has the advantages of the spatial-confinement effect, resistance to nuclease degradation and easy penetration into cells, rapid and excellent signal amplification FRET detection and bioimaging of endogenous circHIPK3 can be achieved in various cells. This study provides a high-precision assay platform to explore the possibility of using circRNA as a biomarker, and it is valuable for circRNA-related early diagnosis and treatment of diseases.

Ultrasound-enhanced catalytic hairpin assembly capable of ultrasensitive microRNA biosensing for the early screening of Alzheimer's disease

Catalytic hairpin assembly (CHA) is a promising enzyme-free, isothermal signal amplification strategy, but the relatively time-consuming strand replacement limits its application scenarios. Here, we developed an ultrasound-enhanced catalytic hairpin assembly (UECHA) biosensing platform for early screening of Alzheimer's disease by introducing a portable acoustic-drive platform with functionalized microspheres for effective biomarkers enrichment and fluorescence enhancement. By constructing a gradient ultrasonic field in a microcavity, the platform concentrates the functionalized microspheres in a central position, accompanied by an enhanced fluorescence signal with a specific release. In addition, the programmable frequency modulation can also modify the acoustic potential well and effectively promote non-equilibrium chemical reactions such as CHA (25 min). Compared with the conventional catalytic hairpin assembly (CHA), UECHA allows for direct and quantitative measurement of AD miRNAs down to 3.55 × 10-15 M in 1 μL samples. This visual analysis of ultra-trace biomarkers based on acoustic enrichment and promotion provides a new perspective for the rapid and highly sensitive clinical detection of Alzheimer's disease.

Stimuli-responsive probes for amplification-based imaging of miRNAs in living cells

MicroRNAs (miRNAs) have emerged as important biomarkers in biomedicine and bioimaging due to their roles in various physiological and pathological processes. Real-time and in situ monitoring of dynamic fluctuation of miRNAs in living cells is crucial for understanding these processes. However, current miRNA imaging probes still have some limitations, including the lack of effective amplification methods for low abundance miRNAs bioanalysis and uncontrollable activation, leading to background signals and potential false-positive results. Therefore, researchers have been integrating activatable devices with miRNA amplification techniques to design stimuli-responsive nanoprobes for "on-demand" and precise imaging of miRNAs in living cells. In this review, we summarize recent advances of stimuli-responsive probes for the amplification-based imaging of miRNAs in living cells and discuss the future challenges and opportunities in this field, aiming to provide valuable insights for accurate disease diagnosis and monitoring.

A Novel miRNA Detection Method Using Loop-Mediated Isothermal Amplification

A novel ligation-based loop-mediated isothermal amplification has been developed for miRNA detection. Two stem-loop structure DNA linker A/B probes which hybridized with miRNA were designed to establish a rapid and ultrasensitive miRNA-LAMP system for miRNA detection. Target miR-200a was used to template the ligation of Linker A/B probes with SplintR Ligase and used as a dumbbell-shaped amplicon. By adding BIP/FIP and Bst 2.0 DNA polymerase, the LAMP reaction was carried out, which brought greatly improved amplification efficiency. The double-stranded DNA fluorescent dye EvaGreen was added for the detection of amplification product to achieve the quantification of the target miRNA. This method can detect miRNA in a linear range of seven orders of magnitude, with a detection limit of 100 fM. Therefore, this ultrasensitive miRNA-LAMP assay provides a new path for the highly sensitive quantitative analysis of miRNA, thereby bringing convenience to clinical diagnosis and prognostic research.

In situ imaging miRNAs using multifunctional linear DNA nanostructure

The microRNAs (miRNAs) play a critical role in many biological processes and are essential biomarkers for diagnosing disease. However, the sensitive and specific quantification of microRNAs (miRNAs) expression in living cells still faces a huge challenge. Our study designed a multifunctional linear DNA nanostructure (MLN) as a carrier of molecular beacons (MB-21) for detecting and intracellular imaging miRNA-21. The MLN-MB consists of three parts: aptamer, MLN, and MB-21. The aptamer (AS1411) could media MLN-MB enter live cells without additional transfection reagents. Once inside the cells, the intracellular miRNA-21 could hybridize the MB-21s, resulting in significantly enhanced fluorescence signals. The whole process was enzyme-free, autonomous, and continuous, which avoided the necessity of adding external fuel strands or enzymes. We demonstrated that the MLN-MB could be used to screen the miRNA-21 with a detection limit of 320 pM in a short time (10 min) and show high specificity toward miRNA-21 against other miRNAs. Moreover, the proposed MLN-MB could detect the miRNA-21 in complex matrixes stably. With its outstanding stability, dual recognition, and biocompatibility, MLN-MB is capable of delivering into living cells to identify specific cancer cells. Therefore, our sensing approach, with high sensitivity, specificity, and simplicity advantages, holds great potential for early cancer diagnosis.

Electrochemiluminescence resonance energy transfer biosensing platform between g-C3N4 nanosheet and Ru-SiO2@FA for dual-wavelength ratiometric detection of SARS-CoV-2 RdRp gene

Rational detection of syndrome coronavirus 2 (SARS-CoV-2) is crucial to prevention, control, and treatment of disease. Herein, a dual-wavelength ratiometric electrochemiluminescence (ECL) biosensor based on resonance energy transfer (RET) between g-C₃N₄ nanosheets and Ru-SiO₂@folic acid (FA) nanomaterials was designed to realize ultrasensitive detection of SARS-CoV-2 virus (RdRp gene). Firstly, the unique g-C₃N₄ nanosheets displayed very intense and stable ECL at 460 nm, then the triple helix DNA was stably and vertically bound to g-C₃N₄ on electrode by high binding affinity between ssDNA and g-C₃N₄. Meanwhile, trace amounts of target genes were converted to a large number of output by three-dimensional (3D) DNA walker multiple amplification, and the output bridged a multifunctional probe Ru-SiO₂@FA to electrode. Ru-SiO₂@FA not only showed high ECL at 620 nm, but also effectively quenched g-C₃N₄ ECL. As a result, ECL decreased at 460 nm and increased at 620 nm, which was used to design a rational ECL biosensor for detection of SARS gene. The results show that the biosensor has excellent detection sensitivity for RdRp gene with a dynamic detection range of 1 fM to 10 nM and a limit of detection (LOD) of 0.18 fM. The dual-wavelength ratio ECL biosensor has inestimable value and application prospects in the fields of biosensing and clinical diagnosis.

Programmable mismatch-fueled high-efficiency DNA signal amplifier

Herein, by introducing mismatches, a high-efficiency mismatch-fueled catalytic multiple-arm DNA junction assembly (M-CMDJA) with high-reactivity and a high-threshold is developed as a programmable DNA signal amplifier for rapid detection and ultrasensitive intracellular imaging of miRNA. Compared with traditional nucleic acid signal amplification (NASA) with a perfect complement, the M-CMDJA possesses larger kinetic and thermodynamic favorability owing to the more negative reaction standard free energy (ΔG) as driving force, resulting in much higher efficiency and rates. Once traces of the input initiator react with the mismatched substrate DNA, it could be converted into amounts of output multiple-arm DNA junctions via the M-CMDJA as the functional DNA conversion nanodevice. Impressively, the mismatch-fueled catalytic four-arm DNA junction assembly (M-CFDJA) exhibits high conversion efficiency up to 1.05 × 108 in 30 min, which is almost ten times more than those of conventional methods. Therefore, the M-CMDJA could easily address the challenges of traditional methods: slow rates and low efficiency. In application, the M-CFDJA as a DNA signal amplifier was successfully used to develop a biosensing platform for rapid miRNA detection with a LOD of 6.11 aM and the ultrasensitive intracellular imaging of miRNA, providing a basis for the next-generation of versatile DNA signal amplification methods for ultimate applications in DNA nanobiotechnology, biosensing assay, and clinical diagnoses.

Mitochondria MicroRNA Spatial Imaging via pH-Responsive Exonuclease-Assisted AIE Nanoreporter

Mitochondrial microRNAs (mitomiRs) critically orchestrate mitochondrial functions. Spatial imaging of mitomiRs is essential to understand its clinical value in diagnosis and prognosis. However, the direct monitoring of mitomiRs in living cells remains a key challenge. Herein, we report an AIE nanoreporter strategy for mitomiRs imaging in living cells through pH-controlled exonuclease (Exo)-assisted target cycle signal amplification. The AIE-labeled DNA detection probes are conjugated on Exo III encapsulated polymeric nanoparticles (NPs) via consecutive adenines (polyA). The amplified sensing functions are off during the cytoplasm delivery process, and it can be spatially switched from off to on when in the alkaline mitochondria (about pH 8) after triphenylphosphonium (TPP)-mediated mitochondrial targeting. Where the NPs degraded to release Exo III and cancer-specific mitomiRs hybridize with AIE-labeled DNA detection probes to expose the cleavage site of released Exo III, enabling spatially restricted mitomiRs imaging. The mitomiRs expression fluctuation was also realized. This study contributes to a facile strategy that could easily extend to a broad application for the understanding of mitomiRs-related pathological processes.

Computer-Aided Design of DNA Self-Limited Assembly for Relative Quantification of Membrane Proteins

Immunofluorescence imaging of cells plays a vital role in biomedical research and clinical diagnosis. However, when it is applied to relative quantification of proteins, it suffers from insufficient fluorescence intensity or partial overexposure, resulting in inaccurate relative quantification. Herein, we report a computer-aided design of DNA self-limited assembly (CAD-SLA) technology and apply it for relative quantification of membrane proteins, a concept proposed for the first time. CAD-SLA can achieve exponential cascade signal amplification in one pot and terminate at any desired level. By conjugating CAD-SLA with immunofluorescence, in situ imaging of cell membrane proteins is achieved with a controllable amplification level. Besides, comprehensive fluorescence intensity information from fluorescent images can be obtained, accurately showing relative quantitative information. Slight protein expression differences previously indistinguishable by immunofluorescence or Western blotting can now be discriminated, making fluorescence imaging-based relative quantification a promising tool for membrane protein analysis. From the perspectives of both DNA self-assembly technology and immunofluorescence technology, this work has solved difficult problems and provided important reference for future development.

CRISPR/Cas12a-Triggered Chemiluminescence Enhancement Biosensor for Sensitive Detection of Nucleic Acids by Introducing a Tyramide Signal Amplification Strategy

CRISPR-based biosensors have attracted increasing attention in accurate and sensitive nucleic acid detection. In this work, we report a CRISPR/Cas12a-triggered chemiluminescence enhancement biosensor for the ultrasensitive detection of nucleic acids by introducing tyramide signal amplification for the first time (termed CRICED). The hybrid chain DNA (crDNA) formed by NH₂-capture DNA (capDNA) and biotin-recognition DNA (recDNA) was preferentially attached to the magnetic beads (MBs), and the streptavidin-HRP was subsequently introduced to obtain MB@HRP-crDNA. In the presence of the DNA target, the activated CRISPR/Cas12a is capable of randomly cutting initiator DNA (intDNA) into vast short products, and thus the fractured intDNA could not trigger the toehold-mediated DNA-strand displacement reaction (TSDR) event with MB@HRP-crDNA. After the addition of tyramine-AP and H₂O₂, abundant HRP-tyramine-AP emerges through the covalent attachment of HRP-tyramine, exhibiting enhanced chemiluminescence (CL) signals or visual image readouts. By virtue of this biosensor, we achieved high sensitivity of synthetic DNA target and amplified DNA plasmid using recombinase polymerase amplification (RPA) as low as 17 pM and single-copy detection, respectively. Our proposed CRICED was further evaluated to test 20 HPV clinical samples, showing a superior sensitivity of 87.50% and specificity of 100.00%. Consequently, the CRICED platform could be an attractive means for ultrasensitive and imaging detection of nucleic acids and holds a promising strategy for the practical application of CRISPR-based diagnostics.

Multistage Photoactivatable Zinc-Responsive Nanodevices for Monitoring and Regulating Dysfunctional Islet β-Cells

The dysfunctional islet β-cell triggered by excessive deposition of Zn²⁺ constituted a striking indicator of the occurrence of diabetic disease. However, it remained a formidable challenge to reflect the real-time function of β-cell by monitoring the Zn²⁺ content. Herein, multistage photoactivatable Zn²⁺-responsive nanodevice (denoted as AD2@USD1) was presented for sensing, regulating, and evaluating Zn²⁺ levels in dysfunctional islet β-cells. The photoactivated signatures on the satellite shell layer of the nanodevices and the internally loaded chelating factors effectively identified and intervened in the real-time concentration of Zn²⁺, the photothermal feedback component decorated on the inner core permitted the assessment of the post-intervention Zn²⁺ levels, achieving an integrated intervention and prognostic assessment in response to the abnormal islet β-cell function induced by Zn²⁺ deposition. In this way, one strategy for sensing and regulating islet β-cell function-oriented to Zn²⁺ was established. Our study introduced AD2@USD1 as a tool for effectively sensing, adjusting, and assessing the Zn²⁺ level in islet β-cells with abnormalities, gaining a potential breakthrough in the treatment of diabetes.

Label-free and highly sensitive APE1 detection based on rolling circle amplification combined with G-quadruplex

The highly sensitive detection of low-abundant apurinic/apyrimidinic endonuclease 1 (APE1) activity is of great significance for early diagnosis of disease and pathological research. Many methods for detecting APE1 based on isothermal nucleic acids amplification have been developed for improving its sensitivity. However, some of these methods have certain limitations, such as multiple reaction steps, narrow linear range, and complicated processes for fluorescent labeling. Herein, we develop a highly sensitive and label-free APE1 fluorescence detection method based on rolling circle amplification combined with G-quadruplex (RCA-G4). A hairpin probe (HP) labeled with the AP site can be recognized and cleaved by APE1, leading to the release of the primer sequence, which triggered RCA to produce long chain amplification products with a great amount of repeated sequences. The formed amplicon contains a series G-quadruplex structure, which can be combined with Thioflavin T (ThT) to produce fluorescence and achieve high sensitivity label-free detection of APE1. Benefit from the high amplification efficiency of RCA and the high fluorescence quantum yield of G-quadruplex/ThT, a detection limit as low as 1.52 × 10^-6 U/mL and the linear range from 2 × 10^-6 to 10 U/mL were obtained. The developed RCA-G4 method can be successfully used to detect APE1 in serum samples with a recovery from 96.3% to 105.7%. We believe that this approach is expected to play an important role in APE1-related disease research and drug development.

Circulating Abnormal Extracellular Vesicles: Their Mechanism for Crossing Blood-Brain Barrier, Effects on Central Nervous System and Detection Methods

Central nervous system (CNS) diseases are difficult to treat and harmful. Many CNS diseases are secondary to peripheral diseases, such as tumor brain metastases (BMS), viral infections and inflammation of the brain, and their pathogenic factors travel through the circulatory system to the brain, eventually leading to lesions. Extracellular vesicles (EVs) play an important role in this process. Recent studies have shown that, extracellular EVs can effectively cross the blood- brain barrier (BBB) through endocytosis and they transmit molecular signals in cell-to-cell communication. Abnormal EVs produced in the lesion portion transport pathogenic factors, including miRNAs, proteins, and virions into the CNS. These pathogenic factors participate in cellular pathways to interfere with homeostasis or are themselves pathogens that directly damage CNS. In addition, different or specific pathological molecules in EVs are potential disease markers. We herein reviewed pathways through which the abnormal EVs cross BBB and adverse effects of abnormal exosomes. We also and summarized their existing detection techniques, so as to provide basis for prevention and early diagnosis of secondary diseases.

Shedding Light on DNA-Based Nanoprobes for Live-Cell MicroRNA Imaging

DNA-based nanoprobes integrated with various imaging signals have been employed for fabricating versatile biosensor platforms for the study of intracellular biological process and biomarker detection. The nanoprobes developments also provide opportunities for endogenous microRNA (miRNA) in situ analysis. In this review, the authors are primarily interested in various DNA-based nanoprobes for miRNA biosensors and declare strategies to reveal how to customize the desired nanoplatforms. Initially, various delivery vehicles for nanoprobe architectures transmembrane transport are delineated, and their biosecurity and ability for resisting the complex cellular environment are evaluated. Then, the novel strategies for designing DNA sequences as target miRNA specific recognition and signal amplification modules for miRNA detection are presented. Afterward, recent advances in imaging technologies to accurately respond and produce significant signal output are summarized. Finally, the challenges and future directions in the field are discussed.

A sensing system constructed by combining a structure-switchable molecular beacon with nicking-enhanced rolling circle amplification for highly sensitive miRNA detection

A novel amplification assay strategy is developed for the highly sensitive detection of miRNA-21 based on a combination of a structure-switchable molecular beacon with nicking-enhanced rolling circle amplification.

Advances in the DNA Nanotechnology for the Cancer Biomarkers Analysis: Attributes and Applications

The most commonly used clinical methods are enzyme-linked immunosorbent assay (ELISA) and quantitative PCR (qPCR) in which ELISA was applied for the detection of protein biomarkers and qPCR was especially applied for nucleic acid biomarker analysis. Although these constructed methods have been applied in wide range, they also showed some inherent shortcomings such as low sensitivity, large sample volume and complex operations. At present, many methods have been successfully constructed on the basis of DNA nanotechnology with the merits of high accuracy, rapid and simple operation for cancer biomarkers assay. In this review, we summarized the bioassay strategies based on DNA nanotechnology from the perspective of the analytical attributes for the first time and discussed and the feasibility of the reported strategies for clinical application in the future.

Sensitive Quantification of MicroRNA in Blood through Multi-amplification Toehold-Mediated DNA-Strand-Displacement Paper-Spray Mass Spectrometry (TSD-PS MS)

Accurate quantification of disease-signature microRNAs (miRNAs) in biomedical samples is in high demand for clinical diagnosis but still challenging because of low miRNAs abundance and complicating interferences in the milieus. Here, we report a multi-amplification strategy for blood miRNAs analysis based on paper-spray mass spectrometry (PS MS). A toehold-mediated DNA-strand-displacement reaction (TSD) is employed to amplify the signal chain and to ensure the specificity. The signal chain is then cleaved by UV to release signal molecules for detection. Moreover, paper spray can efficiently filter out the interfering substances in blood and further enhances the detecting sensitivity. This concept is successfully demonstrated in the prototype detection of a cancer biomarker miRNA-141 in blood and serum. The proposed TSD-PS MS approach provides an efficient way for sensitive detection of oligonucleotides with low concentration in complicating milieus.

Soft nanoball-encapsulated carbon dots for reactive oxygen species scavenging and the highly sensitive chemiluminescent assay of nucleic acid biomarkers

The expression level of nucleic acids is closely related to a variety of diseases. Herein, a highly sensitive detection of a nucleic acid based on a CoOOH-luminol chemiluminescence (CL) system without the addition of oxidants was proposed by the toehold-mediated strand displacement reaction (TSDR) and the liposome dual signal amplification strategy with the hybrid probe formed by linking soft nanoballs (SNBs) to magnetic beads (MBs) through DNA hybridization. Inspired by the free radical scavenging effect of the as-prepared carbon dots (CDs), CDs were successfully employed to quench the CL intensity of the CoOOH-luminol system. And the CDs were further encapsulated into liposomes to construct SNBs, which avoided the complex modification of CDs to maintain their original properties, as well as loaded a large number of CDs to scavenge free radicals to achieve signal amplification. Based on this, target DNA (tDNA) could be sensitively detected based on the reduced CL intensity, which achieved a dynamic detection range from 0.1 nM to 20 nM with a limit of detection as low as 59 pM (3σ/k), showing amazing promise in the biosensing of nucleic acid biomarkers.

Ratiometric and amplified fluorescence nanosensor based on a DNA tetrahedron for miRNA imaging in living cells

Enzyme-free signal amplification approaches have attracted considerable attention in the field of intracellular miRNA analysis. However, the application of nucleic acid amplification has been limited by intracellular delivery of multiple oligonucleotide components with precise stoichiometry. In this work, we propose a new DNA tetrahedron (DTN)-based sensing platform addressing the delivery and stoichiometric control of nucleic components for enzyme-free amplification. The nanosensor is composed of two DTN probes; DTN-F served as the target recognition and signal output unit, and DTN-H served as the signal amplification unit. DTNs could facilitate the cell internalization of the nucleic acid probes and protect them from nuclease degradation. In the absence of target miRNA, the fluorescent strands (F) hybridize with the hanging sequences of DTN, and FAM and TAMRA labeled on F will be separated, blocking fluorescence resonance energy transfer (FRET). In the presence of the target miRNA, F will be displaced by the target and the hairpin structure will be restored, bringing the FRET pair into close proximity and inducing a FRET signal. Moreover, the helper strands (H) on DTN-H could liberate target miRNA through strand displacement, which will initiate a new round of reaction, generating an amplified FRET signal. The DTN nanosensor realized sensitive and selective detection of let-7a in buffer solution and 10% FBS solution. In addition, imaging of miRNA in the different cell lines and monitoring of intracellular miRNA fluctuations were carried out The developed method offers a new tool for bioanalytical and biomedical research.

Ratiometric Fluorescence Imaging of Intracellular MicroRNA with NIR-Assisted Signal Amplification by a Ru-SiO2@Polydopamine Nanoplatform

Accurate and sensitive fluorescence imaging of intracellular miRNA is essential for understanding the mechanism underlying some physiological and pathological events, as well as the prevention and diagnosis of diseases. Herein, a highly sensitive ratiometric fluorescent nanoprobe for intracellular miRNA imaging was fabricated by integrating a Ru-SiO₂@polydopamine (Ru-SiO₂@PDA) nanoplatform with a near-infrared light (NIR)-assisted DNA strand displacement signal amplification strategy. The Ru-SiO₂@PDA spheres have excellent biosafety, high photothermal effect, and unique photophysical properties that can both emit a stable red fluorescence and well quench the fluorophores getting closer to them. So, when the fuel DNA and carboxyfluorescein (FAM)-labeled signal DNA are co-assembled on their outer surfaces, the FAM's green fluorescence is quenched, and a low ratiometric signal is obtained. However, in the presence of miRNA, the target displaces the signal DNA from the capture DNA, releasing the signal DNA far away from the Ru-SiO₂@PDA. Then, the green fluorescence recovers and leads to an enhanced I_green/I_red value. Under NIR light irradiation, the Ru-SiO₂@PDA increases the local temperature around the probe and triggers the release of fuel DNA, which thus recycles the target miRNA and effectively amplifies the ratiometric signal. Using A549 cells as a model, the nanoprobe realizes the highly sensitive ratiometric fluorescence imaging of miRNA let-7a, as well as its in vivo up- and down-regulation expressions. It provides a facile tool for highly sensitive and accurate intracellular miRNA detection through one-step incubation and may pave a new avenue for single-cell analysis.

Near-Infrared Light Controllable DNA Walker Driven by Endogenous Adenosine Triphosphate for in Situ Spatiotemporal Imaging of Intracellular MicroRNA

As a powerful signal amplification tool, the DNA walker has been widely applied to detect rare microRNA (miRNA) in vivo. Despite the significant advances, a near-infrared (NIR) light controllable DNA walker for signal amplification powered by an endogenous initiator has not been realized, which is crucial for spatiotemporal imaging of miRNA in living cells with high sensitivity. Herein, we constructed a NIR-photoactivatable DNA walker system, which was powered by endogenous adenosine triphosphate (ATP) for in situ miRNA imaging with spatial and temporal resolution. The system was very stable with an extremely low fluorescent background for the bioimaging in living cells. We employed upconversion nanoparticles (UCNPs) as the carriers of the DNA probe and transducers of converting NIR to UV light. Coupled with the DNA walker fueled by intracellular ATP, a smart system based on the NIR light initiated DNA walker was successfully developed for precise spatiotemporal control in living cells. Triggered by NIR light, the DNA walker could autonomously and progressively travel along the track with the assistance of intracellular ATP. The system has been successfully applied for in situ miRNA imaging in different cell lines with highly spatial and temporal resolution. This strategy can expand NIR photocontrol the DNA walker for precise imaging in a biological system.

Self-assembled nanomaterials for biosensing and therapeutics: recent advances and challenges

Self-assembled nanomaterials (SANs) exhibit designable biofunctions owing to their tunable nanostructures and modifiable surface. Various constituent units and multi-dimensional structures of SANs provide unlimited possibilities for numerous applications. This review emphasizes the recent development of SANs in the fields of biosensing, bioimaging, and nano-drug engineering. The unit type, design concepts, material advantages, assembly driving force, nanostructure effects, drug loading performance, etc. are discussed and summarized. Finally, we briefly summarize how to assemble unique nanomaterials and point out the key challenges in this field.

MnO2 nanosheet-mediated target-binding-induced FRET strategy for multiplexed microRNAs detection and imaging in living cells

In the regulatory network, miRNAs play a regulatory role in a cooperative or antagonistic manner. Simultaneous accurate detection and imaging of multiplexed miRNAs in living cells are of great significance for miRNA-associated biological research and disease diagnosis and treatment. Herein, a MnO₂ nanosheet-mediated target-binding-induced fluorescence resonance energy transfer (FRET) strategy was developed for detection and imaging of multiplexed miRNAs in living cells. Two pairs of DNA probes (P1-AF 488/P1'-Cy3 and P2-AF 488/P2'-AF 594) contained the complementary sequence to target miRNAs (miRNA-373 and miRNA-96) and labelled with different fluorescence dyes were designed. They were adsorbed onto MnO₂ nanosheets by physisorption to form DNA/MnO₂ nanocomposite probes. When the DNA/MnO₂ nanocomposite probes were taken up by cells, the MnO₂ nanosheets were reduced by intracellular glutathione, accompanying the release of DNA probe pairs. Then the DNA probe pairs specifically recognized and combined with miRNA-373 and miRNA-96 to form stable duplexes, respectively, bringing labelled fluorophores into close proximity to occur FRET. Based on this, the simultaneous imaging of miRNA-373 and miRNA-96 in MDA-MB-231 and L02 cells was successfully implemented. The results displayed a higher expression level of target miRNAs in MDA-MB-231 cells compared to L02 cells. The changes in expression levels of miRNA-96 induced by anti-miRNA-96 or mimics in MDA-MB-231 cells could also be monitored. In addition, the ratiometric detections of multiplexed miRNAs were achieved by utilizing the DNA probe pairs. The proposed strategy provides an alternative method for simultaneous accurate detection and imaging of multiplexed miRNAs and has potential application in biomedical applications.

Flexible paper-based label-free electrochemical biosensor for the monitoring of miRNA-21 using core-shell Ag@Au/GQD nano-ink: a new platform for the accurate and rapid analysis by low cost lab-on-paper technology

miRNA-21 is one of the most famous and prominent microRNAs that is important in the development and emergence of cancers. So, the sensitive and selective monitoring of miRNA-21 as a very common biomarker in cancer treatment is necessary. In this work, a novel paper-based electrochemical peptide nucleic acid (PNA) sensor was developed for the detection of miRNA-21 in human plasma samples by using Ag@Au core-shell nanoparticles electrodeposited on graphene quantum dots (GQD) conductive nano-ink (Ag@Au core-shell/GQD nano-ink), which was designed directly by writing pen-on paper technology on the surface of photographic paper. This nano-ink has a great surface area for biomarker immobilization. The prepared paper-based biosensor is very small and cheap, and also has high stability and sensitivity. Hybridization of PNA was measured using various electrochemical techniques, such as cyclic voltammetry (CV), square wave voltammetry (SWV) and chronoamperometry (ChA). FE-SEM (Field Scanning Electron Microscope), TEM (Transmission Electron Microscope), EDS and DLS (Dynamic Light Scattering) tests were performed to identify the engineering safety sensor. Under optimal conditions, the linear range for the calibration curve was from 5 pM to 5 μM, and the achieved LLOQ was 5 pM. The obtained results recommended that the proposed bioassay might be suitable for an early diagnosis of cancer based on the inhibition of the expression of miRNA-21, which activates the enzyme caspase and accelerates apoptotic proteins and death in tumor cells.

A controlled T7 transcription-driven symmetric amplification cascade machinery for single-molecule detection of multiple repair glycosylases

Genomic oxidation and alkylation are two of the most important forms of cytotoxic damage that may induce mutagenesis, carcinogenicity, and teratogenicity. Human 8-oxoguanine (hOGG1) and alkyladenine DNA glycosylases (hAAG) are responsible for two major forms of oxidative and alkylative damage repair, and their aberrant activities may cause repair deficiencies that are associated with a variety of human diseases, including cancers. Due to their complicated catalytic pathways and hydrolysis mechanisms, simultaneous and accurate detection of multiple repair glycosylases has remained a great challenge. Herein, by taking advantage of unique features of T7-based transcription and the intrinsic superiorities of single-molecule imaging techniques, we demonstrate for the first time the development of a controlled T7 transcription-driven symmetric amplification cascade machinery for single-molecule detection of hOGG1 and hAAG. The presence of hOGG1 and hAAG can remove damaged 8-oxoG and deoxyinosine, respectively, from the dumbbell substrate, resulting in breaking of the dumbbell substrate, unfolding of two loops, and exposure of two T7 promoters simultaneously. The T7 promoters can activate symmetric transcription amplifications with the unfolded loops as the templates, inducing efficient transcription to produce two different single-stranded RNA transcripts (i.e., reporter probes 1 and 2). Reporter probes 1 and 2 hybridize with signal probes 1 and 2, respectively, to initiate duplex-specific nuclease-directed cyclic digestion of the signal probes, liberating large amounts of Cy3 and Cy5 fluorescent molecules. The released Cy3 and Cy5 molecules can be simply measured by total internal reflection fluorescence-based single-molecule detection, with the Cy3 signal indicating the presence of hOGG1 and the Cy5 signal indicating the presence of hAAG. This method exhibits good specificity and high sensitivity with a detection limit of 3.52 × 10-8 U μL-1 for hOGG1 and 3.55 × 10-7 U μL-1 for hAAG, and it can even quantify repair glycosylases at the single-cell level. Moreover, it can be applied for the measurement of kinetic parameters, the screening of potential inhibitors, and the detection of repair glycosylases in human serum, providing a new paradigm for repair enzyme-related biomedical research, drug discovery, and clinical diagnosis.

MNAzyme probes mediated DNA logic platform for microRNAs logic detection and cancer cell identification

Here, a MNAzyme probes mediated DNA logic platform was developed for microRNAs (miRNAs) logic detection and cancer cells identification. A series of MNAzyme probes containing the cleavage active center were designed. Four types of logic gates were constructed, including YES, AND, XOR and NOR gate. These logic gates used miRNAs that were high expression in cancer cells as logic inputs and used MNAzyme cleavage amplification reaction to output signals. For the construction of intracellular logic gates, MnO₂ nanosheets were used as carriers and cofactor providers. When MnO₂ nanoprobes entered the cells through endocytosis, the intracellular glutathione degraded the MnO₂ nanosheets to release the cofactor Mn²⁺ and MNAzyme probes. The MNAzyme probes bound to the miRNAs and catalyze the MNAzyme cleavage amplification reaction, producing enhanced fluorescent signal with "true" output. The logic detection of miRNAs was achieved by integrating information from the AND, XOR and NOR logic gates. Moreover, through the construction of intracellular YES and AND logic gates, the cancer cells identification, especially the identification of same type of cancer cells with different phenotypes was achieved. These experimental results showed that this platform held great promise in accurate diagnosis and treatment of cancer.

NIR Light-Propelled Janus-Based Nanoplatform for Cytosolic-Fueled microRNA Imaging

Various nanoplatforms have been developed to visualize intracellular microRNAs (miRNAs) because of their clinical significance in tumor progression and diagnosis. However, the diffusion-limited motion of the nanoplatforms penalizes the miRNA imaging efficiency in cells. Herein, we fabricated a near-infrared (NIR) light-propelled Janus-based nanoplatform to advance the imaging response. The Janus nanomotor covered with an Au half-shell was loaded by the endocytosis adjuvant of the MnO₂ nanosheet for delivering a miRNA-responsive hQN (hairpin DNA quadrangular nanostructure) probe with a catalyzed hairpin assembly (CHA). Once the nanoplatform entered into cells, the MnO₂ nanosheet was degraded to Mn²⁺ by endogenous fuels (such as glutathione) to release the hQN probe. The NIR light irradiation of the nanoplatform generated a heat gradient and thus propelled motion of the nanoplatform. This process accelerated the intracellular reaction of the hQN probe with miRNAs to trigger the cascade CHA amplification with an enhanced fluorescence readout.

Target-Cell-Specific Bioorthogonal and Endogenous ATP Control of Signal Amplification for Intracellular MicroRNA Imaging

A stringent signal amplification method to profile microRNA (miRNA) expression within a specific cell remains a key challenge in biology. To address this issue, we report a target-cell-specific DNA nanosystem for endogenous adenosine-5'-triphosphate (ATP) bioorthogonal activation of the hybridization chain reaction (HCR) to spatiotemporally controlled signal amplification detection of miRNA in vitro and in vivo. The system consists of ATP aptamer-sealed engineered HCR functional units combined with a cancer cell membrane-encapsulated glutathione (GSH)-responsive metal-organic framework (MOF). Once the nanosystem is specifically and efficiently internalized into a cancer cell through membrane-mediated homing targeting, the MOF structure degrades and releases HCR functional units. The endogenous high expressional ATP recognizes the aptamer, allowing the HCR functional units to adopt its active modality. The activated HCR functional units are then able to spatiotemporally and bioorthogonally image miRNA with high sensitivity in vitro and in vivo.

Novel Luminescent Nanostructured Coordination Polymer: Facile Fabrication and Application in Electrochemiluminescence Biosensor for microRNA-141 Detection

A series of novel luminescent nanostructured coordination polymers (Ce-Ru-NCPs) with tunable morphologies have been successfully synthesized on a large scale at room temperature by a facile and rapid solution-phase method using Ce³⁺ and tris(4,4'-dicarboxylicacid-2,2'-bipyridyl) ruthenium(II) dichloride (Ru(dcbpy)₃²⁺). Among them, the flowerlike Ce-Ru-NCP shows good cathodic electrochemiluminescence (ECL) characteristics. The ECL efficiency of the Ce-Ru-NCP/S₂O₈^2- system is about 2.34 times that of the classic tris(2,2'-bipyridyl) ruthenium(II) dichloride/S₂O₈^2- (Ru(bpy)₃²⁺/S₂O₈^2-) system. Hence, we report a sensitive ECL biosensor for microRNA-141 (miRNA-141) detection based on the flowerlike Ce-Ru-NCP as a cathodic ECL luminophore and a bipedal three-dimensional (3D) DNA walking machine as a signal amplifier. Through the bipedal 3D DNA walking machine, trace targets can be converted to substantial secondary targets (marked with the quencher dopamine), and a significant quenching effect on the ECL signal is achieved. As a result, the proposed biosensor exhibits a relatively good sensitivity for miRNA-141 detection and shows a dynamic range from 1.0 × 10^-16 to 1.0 × 10^-6 mol·L^-1 with a limit of detection (LOD) of 33 amol·L^-1 (S/N = 3). The Ce-Ru-NCP with tunable morphologies and high ECL efficiency, intensity, and stability possesses potential applications in ECL analysis.

Reverse transcription-based loop-mediated isothermal amplification strategy for real-time miRNA detection with phosphorothioated probes

A novel reverse transcription-based loop-mediated isothermal amplification (LAMP) strategy for miRNA detection has been developed. This method consists of two stem-loop probes inspired by the dumbbell-shaped amplicons and inner primers used in conventional LAMP reactions. Termed "terminal hairpin formation and self-priming" (THSP), this reaction incorporates phosphorothioated (PS) modifications to achieve DNA folding and extension without primers. The final signal is monitored by a sequence-specific detection probe, which minimizes the background noise. We suggest that our rapid, facile, and reliable LAMP method will be a promising candidate for detecting miRNA in biomedical applications.

Multi-Dimensionally Extended Functionalization Innovates to an Entropy-Driven Detection of Multi-miRNAs for One-Step Cancer Screening and Diagnosis in Living Cells

Compared with tedious multi-step detections, multi-functional nanoprobes are effective for one-step screening and diagnosis of cancers by multi-detection of microRNAs (miRNAs). However, limited probe density, spatial mutual interference, and low target-triggered hybridization efficiency of nanoprobes will hinder intracellular applications. Here, for obtaining high loading density but low spatial mutual interference between functional biomolecules on nanoprobes, an extended biofunctionalization in three dimensions (the two-dimensional surface and a special "height" direction) is designed. Therefore, a multi-functional probe is constructed for one-step detection of multi-miRNAs for cancer screening and diagnosis. With linker-bridged multiple single-stranded DNAs swung out rigidly, multi-dimensionally extended upconversion nanorods (ME-UCNRs) covered by chitosan are constructed to load and deliver multiple biomolecules into living cells. Escaping from endolysosomes, ME-UCNRs maintain good biological activities of functionalized DNAs for effective detection of multi-miRNAs in living cells. Thereby, with multiple targets of miRNAs, toehold-mediated entropy-driven strand displacements are employed to give respectively changed fluorescent signals via fluorescence resonance energy transfer. Thus, a universal cancer biomarker of miR-21 and two specific liver-cancer biomarkers (miR-199a and miR-224) are efficiently detected through a one-step detection. By discriminating cancer cells from normal ones and determining liver-cancer cells simultaneously, this work innovates an efficient and definite one-step strategy for fast screening and early cancer diagnosis.

Autophagy regulation by microRNAs: Novel insights into osteosarcoma therapy

Osteosarcoma (OS) is a kind of primary bone cancer that is considered as the leading cause of children death. Surgery and chemotherapy are considered as common treatment approaches for OS; the rate of survival for patients is almost 60-70%. Besides the used therapeutic approaches, it seems that there is a crucial need to launch new treatments for OS. In this regard, more understanding about cellular and molecular pathways involved in OS can contribute to recovery and develop new therapeutic platforms. Autophagy is a cellular machinery that digests and degrades dysfunctional proteins and organelles, so it can regulate the cell proliferation and survival. Most of the time, OS cells use autophagy to increase their survival and proliferation and to gain the ability to resist chemotherapy. Although, there are several controversial evidences on how OS cells use autophagy. A variety of cellular and molecular pathways, that is, microRNAs (miRNAs) can modulate autophagy. MiRNAs are some endogenous, approximately 22 nucleotide RNAs that have an important role in posttranscriptional regulation of mRNAs by targeting them. There are many evidences that the various miRNA expressions in OS cells are dysregulated, so it can propel a normal cell to cancerous one by influencing the cell survival, apoptosis, and autophagy, and eventually increased chemoresitance. Hence, miRNAs can be considered as new biomarkers for OS diagnosis, and according to the role of autophagy in OS progression, miRNAs can use inhibiting or promoting autophagy agents. The present review summarizes the effects of aberrant expression of miRNAs in OS diagnosis and treatment with focus on their roles in autophagy.

Fluorescent dye nano-assemblies by thiol attachment directed to the tips of gold nanorods for effective emission enhancement

The conjugation of dye-labelled DNA oligonucleotides with gold nanorods has been widely explored for the development of multifunctional fluorescent nanoprobes. Here, we show that the functionalization route is crucial to achieve enhanced emission in dye nano-assemblies based on gold nanorods. By using a tip-selective approach for thiol attachment of dye molecules onto gold nanorods, it was possible to effectively increase the emission by more than 10-fold relatively to that of a free dye. On the other hand, a non-selective approach revealed that indiscriminate surface functionalization has a detrimental effect on the enhancement. Simulations of discrete dipole approximation gave further insight into the surface distribution of plasmon-enhanced emission by confirming that tip regions afford an effective enhancement, while side regions exhibit a negligible effect or even emission quenching. The contrast between dye nano-assemblies obtained from tip- and non-selective functionalization was further characterized by single-particle fluorescence emission. These studies showed that tip-functionalized gold nanorods with an average of only 30 dye molecules have a comparable to or even stronger emission than non-selectively functionalized particles with approximately 10 times more dye molecules. The results herein reported could significantly improve the performance of dye nano-assemblies for imaging or sensing applications.

Environment-Recognizing DNA-Computation Circuits for the Intracellular Transport of Molecular Payloads for mRNA Imaging

Programming intelligent DNA nanocarriers for the targeted transport of molecular payloads in living cells has attracted extensive attention. In vivo activation of these nanocarriers usually relies on external light irradiation. An interest is emerging in the automatic recognition of intracellular surroundings by nanocarriers and their in situ activation under the control of programmed DNA-computation circuits. Herein, we report the integration of DNA circuits with framework nucleic acid (FNA) nanocarriers that consist of a truncated square pyramid (TSP) cage and a built-in duplex cargo containing an antisense strand of the target mRNA. An i-motif and ATP aptamer embedded in the TSP are employed as logic-controlling units to respond to H⁺ and ATP inside cellular compartments, triggering the release of the sensing element for fluorescent mRNA imaging. Logic-controlled FNA devices could be used to target drug delivery, enabling precise disease treatment.

A self-powered 3D DNA walker with programmability and signal-amplification for illuminating microRNA in living cells

We construct a target-triggered, self-powered 3D DNA walker for achieving intracellular signal amplification and sensitive imaging analysis of microRNAs.

Sensitive and enzyme-free fluorescence polarization detection for miRNA-21 based on decahedral sliver nanoparticles and strand displacement reaction

A highly sensitive method for miRNA-21 detection has been developed, which relied on the principle of strand displacement reaction to achieve asymmetric signal amplification and combined with the enhanced effect of Ag₁₀NPs.

An intramolecular catalytic hairpin assembly on a DNA tetrahedron for mRNA imaging in living cells: improving reaction kinetics and signal stability

Enzyme-free amplification techniques based on dynamic DNA self-assembly (DDSA) have recently been developed for the in situ detection of mRNA in living cells. However, signal generation in traditional DDSA amplifiers is mainly dependent on the random diffusion of dissociative probes in a bulk solution, which is generally accompanied by poor kinetics and interference from complex biological systems. In this work, a new amplifier based on the design of an intramolecular catalytic hairpin assembly (intra-CHA) is proposed for the FRET imaging of mRNA in living cells. Compared with that in the free catalytic hairpin assembly (free-CHA), probes H1 and H2 in intra-CHA were simultaneously fixed on a DNA tetrahedron. The distance between them was closer, the local concentration of H1 and H2 in intra-CHA was theoretically approximately 808-times higher than that in free-CHA, and the initial reaction rate was enhanced 15.6 fold. Due to the spatial confinement effect, the reaction kinetics for target-catalyzed signal generation were significantly improved. By virtue of the three-dimensional nanostructure, H1 and H2 in the intra-CHA amplifier entered cells without any transfection or nanocarrier, and the probes and their products were free from biological interference, providing much higher signal stability for the reliable imaging of mRNA in living cells.

An intramolecular catalytic hairpin assembly is implemented on a DNA tetrahedron for mRNA imaging in living cells. The spatial confinement effect enables the acceleration of target-triggered signal generation, with excellent cell permeability and FRET signal stability.

Dandelion flower-like micelles

Dandelion flower-like micelles (DFMs) were prepared by self-assembly of polycaprolactone (PCL) functionalized surface cross-linked micelles (SCMs). Upon reductive stimuli, the SCMs can be released from the DFMs by non-Brownian motion at an average speed of 19.09 μm s-1. Similar to the property of dandelion flowers dispersing their seeds over a long distance, the DFMs demonstrated enhanced multicellular tumor spheroid (MTS) penetration, a useful property in the treatment of many diseases including cancer, infection-of-biofilm diseases and ocular problems.