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

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

Spatiotemporal control of DNAzyme activity for fluorescent imaging of telomerase RNA in living cells.

BACKGROUND: Human telomerase is a ribonucleoprotein complex that includes proteins and human telomerase RNA (hTR). Emerging evidence suggested that the expression level of hTR was high related with the development of tumor, so it is important to accurately detect the content of hTR. Optical control of DNAzyme activity shows a promising strategy for precise biosensing, biomedical imaging and modulation of biological processes. Although DNAzyme-based sensors can be controlled spatiotemporally by light, its application in the detection of hTR in living cells is still rare. Therefore, designing DNAzyme activity spatiotemporal controllable sensors for hTR detection is highly needed. RESULTS: We developed a UV light-activated DNAzyme-based nanoprobe for spatially accurate imaging of intracellular hTR. The proposed nanoprobe was named MDPH, which composed of an 8-17 DNAzyme (D) inactivated by a protector strand (P), a substrate strand (H), and MnO2 nanosheets. The MnO2 nanosheets can enhance the cellular uptake of DNA strands, so that MDPH probe can enter cells autonomously through endocytosis. Under the high concentration of GSH in cancer cells, MnO2 nanosheets can self-generate cofactors to maintain the catalytic activity of DNAzyme. When exposing UV light and in presence of target hTR, DNAzyme could cleave substrate H, resulting in the recovery of fluorescence of the system. The cells imaging results show that MDPH probe could be spatiotemporally controlled to image endogenous hTR in cancer cells. SIGNIFICANCE: With this design, telomerase RNA-specific fluorescent imaging was achieved by MDPH probe in both cancer and normal cells. Our probe made a promising new platform for spatiotemporal controllable intracellular hTR monitoring. This current method can be applied to monitor a variety of other biomarkers in living cells and perform medical diagnosis, so it may has broad applications in the field of medicine.

DNA Dendrimer-Based Directed 3D Walking Nanomachine for the Sensitive Detection and Intracellular Imaging of miRNA.

Taking advantage of the remarkable processivity and membrane penetrability, the gold nanoparticle (AuNP)-based three-dimensional (3D) DNA walking nanomachine has induced tremendous promise in molecular diagnostics and cancer therapy, whereas the executive ability of this nanomachine was eventually limited because of the disordered assembly between the walker and the track. Therefore, we developed a well-directed 3D DNA walking nanomachine by employing a DNA dendrimer as the track for intracellular imaging with high directionality and controllability. The nanomachine was constructed on a DNA dendrimer decorated with a substrate strand serving as the DNA track and a DNAzyme restrained by a locking strand as the walker. In this system, the distribution of the substrate strand and DNAzyme on the DNA dendrimer could be precisely regulated to achieve expected goals because of the specificity and predictability of the Watson-Crick base pairing, paving an explicit route for each walker to move along the track. Moreover, such a DNA dendrimer-based nanomachine owned prominent stability and anti-interference ability. By choosing microRNA-21 as a model analyte, the nanomachine was applied for the imaging of microRNA-21 in different cell lines and the monitoring of the dynamic microRNA-21 expression level in cancer cells. Therefore, we believe that this directed DNA walking nanomachine will have a variety of applications in molecular diagnostics and biological function modulation.

Split-aptamer mediated regenerable temperature-sensitive electrochemical biosensor for the detection of tumour exosomes.

In this paper, a split-aptamer mediated regenerable temperature-sensitive (SMRT) electrochemical biosensor was constructed for the detection of exosomes. The split-aptamer used in this SMRT biosensor was composed of two fragments, one of which was immobilized on the surface of an electrode via sulfhydryl groups and named split-a and the other was labelled with methylene blue and named split-b. The two fragments could form sandwich structures at the electrode surface via target-induced self-assembly in the presence of target exosomes at 4 °C in PBS, and then realizing the detection of exosomes via voltammetry. In addition, due to the temperature sensitivity of the split-aptamer, the electrode could be regenerated through temperature-induced disassembly of the sandwich structures. Consequently, the SMRT biosensor realized sensitive and specific analysis of target exosomes with a limit of detection of 1.5 × 106 particles/mL and could be quickly and easily regenerated by washing with PBS at 37 °C for 30 s without any additives. This is the first study on the construction of a reproducible electrochemical biosensor using a split-aptamer for the specific detection of tumour exosomes, and may provide an innovative strategy for the economical and efficient design of regenerable electrochemical biosensors.

Multivalent self-assembled nano string lights for tumor-targeted delivery and accelerated biomarker imaging in living cells and in vivo.

Highly efficient monitoring of microRNA is of great significance for cancer research. By attaching aptamers to DNA nanowires through base pairing, here we designed a multivalent self-assembled DNA nanowire for fast quantification of intracellular target miRNAs in special cancer cells. In this work, an aptamer AS1411 and a microRNA-21 anti-sequence labeled with Cy5 were fixed on DNA nanowires, and then a short DNA strand with black hole quencher 2 (BHQ2) hybridizes with the microRNA-21 anti-sequence to quench Cy5. With the aid of AS1411, the probe can recognize and enter the target special cells efficiently. In addition, because of the banding between microRNA-21 and microRNA-21 anti-sequence, short DNA strands with BHQ2 are detached from the DNA nanowire and result in the recovery of Cy5 fluorescence signals. Ultimately, the fluorescence of Cy5 was activated quickly due to the high local concentration of recognition units on the nanowire, resulting in a large number of activated Cy5 dyes in a short time just like DNA nano string lights. Experimental results revealed that the designed DNA nanowire probe shows great performance for specifically and quickly monitoring microRNA-21 in living cells and in vivo. This developed strategy may become a general platform for detecting targets in living cells and possess great potential for biological and diagnostic research.

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

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

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

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

Near-infrared inorganic nanomaterial-based nanosystems for photothermal therapy.

The development of robust materials for treating diseases through non-invasive photothermal therapy (PTT) has attracted increasing attention in recent years. Among various types of nanomaterials, inorganic nanomaterials with strong absorption in the near-infrared (NIR) window can be employed as high-efficiency photothermal agents to treat cancer and bacterial infections. In addition, inorganic nanomaterials can be easily combined with other drugs or chemical reagents to construct multifunctional nanomaterials to cascade stimulation responses, enhance therapeutic effects, and perform precise medical treatments. In this review, focusing on the latest developments of inorganic nanomaterials in photothermal therapy, we firstly introduced the light-to-heat conversion mechanism of inorganic nanomaterials. Secondly, we summarized the application of common inorganic nanomaterials, such as metallic nanoparticles, transition metal oxide nanoparticles and two dimensional (2D) nanosheets. In addition, the strategy of developing multifunctional nano-platforms with excellent biocompatibility as well as good targeted capability was also expounded. Finally, challenges and new perspectives for designing effective inorganic nanomaterial-based nanosystems for photothermal assisted therapy were also discussed.

Zinc-Based Metal-Organic Frameworks in Drug Delivery, Cell Imaging, and Sensing.

The design and structural frameworks for targeted drug delivery of medicinal compounds and improved cell imaging have been developed with several advantages. However, metal-organic frameworks (MOFs) are supplemented tremendously for medical uses with efficient efficacy. These MOFs are considered as an absolutely new class of porous materials, extensively used in drug delivery systems, cell imaging, and detecting the analytes, especially for cancer biomarkers, due to their excellent biocompatibility, easy functionalization, high storage capacity, and excellent biodegradability. While Zn-metal centers in MOFs have been found by enhanced efficient detection and improved drug delivery, these Zn-based MOFs have appeared to be safe as elucidated by different cytotoxicity assays for targeted drug delivery. On the other hand, the MOF-based heterogeneous catalyst is durable and can regenerate multiple times without losing activity. Therefore, as functional carriers for drug delivery, cell imaging, and chemosensory, MOFs' chemical composition and flexible porous structure allowed engineering to improve their medical formulation and functionality. This review summarizes the methodology for fabricating ultrasensitive and selective Zn-MOF-based sensors, as well as their application in early cancer diagnosis and therapy. This review also offers a systematic approach to understanding the development of MOFs as efficient drug carriers and provides new insights on their applications and limitations in utility with possible solutions.

Aptamer-based fluorescent sensors for the detection of cancer biomarkers.

Aptamers are short single-stranded RNA or DNA molecules that can recognize a series of targets with high affinity and specificity. Known as "chemical antibodies", aptamers have many unique merits, including ease of chemical synthesis, high chemical stability, low molecular weight, lack of immunogenicity, and ease of modification and manipulation compared to their protein counterparts. Using aptamers as the recognition groups, fluorescent aptasensors provide exciting opportunities for sensitive detection and quantification of analytes. Herein, we give an overview on the recent development of aptamer-based fluorescent sensors for the detection of cancer biomarkers. Based on various nanostructured sensor designs, we extended our discussions on sensitivity, specificity and the potential applications of aptamer-based fluorescent sensors in early diagnosis, treatment and prognosis of cancers.

A DNAzyme-based label-free fluorescent probe for guanosine-5'-triphosphate detection.

Guanosine-5'-triphosphate (GTP) plays a key role in many important biological processes of cells. It is not only a primer for DNA replication and one of the four essential nucleoside triphosphates for mRNA synthesis, but also an energy source for translation and other important cellular processes. It can be converted to adenine nucleoside triphosphate (ATP), and the intracellular GTP level is closely related to the specific pathological state, so it is crucial to establish a simple and accurate method for the detection of GTP. Deoxyribozymes have unique catalytic and structural properties. One of the deoxyribozymes which is named DK2 with self-phosphorylation ability can transfer a phosphate from GTP to the 5' end in the presence of manganese(ii), while lambda exonuclease (λexo) catalyzes the gradual hydrolysis of double-stranded DNA molecules phosphorylated at the 5'-end from 5' to 3', but cannot cleave the 5'-OH end. The fluorescent dye SYBR Green I (SG I) can bind to dsDNA and produce significant fluorescence, but it can only give out weak fluorescence when it is mixed with a single strand. Here, we present a novel unlabeled fluorescence assay for GTP based on the self-phosphorylation of deoxyribozyme DK2 and the specific hydrolysis of λexo. Owing to the advantages of simple operation, high sensitivity, good specificity, low cost and without fluorophore (quenching group) labeling, this method has great potential in biological applications.

Recognition triggered assembly of split aptamers to initiate a hybridization chain reaction for wash-free and amplified detection of exosomes.

Here, we develop a facile split aptamer-based system for the amplified, specific and wash-free detection of exosomes in situ assisted by a target-induced hybridization chain reaction (HCR). This design was successfully used to detect target exosomes in a bio-matrix and distinguish cancer patients from healthy individuals.

Aptamer-Functionalized DNA Nanostructures for Biological Applications.

DNA nanostructures hold great promise for various applications due to their remarkable properties, including programmable assembly, nanometric positional precision, and dynamic structural control. The past few decades have seen the development of various kinds of DNA nanostructures that can be employed as useful tools in fields such as chemistry, materials, biology, and medicine. Aptamers are short single-stranded nucleic acids that bind to specific targets with excellent selectivity and high affinity and play critical roles in molecular recognition. Recently, many attempts have been made to integrate aptamers with DNA nanostructures for a range of biological applications. This review starts with an introduction to the features of aptamer-functionalized DNA nanostructures. The discussion then focuses on recent progress (particularly during the last five years) in the applications of these nanostructures in areas such as biosensing, bioimaging, cancer therapy, and biophysics. Finally, challenges involved in the practical application of aptamer-functionalized DNA nanostructures are discussed, and perspectives on future directions for research into and applications of aptamer-functionalized DNA nanostructures are provided.

DNA Amplifier-Functionalized Metal-Organic Frameworks for Multiplexed Detection and Imaging of Intracellular mRNA.

DNA amplification is a useful technique for low-abundance biomarker detection and environmental monitoring because of its high signal-amplifying ability. However, intracellular application of DNA amplifiers remains challenging due to poor delivery efficiency and stability. Herein, we report an entropy-driven DNA amplifier-functionalized metal-organic framework (DNA amplifier-MOF) for the detection and imaging of multiple intracellular messenger RNAs (mRNAs). The DNA amplifier-MOF conjugate exhibits high cellular uptake, enhanced enzymatic stability, and good biocompatibility. Importantly, in the presence of phosphate ions, a surface-functionalized DNA amplifier can be released in cells with high efficiency, which facilitates the imaging of mRNA. This method is rapid and of high sensitivity/specificity, as validated in HepG2 and HL7702 cells for the imaging of TK1 and survivin mRNA, respectively. With further optimization, the strategy can become a powerful biotechnology tool for the detection of cancers at early stages and for elucidating biological processes.

Structure-switching aptamer triggering hybridization displacement reaction for label-free detection of exosomes.

Exosomes play important roles in intercellular communications, tumor migration and invasion. However, the specific detection of cancer exosomes remains as a big challenge due to its low concentration in biofluids. Therefore, the sensitive and selective detection of cancer cells-derived exosomes has attracted growing attention owing to their potential in diagnostic and prognostic applications. Activatable strategies have received great attention for the detection of low abundant analytes due to their high sensitivity. Herein, based on molecular recognition between DNA aptamer and exosome surface biomarker (protein tyrosine kinase-7), a novel activatable and label-free strategy was designed for highly sensitive and specific sensing of exosomes. In this work, the target exosomes trigger strand replacement reaction to form G-quadruplex, which result in an obvious fluorescence enhancement of N-methylmesoporphyrin IX due to the bonding between G-quadruplex and N-methylmesoporphyrin IX. Under the optimum experimental conditions, the linear range for exosomes was measured to be 5.0 × 105-5.0 × 107 particles/µL and the detection limit (LOD) was calculated to be 3.4 × 105 particles/µL (3σ). This assay possesses high specificity to distinguish exosomes derived from different cell lines, and has successfully been validated in patient and healthy plasma samples. Furthermore, the probe can effectively detect the exosomes in 30% fetal bovine serum, indicating that the biological matrix has a negligible effect on this method. This developed label-free, convenient and highly sensitive biosensor will offer a great opportunity for exosomes quantification in biological study and clinical application.

"Apollo Program" in Nanoscale: Landing and Exploring Cell-Surface with DNA Nanotechnology.

Plasma membranes are the fundamental mediators through which cells communicate with their surrounding environment. The techniques to monitor or synthetically manipulate the cell membranes are attractive tools to engineer the functions of cells as well as their local microenvironment. Current advances of biomolecular science enable the insertion of functional compounds onto cell-surface via external integration or genetic engineering to manipulate cell membrane function. Recently, the DNA nanotechnology made it possible to use synthetic DNA as an emerging and promising molecular toolkit for anchoring and exploring cell-surface. In this review, the latest advances of DNA nanotechnology on cell-surface are summarized. We first give an overview of commonly used strategies for installing DNA nanodevices onto cell-surface including amphiphilic interaction, covalent modification, and affinity labeling. Then the biological applications of DNA nanodevices on cell membranes are reviewed. By integrating functional nucleic acids as recognition elements, DNA sensors are fabricated to monitor the cellular microenvironment and membrane activities. In addition, the programmable behaviors of DNA on cell-surface are also discussed, which include biomimicry and the regulation of membrane functions. Finally, we analyze the current challenges in the development of DNA nanotechnology on cell-surface as well as their prospects in bioimaging and cancer therapy.

Accelerated DNAzyme-based fluorescent nanoprobe for highly sensitive microRNA detection in live cells.

By assembling DNAzyme on DNA nanowires through DNA hybridization, we have developed a novel accelerated DNAzyme-based fluorescent nanoprobe for fast, sensitive and selective detection of miRNA. Moreover, the strategy was successfully applied for in situ imaging of miRNA-21 in different cell lines.

Two-photon excited fluorescent silica nanoparticles loaded with iron(II) as a probe for determination and imaging of hydrogen peroxide in living cells.

A method is described for determination and optical imaging of hydrogen peroxide (H2O2) by using the two-photon (TP) excited fluorescence of silica (SiO2) nanoparticles containing Fe(II) ions. In the presence of H2O2, hydroxyl radicals (•OH) are produced via the Fenton reaction. This leads to quenching of the green fluorescence of a TP-excitable organic dye loaded into the SiO2NPs. Fluorescence is excited at 370 nm and has an emission peaking at 447 nm. The degree of quenching increases linearly in the 2.5 to 100 µM H2O2 concentration range. The nanoprobe is highly selective and sensitive, with a detection limit of 336 nM. The nanoprobe is biocompatible and was successfully used to image changes in the H2O2 concentration in HeLa cells via TP fluorescence imaging. Graphical abstractSchematic rpresentation of the detection of H2O2 by using the two-photon excited fluorescence of silica nanoparticles (TP-SiO2NPs) containing Fe2+. H2O2 triggers the Fenton reaction to produce hydroxyl radicals (•OH), which quench the green fluorescence of the SiO2NPs.

Recent advances in functionalized MnO2 nanosheets for biosensing and biomedicine applications.

As one kind of redox active layered transition-metal dioxide nanomaterials, single-layer manganese dioxide (MnO2) nanosheets have gained significant research attention in the fields of biosensing and biomedicine because of their large surface area, intense and broad optical absorption, strong oxidation ability, catalytic activity, and robust mechanical properties. This review provides a brief overview of the recent advances in the development of MnO2 nanosheet-based biosensors, bioimaging as well as drug delivery for cancer therapy. The methodologies for the preparation of MnO2 nanosheets are summarized, followed by an introduction of the nanostructure and properties of MnO2 nanosheets. Special attention is paid to their applications in biosensing, bioimaging and cancer therapy. Future perspectives and the challenges of high-performance MnO2 nanosheets are also discussed.

A graphene quantum dot-based multifunctional two-photon nanoprobe for the detection and imaging of intracellular glutathione and enhanced photodynamic therapy.

A multifunctional nanosystem, which integrates biosensing, bioimaging, and therapeutic functions into a single nanoprobe, is of great significance for biosensing and biomedicine. Near-infrared (NIR) graphene quantum dots (GQDs) have emerged as an attractive bioimaging and therapy tool for exploring biological events because they can provide deep imaging penetration and low fluorescence background and produce 1O2 for PDT. Here, we reported a GQD-based multifunctional two-photon nanoprobe for intracellular tumor-related glutathione (GSH) detection and enhanced photodynamic therapy by reducing GSH levels in cancer cells. By taking the excellent quenching property of MnO2 nanosheets and the reduction ability of GSH, a GQD@MnO2 nanoprobe was developed through adsorption of MnO2 nanosheets onto the surface of GQDs for sensing intracellular tumor-related GSH. The nanoprobe shows a highly sensitive response to GSH in aqueous solutions with a detection limit of 83 nM. It also exhibits a high selectivity toward GSH relative to other biomolecules and electrolytes. In addition, once endocytosed, the MnO2 nanosheets are reduced by intracellular GSH, simultaneously releasing GQDs and decreasing the level of GSH for highly efficient PDT.