Aptamer-Based DNA Allosteric Switch for Regulation of Protein Activity.

Allostery is a fundamental way to regulate the function of biomolecules playing crucial roles in cell metabolism and proliferation and is deemed the second secret of life. Given the limited understanding of the structure of natural allosteric molecules, the development of artificial allosteric molecules brings a huge opportunity to transform the allosteric mechanism into practical applications. In this study, the concept of bionics is introduced into the design of artificial allosteric molecules and an allosteric DNA switch with an activity site and an allosteric site based on two aptamers for selective inhibition of thrombin activity. Compared with the single aptamer, the allosteric switch possesses a significantly enhanced inhibition ability, which can be precisely regulated by converting the switch states. Moreover, the dynamic allosteric switch is further subjected to the control of the DNA threshold circuit for realizing automatic concentration determination and activity inhibition of thrombin. These compelling results confirm that this allosteric switch equipped with self-sensing and information-processing modules puts a new slant on the research of allosteric mechanisms and further application of allosteric tactics in chemical and biomedical fields.

In situ coupling of carbon dots with zeolitic imidazolate frameworks enabling highly red emission in solid state.

In this work, an extraordinary solid red emissive phosphor was prepared based on red-emitting carbon dots (R-CDs). The synthesis was conducted under an in-situ strategy, with assistance of zeolitic imidazolate frameworks. The obtained phosphor possesses a stronger red emission located at 630 nm in solid state, with CIE coordinate of (0.63, 0.35) and quantum yield of âˆ¼ 45 %. As a consequence, not only aggregation-induced fluorescence quenching of R-CDs is avoided in solid state, but also an enhanced emission with high quantum yield is presented. Fluorescence properties were further explored in detail. The emission is found to be responsive to temperature and applied pressure. Based on the excellent emissive performance, the material has great potentials in anti-counterfeiting, latent fingerprint imaging, and temperature/pressure-sensing. This work provides a facile and promising way of preparing solid carbon-based phosphors for special applications.

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 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.

A dual-mode system based on molybdophosphoric heteropoly acid and fluorescent microspheres for the reliable and ultrasensitive detection of alkaline phosphatase.

A novel colorimetric and fluorescent dual-mode sensing system based on molybdophosphoric heteropoly acid (PMA) and fluorescent microspheres (FMs) was established for monitoring the activity of alkaline phosphatase (ALP). In the presence of ALP, L-ascorbic acid-2-phosphate (AAP) could be hydrolyzed catalytically to ascorbic acid (AA), which could reduce PMA to phosphorus molybdenum blue (PMB), accompanied by the generation of colorimetric signals depending on the level of ALP. Meanwhile, the fluorescence of FMs was quenched markedly by the PMB produced due to the inner-filter effect, which constituted the response mechanism for the dual-mode sensing systems of ALP. On this basis, a PMA-FMs based dual-mode sensing system was used for the detection of ALP, which not only possessed remarkable sensitivity, with a limit of detection of 0.27 U L-1 and 0.11 U L-1, but also exhibited good analytical performance in biological samples with satisfactory results. Moreover, a simple and portable test kit for the visual detection of ALP in real serum samples was fabricated utilizing a smartphone with image-recognition and data-processing capabilities as a visual-detection platform.

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.

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.

2D Co-MOF nanosheet-based nanozyme with ultrahigh peroxidase catalytic activity for detection of biomolecules in human serum samples.

A two-dimensional (2D) Co-MOF nanosheet-based nanozyme was developed for colorimetric detection of disease-related biomolecules. The prepared 2D Co-MOFs exhibited ultrahigh peroxidase catalytic activity. 2D Co-MOFs can catalyze the oxidation of colorless 3,3',5,5'-tetramethylbenzidine (TMB) to the blue product oxTMB, accompanying an obvious change of absorption value at 652 nm. However, alkaline phosphatase can catalyze the hydrolysis of L-ascorbic acid-2-phosphate to produce ascorbic acid which can reduce the oxTMB to TMB, resulting in an obvious color fading. Therefore, by recording the change of absorption value at 652 nm, the 2D Co-MOF nanosheets were used to detect ascorbic acid (AA) and alkaline phosphatase (ALP). The limit of detection for AA and ALP was 0.47 µM and 0.33 U L-1, respectively. The limit of quantification for AA and ALP was 1.56 µM and 1.1 U L-1, respectively. The developed nanozyme was successfully used to determine alkaline phosphatase in clinical human serum samples and the results were consistent with those provided by the hospital. Furthermore, by integrating 2D Co-MOF nanosheets with image recognition and data processing function fixed on a smartphone, a portable test of ascorbic acid was reached. Schematic presentation of the preparation of two-dimensional Co-MOF nanosheet-based nanozyme and their application in portable detection of biomolecules.

Entropy-driven amplification strategy-assisted lateral flow assay biosensor for ultrasensitive and convenient detection of nucleic acids.

Accurate, sensitive and rapid nucleic acid tests are important to implement timely treatment measures and control the spread of disease. Herein, we developed a novel portable platform for highly sensitive and specific detection of nucleic acids by integrating an entropy-driven amplification strategy into lateral flow assay (LFA) biosensor. We find that introducing an entropy-driven amplification strategy yields bright intensities on the test line of LFA stirp, which results in improved sensitivity for targeted nucleic acid detection. The developed LFA biosensor showed good reproducibility, specificity and sensitivity for target DNA and H1N1-RNA detection with a low detection limit of 1.43 pM and 2.02 pM, respectively. Its practical potential was also verified by detecting the target nucleic acid in human serum. More importantly, the design of an entropy-driven amplification strategy in this portable platform retained the convenient, rapid and low-cost characterizations of LFA biosensor due to the compact amplification principle and the elimination of enzyme use. Thus, we believe that this assay biosensor will certainly report its own position in the timely detection of nucleic acid, especially when the medical environment and resources are fewer.

A lysosome-targetable two-photon excited near-infrared fluorescent probe for visualizing hypochlorous acid-involved arthritis and its treatment.

Lysosome of phagocyte is the main site of hypochlorous acid (HClO) production, and HClO can be employed as the biomarker for the diagnosis and treatment evaluation of arthritis. In recent years, developing fluorescent probes for lysosomal HClO has attracted considerable attention, but most of them still have some defects, such as autofluorescence, phototoxicity and photobleaching because of their excitation and emission located in short-wavelength region. Due to the advantages of two-photon fluorescent probes with near-infrared emissions, a lysosome-targetable two-photon fluorescent probe (Lyso-TP-HClO) with a near-infrared emission was reported in this paper. Lyso-TP-HClO has a high selectivity and a high sensitivity to HClO in the linear range (10.0 × 10-8 to 5.0 × 10-6 M), with a detection limit of 3.0 × 10-8 M. Due to the two-photon excited near-infrared emission, Lyso-TP-HClO has excellent imaging performances, such as small autofluorescence, excellent photostability, and large imaging depth. Furthermore, Lyso-TP-HClO was successfully employed for visualizing lysosomal HClO in bacteria-infected cells. At last, we have successfully used Lyso-TP-HClO to image the arthritis and evaluate the treatment of arthritis in mice. All the results confirm that Lyso-TP-HClO is a useful chemical tool for imaging of lysosomal HClO, the diagnosis of arthritis, and treatment evaluation of arthritis.

DNA origami-based protein networks: from basic construction to emerging applications.

Natural living systems are driven by delicate protein networks whose functions are precisely controlled by many parameters, such as number, distance, orientation, and position. Focusing on regulation rather than just imitation, the construction of artificial protein networks is important in many research areas, including biomedicine, synthetic biology and chemical biology. DNA origami, sophisticated nanostructures with rational design, can offer predictable, programmable, and addressable scaffolds for protein assembly with nanometer precision. Recently, many interdisciplinary efforts have achieved the precise construction of DNA origami-based protein networks, and their emerging application in many areas. To inspire more fantastic research and applications, herein we highlight the applicability and potentiality of DNA origami-based protein networks. After a brief introduction to the development and features of DNA origami, some important factors for the precise construction of DNA origami-based protein networks are discussed, including protein-DNA conjugation methods, networks with different patterns and the controllable parameters in the networks. The discussion then focuses on the emerging application of DNA origami-based protein networks in several areas, including enzymatic reaction regulation, sensing, bionics, biophysics, and biomedicine. Finally, current challenges and opportunities in this research field are discussed.

DNAzyme-gold nanoparticle-based probes for biosensing and bioimaging.

The deoxyribozyme (DNAzyme) is a specific nucleic acid with high catalytic activity in the presence of coenzyme factors. Because of its good programmability, high stability and excellent activity, DNAzyme is considered to be a promising material in many fields, such as environmental monitoring, food regulation, biosensing and gene therapy. Gold nanoparticles exhibit excellent photoelectric properties, and can also provide DNAzyme with enhanced cell transfection and excellent resistance to nuclease degradation. Therefore, DNAzyme-gold nanoparticle complexes have attracted much attention in many areas, particularly in biosensing and bioimaging. In this review, we first provide a brief introduction of the structure and catalytic activity of DNAzymes, as well as several methods for preparing DNAzyme-gold nanoparticles. Then, the discussion focuses on applications of DNAzyme-gold nanoparticle-based probes in biosensing and bioimaging in recent years (especially in the past five years). Based on their output signals, these sensors are divided into fluorescence sensors, colorimetric sensors, electrochemical sensors, photoelectrochemical sensors and other sensors. Finally, we discuss several challenges and opportunities in this emerging field.

DNAzyme-Metal-Organic Framework Two-Photon Nanoprobe for In situ Monitoring of Apoptosis-Associated Zn2+ in Living Cells and Tissues.

Monitoring Zn2+ in living cells is critical for fully elucidating the biological process of apoptosis. However, the quantitative intracellular sensing of Zn2+ using DNAzyme remains challenging because of issues related to penetration of the signal through tissue, targeted cellular uptake and activation, and susceptibility toward enzymatic degradation. In this study, we developed a novel phosphate ion-activated DNAzyme-metal-organic frameworks (MOFs) nanoprobe for two-photon imaging of Zn2+ in living cells and tissues. The design of this nanoprobe involved the loading of a Zn2+-specific, RNA-cleaving DNAzyme onto the MOFs through strong coordination between the phosphonate O atoms of the DNAzyme backbone and Zr atoms in the MOFs. This coordination restrained the extracellular activity of DNAzyme; however, after cell entry, the DNAzyme was released from the MOFs through a competitive binding by the phosphate ions present at a high intracellular concentration. Following their release, the two-photon (TP) fluorophore-labeled substrate strands of DNAzyme were cleaved with the aid of Zn2+, which resulted in a strong fluorescence signal. The incorporation of a TP fluorophore into the nanoprobe facilitated near-infrared excitation, which allowed the highly sensitive and specific imaging of Zn2+ in living cells and tissues at greater depths than possible previously. The TP-DNAzyme-MOFs nanoprobe achieved a low detection limit of 3.53 nM, extraordinary selectivity toward Zn2+, and a tissue signal penetration of 120 µm. More importantly, this nanoprobe was successfully used to monitor cell apoptosis, and this application of the DNAzyme-MOFs probe holds great potential for future use in biological studies and medical diagnostics.

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.

Detection of Tetanus Antibody Applying a Cu-Zn-In-S/ZnS Quantum Dot-Based Lateral Flow Immunoassay.

Lateral flow test strip (LFTS) enables rapid, portable, and low-cost point-of-care testing (POCT) diagnosis. Quantum dots (QDs), which are fluorescent semiconductor nanocrystals with distinctive and unique photophysical properties, have become promising candidates to serve as labels for LFTS with improved sensitivity. Here, by using QDs as a signal reporter, we report a fluorescent LFTS for detection of tetanus antibody. This LFTS possess a high sensitivity for tetanus antibody, with a detection limit of 0.001 IU/mL. This assay was also applied for detection of tetanus antibody in human serum. More importantly, these strips can retain their specificity and sensitivity for at least 4 months when they are stored at 4 °C.

Biomineralized nanoparticles enable an enzyme-assisted DNA signal amplification in living cells.

The enzymatic-assisted signal amplification of DNA sensors is rarely applied in living cells due to the difficulties in protein delivery. In this study, we have proposed a biomineralization-based DNA nanoprobe to transport nucleases and DNA sensors for enzyme-assisted imaging of microRNA in living cells.