DNA nanosensor based on bipedal 3D DNA walker-driven proximal catalytic hairpin assembly for sensitive and fast TK1 mRNA detection.

Hyperproliferative  diseases are the first step for tumor formation; thymidine kinase 1 (TK1) mRNA is closely related to cell proliferation. Therefore, the risk of malignant proliferation can be identified by sensitively detecting the variance in TK1 mRNA concentration, which can be used for tumor auxiliary diagnosis and monitoring tumor treatment. Owing to the low abundance and instability of TK1 mRNA in real samples, the development of a sensitive and fast mRNA detection method is necessary. A DNA nanosensor that can be used for detecting TK1 mRNA based on bipedal 3D DNA walker-driven proximal catalytic hairpin assembly (P-CHA) was developed. P-CHA hairpins were hybridized to a linker DNA strand coupled with magnetic nanoparticles to increase their local concentrations. The bipedal DNA walking on the surface of NPs accelerates reaction kinetics using the proximity effect. Taking advantage of the signal amplification of P-CHA as well as the rapid reaction rate of the DNA walker in 80 min, the proposed sensor detects TK1 mRNA with a low detection limit of 14 pM and may then be applied to clinical diagnosis.

Pyridine-Based Covalent Organic Frameworks with Pyridyl-Imine Structures for Boosting Photocatalytic H2O2 Production via One-Step 2e- Oxygen Reduction.

Bipyridine-based covalent organic frameworks (COFs) have emerged as promising contenders for the photocatalytic generation of hydrogen peroxide (H2O2). However, the presence of imine nitrogen alters the mode of H2O2 generation from an efficient one-step two-electron (2e-) route to a two-step 2e- oxygen reduction pathway. In this work, we introduce 3,3'-bipyridine units into imine-based COF skeletons, creating a pyridyl-imine structure with two adjacent nitrogen atoms between the pyridine ring and imine linkage. This unique bipyridine-like architecture can effectively suppress the two-step 2e- ORR process at the single imine-nitrogen site, facilitating a more efficient one-step 2e- pathway. Consequently, the optimized pyridyl-imine COF (PyIm-COF) exhibits a remarkable H2O2 production rate of up to 5850 µmol h-1 g-1, nearly double that of pristine bipyridine COFs. This work provides valuable insight into the rational design of functionalized COFs for enhanced H2O2 production in photocatalysis.

Construction of Covalent Organic Framework Nanofiber Membranes for Efficient Adsorption of Antibiotics.

Techniques beyond crystal engineering are critical for manufacturing covalent organic frameworks (COFs) and to explore them for advanced applications. However, COFs are normally obtained as insoluble, unmeltable, and thus nonprocessible microcrystalline powders. Therefore, it is a significant challenge to implement COFs into larger architectures and structural control on different length scales. Herein, a facile strategy is presented to prepare flexible COF nanofiber membranes by in-situ growth of COFs on polyacrylonitrile (PAN) nanofiber substrates via a reversible polycondensation-termination approach. The obtained PAN@COF nanofiber membranes with vertically aligned COF nanoplates combine a large functional surface with efficient mass transport, thus making it a promising adsorbent, for example, for water purification. The antibiotic pollutant ofloxacin (OFX) is removed from water with a superior absorption capacity of ≈236 mg g-1 and removal efficiency as high as 98%. The here presented in-situ growth of COFs on nanofiber membranes can be extended to various Schiff base-derived COF materials with different compositions, providing a highly efficient way to construct flexible COF-based membranes for several applications.

pH-activated DNA nanomachine for miRNA-21 imaging to accurately identify cancer cell.

MicroRNA (miRNA) imaging has been employed to distinguish cancer cells from normal cells by exploiting the overexpression of miRNA in cancer. Inspired by the acidic extracellular tumor microenvironment, we designed a pH-activated DNA nanomachine to enable the specific detection of cancer cells using miRNA imaging. The DNA nanomachine was engineered by assembling two hairpins (Y1 and Y2) onto the surface of a ZIF-8 metal-organic framework (MOF), which decomposed under acidic conditions to release the adsorbed DNA hairpin molecules in situ. The released hairpins were captured by the target miRNA-21 and underwent catalytic hairpin assembly amplification between Y1 and Y2. The detection limit for miRNA assays using the DNA nanomachine was determined to be 27 pM, which is low enough for sensitive detection in living cells. Living cell imaging of miRNA-21 further corroborated the application of the DNA nanomachine in the identification of cancer cell.

Covalent organic frameworks (COFs) for electrochemical applications.

Covalent organic frameworks are a class of extended crystalline organic materials that possess unique architectures with high surface areas and tuneable pore sizes. Since the first discovery of the topological frameworks in 2005, COFs have been applied as promising materials in diverse areas such as separation and purification, sensing or catalysis. Considering the need for renewable and clean energy production, many research efforts have recently focused on the application of porous materials for electrochemical energy storage and conversion. In this respect, considerable efforts have been devoted to the design and synthesis of COF-based materials for electrochemical applications, including electrodes and membranes for fuel cells, supercapacitors and batteries. This review article highlights the design principles and strategies for the synthesis of COFs with a special focus on their potential for electrochemical applications. Recently suggested hybrid COF materials or COFs with hierarchical porosity will be discussed, which can alleviate the most challenging drawback of COFs for these applications. Finally, the major challenges and future trends of COF materials in electrochemical applications are outlined.

An enzyme-free probe based on G-triplex assisted by silver nanocluster pairs for sensitive detection of microRNA-21.

A sensitive ratiometric fluorescence probe based on hybridization chain reaction (HCR) was constructed for sensitive detection of miRNA-21 by using G-triplex and silver nanocluster pairs (AgNC pairs) as an enzyme-free and label-free signal output group. miRNA-21 was used as the primer for the hybridization chain reaction of molecular beacon 1 (MB1) containing the locked G-triplex sequence and molecular beacon 2 (MB2) with intact AgNC pairs at the 5' and 3' end activation. The double-stranded product was obtained along with the opening of the G-triplex and the separation of the AgNC pairs. A detection limit of 67 pM and a linear detection range of 0.1-300 nM were obtained for miRNA-21 determination. The proposed strategy enabled the monitoring of miRNA-21 levels in at least three cell lines, indicating that it provided new ideas for detecting miRNA in real samples. MB1 and MB2 contained the locked G-triplex sequence and silver nanocluster pairs (AgNC pairs), respectively. In the presence of target, the hybridization chain reaction (HCR) between MB1 and MB2 was initiated. At the same time, the locked G-triplex was released and combined to the dye thioflavin T (THT) to increase fluorescence, while the separation of the AgNC pairs caused the fluorescence to decrease. The double-stranded (ds) DNA product was generated to form a ratiometric signal to be detected.

DNA Structural Distortions Induced by a Monofunctional Trinuclear Platinum Complex with Various Cross-Links Using Molecular Dynamics Simulation.

The monofunctional trinuclear platinum complex (MTPC), as a promising antitumor agent, can form MTPC-DNA adducts via bifunctional and trifunctional cross-links. Molecular dynamics simulations were used to investigate DNA structural distortions of the MTPC-DNA adducts. MTPC coordinating to DNA results in the decrease of base-pair thermal stability and DNA structural distortions. It is found that there are more significant DNA structural distortions in the trifunctional cross-link than in the bifunctional cross-link, in the 1,4-GG than in the 1,3-GG cross-link, and in the intrastrand than in the interstrand cross-link with the same spans. The results provide a better understanding of DNA structural distortions induced by MTPC with various cross-links at the nucleotide level and are helpful for exploring novel Pt-based anticancer drugs.

Macro/Microporous Covalent Organic Frameworks for Efficient Electrocatalysis.

Covalent organic frameworks (COFs) are of interest for many applications originating from their mechanically robust architectures, low density, and high accessible surface area. Depending on their linkers and binding patterns, COFs mainly exhibit microporosity, even though COFs with small mesopores have been reported using extended linkers. For some applications, especially when fast mass transport is desired, hierarchical pore structures are an ideal solution, e.g., with small micropores providing large surface areas and larger macropores providing unhindered transport to and from the materials surface. Herein, we have developed a facile strategy for the fabrication of crystalline COFs with inherent microporosity and template-induced, homogeneously distributed, yet tunable, macroporous structures. This method has been successfully applied to obtain various ß-ketoenamine-based COFs with interconnected macro-microporous structures. The as-synthesized macroporous COFs preserve high crystallinity with high specific surface area. When bipyridine moieties are introduced into the COF backbone, metals such as Co2+ can be coordinated within the hierarchical pore structure (macro-TpBpy-Co). The resulting macro-TpBpy-Co exhibits a high oxygen evolution reaction (OER) activity, which is much improved compared to the purely microporous COF with a competitive overpotential of 380 mV at 10 mA/cm2. This can be attributed to the improved mass diffusion properties in the hierarchically porous COF structures, together with the easily accessible active Co2+-bipyridine sites.

Molecular dynamics simulation on the allosteric analysis of the c-di-GMP class I riboswitch induced by ligand binding.

Riboswitches are RNA molecules that regulate gene expression using conformation change, affected by binding of small molecule ligands. Although a number of ligand-bound aptamer complex structures have been solved, it is important to know ligand-free conformations of the aptamers in order to understand the mechanism of specific binding by ligands. In this paper, we use dynamics simulations on a series of models to characterize the ligand-free and ligand-bound aptamer domain of the c-di-GMP class I (GEMM-I) riboswitch. The results revealed that the ligand-free aptamer has a stable state with a folded P2 and P3 helix, an unfolded P1 helix and open binding pocket. The first Mg ions binding to the aptamer is structurally favorable for the successive c-di-GMP binding. The P1 helix forms when c-di-GMP is successive bound. Three key junctions J1/2, J2/3 and J1/3 in the GEMM-I riboswitch contributing to the formation of P1 helix have been found. The binding of the c-di-GMP ligand to the GEMM-I riboswitch induces the riboswitch's regulation through the direct allosteric communication network in GEMM-I riboswitch from the c-di-GMP binding sites in the J1/2 and J1/3 junctions to the P1 helix, the indirect ones from those in the J2/3 and P2 communicating to P1 helix via the J1/2 and J1/3 media.

Structural Studies of the 3',3'-cGAMP Riboswitch Induced by Cognate and Noncognate Ligands Using Molecular Dynamics Simulation.

Riboswtich RNAs can control gene expression through the structural change induced by the corresponding small-molecule ligands. Molecular dynamics simulations and free energy calculations on the aptamer domain of the 3',3'-cGAMP riboswitch in the ligand-free, cognate-bound and noncognate-bound states were performed to investigate the structural features of the 3',3'-cGAMP riboswitch induced by the 3',3'-cGAMP ligand and the specificity of ligand recognition. The results revealed that the aptamer of the 3',3'-cGAMP riboswitch in the ligand-free state has a smaller binding pocket and a relatively compact structure versus that in the 3',3'-cGAMP-bound state. The binding of the 3',3'-cGAMP molecule to the 3',3'-cGAMP riboswitch induces the rotation of P1 helix through the allosteric communication from the binding sites pocket containing the J1/2, J1/3 and J2/3 junction to the P1 helix. Simultaneously, these simulations also revealed that the preferential binding of the 3',3'-cGAMP riboswitch to its cognate ligand, 3',3'-cGAMP, over its noncognate ligand, c-di-GMP and c-di-AMP. The J1/2 junction in the 3',3'-cGAMP riboswitch contributing to the specificity of ligand recognition have also been found.

Active Salt/Silica-Templated 2D Mesoporous FeCo-Nx -Carbon as Bifunctional Oxygen Electrodes for Zinc-Air Batteries.

Two types of templates, an active metal salt and silica nanoparticles, are used concurrently to achieve the facile synthesis of hierarchical meso/microporous FeCo-Nx -carbon nanosheets (meso/micro-FeCo-Nx -CN) with highly dispersed metal sites. The resulting meso/micro-FeCo-Nx -CN shows high and reversible oxygen electrocatalytic performances for both ORR and OER, thus having potential for applications in rechargeable Zn-air battery. Our approach creates a new pathway to fabricate 2D meso/microporous structured carbon architectures for bifunctional oxygen electrodes in rechargeable Zn-air battery as well as opens avenues to the scale-up production of rationally designed heteroatom-doped catalytic materials for a broad range of applications.

Bifunctional Electrocatalysts for Overall Water Splitting from an Iron/Nickel-Based Bimetallic Metal-Organic Framework/Dicyandiamide Composite.

Pyrolysis of a bimetallic metal-organic framework (MIL-88-Fe/Ni)-dicyandiamide composite yield a Fe and Ni containing carbonaceous material, which is an efficient bifunctional electrocatalyst for overall water splitting. FeNi3 and NiFe2 O4 are found as metallic and metal oxide compounds closely embedded in an N-doped carbon-carbon nanotube matrix. This hybrid catalyst (Fe-Ni@NC-CNTs) significantly promotes the charge transfer efficiency and restrains the corrosion of the metallic catalysts, which is shown in a high OER and HER activity with an overpotential of 274 and 202 mV, respectively at 10 mA cm-2 in alkaline solution. When this bifunctional catalyst was further used for H2 and O2 production in an electrochemical water-splitting unit, it can operate in ambient conditions with a competitive gas production rate of 1.15 and 0.57 µL s-1 for hydrogen and oxygen, respectively, showing its potential for practical applications.

Facile Synthesis for Benzo-1,4-Oxazepine Derivatives by Tandem Transformation of C-N Coupling/C-H Carbonylation.

A tandem transformation of C-N coupling/C-H carbonylation has been developed for the synthesis of benzo-1,4-oxazepine pharmaceutically derivatives. Notably, this reaction was accomplished by various phenylamine with ally halides under carbon dioxide atmosphere employing 2-(2-dimethylamino-vinyl)-1H-inden-1-olcatalyzed. Furthermore, under the optimized conditions, various benzo-1,4-oxazepine derivatives were obtained in good yields. Finally, a plausible CuI/CuIII mechanism of C-N coupling/C-H carbonylation transformation was proposed.

Construction of an autofluorescence interference-free phosphorescence biosensor for the specific detection of TK1 mRNA.

The anti-interference ability of biosensors is critical for detection in biological samples. Fluorescence-based sensors are subject to interference from self-luminescent substances in biological matrices. Therefore, phosphorescent sensors stand out among biosensors due to their lack of self-luminescence background. In this study, a phosphorescent sensor was constructed, which can accurately detect thymidine kinase 1 (TK1) mRNA in biological samples and avoid autofluorescence interference. When there is no target, polydopamine (PDA) is used as the phosphorescence resonance energy transfer (PRET) acceptor to quench the phosphorescence of the persistently luminescent (PL) nanomaterial. When there is a target, the DNA modified by the PL nanomaterial is replaced by the hairpin H and removed away from the PDA, resulting in a rebound in phosphorescence. The phosphorescent sensor exhibits a good linear relationship in the TK1 mRNA concentration range of 0-200 nM, and the detection limit was 1.74 nM. The sensor fabricated in this study can effectively avoid interference from spontaneous fluorescence in complex biological samples, and sensitively and precisely detect TK1 mRNA in serum samples, providing a powerful tool to more accurately detect biomarkers in biological samples.

Small variation induces a big difference: the effect of polymerization kinetics of graphitic carbon nitride on its photocatalytic activity.

Graphitic carbon nitride (g-CN) has emerged as a promising visible-light-responsive photocatalyst, and its activity is highly sensitive to synthesis conditions. In this work, we attempt to correlate the photocatalytic activity of g-CN with its production yield, which is kinetically determined by the specific condensation process. Bulk g-CN samples were synthesized by the conventional condensation procedure, but in static air and flowing air, respectively. The one synthesized in static air showed a lower production yield with an increased specific surface area and preferential surface chemical states, corresponding to a significantly improved activity for photocatalytic hydrogen evolution (PHE) and dye degradation. We further synthesized a series of g-CN samples by merely changing the synthetic atmosphere, the ramping rate, and the loading amount of the precursor, and the difference in their PHE performance was found to be as high as 7.05 times. The notable changes in their production yields as well as the photocatalytic activities have been discussed from the point of view of polymerization reaction kinetics, and the self-generated NH3 atmosphere plays a crucial role.

Reconstruction the feedback regulation of amino acid metabolism to develop a non-auxotrophic L-threonine producing Corynebacterium glutamicum.

L-Threonine is an important feed additive with the third largest market size among the amino acids produced by microbial fermentation. The GRAS (generally regarded as safe) industrial workhorse Corynebacterium glutamicum is an attractive chassis for L-threonine production. However, the present L-threonine production in C. glutamicum cannot meet the requirement of industrialization due to the relatively low production level of L-threonine and the accumulation of large amounts of by-products (such as L-lysine, L-isoleucine, and glycine). Herein, to enhance the L-threonine biosynthesis in C. glutamicum, releasing the aspartate kinase (LysC) and homoserine dehydrogenase (Hom) from feedback inhibition by L-lysine and L-threonine, respectively, and overexpressing four flux-control genes were performed. Next, to reduce the formation of by-products L-lysine and L-isoleucine without the cause of an auxotrophic phenotype, the feedback regulation of dihydrodipicolinate synthase (DapA) and threonine dehydratase (IlvA) was strengthened by replacing the native enzymes with heterologous analogues with more sensitive feedback inhibition by L-lysine and L-isoleucine, respectively. The resulting strain maintained the capability of synthesizing enough amounts of L-lysine and L-isoleucine for cell biomass formation but exhibited almost no extracellular accumulation of these two amino acids. To further enhance L-threonine production and reduce the by-product glycine, L-threonine exporter and homoserine kinase were overexpressed. Finally, the rationally engineered non-auxotrophic strain ZcglT9 produced 67.63 g/L (17.2% higher) L-threonine with a productivity of 1.20 g/L/h (108.0% higher) in fed-batch fermentation, along with significantly reduced by-product accumulation, representing the record for L-threonine production in C. glutamicum. In this study, we developed a strategy of reconstructing the feedback regulation of amino acid metabolism and successfully applied this strategy to de novo construct a non-auxotrophic L-threonine producing C. glutamicum. The main end by-products including L-lysine, L-isoleucine, and glycine were almost eliminated in fed-batch fermentation of the engineered C. glutamicum strain. This strategy can also be used for engineering producing strains for other amino acids and derivatives.

Tensor Learning Meets Dynamic Anchor Learning: From Complete to Incomplete Multiview Clustering.

Multiview clustering (MVC), which can dexterously uncover the underlying intrinsic clustering structures of the data, has been particularly attractive in recent years. However, previous methods are designed for either complete or incomplete multiview only, without a unified framework that handles both tasks simultaneously. To address this issue, we propose a unified framework to efficiently tackle both tasks in approximately linear complexity, which integrates tensor learning to explore the inter-view low-rankness and dynamic anchor learning to explore the intra-view low-rankness for scalable clustering (TDASC). Specifically, TDASC efficiently learns smaller view-specific graphs by anchor learning, which not only explores the diversity embedded in multiview data, but also yields approximately linear complexity. Meanwhile, unlike most current approaches that only focus on pair-wise relationships, the proposed TDASC incorporates multiple graphs into an inter-view low-rank tensor, which elegantly models the high-order correlations across views and further guides the anchor learning. Extensive experiments on both complete and incomplete multiview datasets clearly demonstrate the effectiveness and efficiency of TDASC compared with several state-of-the-art techniques.

Detection of long mRNA sequences by a Y-shaped DNA probe with three target-binding segments.

Tumor-related mRNA detection is significant and interesting. The current mRNA detection method has the challenge of quantifying long mRNA sequences. Herein, a Y-shaped DNA probe with three target-binding segments was developed to detect tumor-related mRNA. This Y-shaped DNA probe (Y-probe) was assembled by six single DNA strands. Among these DNA strands, two DNA strands contained the split G-quadruplex sequence, and two DNA strands were modified with a pair of fluorophore and quencher, which were used to produce the detectable signal. In the presence of a long target mRNA sequence, target mRNA was hybridized with the three target-binding segments of the Y-probe, resulting in the increased fluorescence of G-quadruplex specific dye Thioflavin T and the decreased fluorescence of fluorophore, which could achieve the ratio detection of target mRNA. The Y-probe exhibited a low detection limit of 17.53 nM. Moreover, this probe showed high accuracy due to the benefits of three target-binding segments.

Molecular dynamics simulation study of DNA conformation changes caused by the dinuclear platinum(II) complexes with the bisphosphonate group.

Bisphosphonate (BP) has been widely used as a bone-targeting group, and the BP-modified platinum(II) complexes have shown potential to as anticancer drugs against bone-related diseases, such as osteosarcoma. DNA conformation changes induced by the BP-modified dinuclear platinum(II) complexes have been investigated using molecular dynamics simulations. The results indicated that the BP-modified dinuclear platinum(II) complexes coordinated to DNA results in DNA structural distortions, including twisting, unwinding and bending. Furthermore, the rigidity of the bridging linkers in the BP-modified platinum(II) complex may induce more significant DNA structural distortions with same spans. The results provide the detail information of DNA conformational changes induced by the BP-modified platinum(II) complexes with different flexibility of bridging linkers, and are helpful for exploring novel platinum-based antitumor drugs.

A covalent organic framework/graphene aerogel electrocatalyst for enhanced overall water splitting.

The rational design of covalent organic framework (COF) based hybrid materials is of paramount importance to address the fundamental challenges of COFs with respect to their poor electron mobilization and the limited number of accessible active sites. Herein, we propose a new strategy for the fabrication of covalently bonded COF grafted graphene aerogel hybrid materials for electrocatalytic application. An in situ step-growth polymerization approach was developed to achieve the hybridization of COFs along the surface of amino-functionalized graphene nanosheets. By taking advantage of the three-dimensional conductive networks and highly accessible active sites, the cobalt-incorporated COF/graphene hybrid aerogel shows high oxygen evolution reaction (OER) and hydrogen evolution reaction (HER) performances with an overpotential of 300 and 275 mV at 10 mA cm-2, respectively, under alkaline conditions. When applied to an electrochemical water-splitting electrolyzer, it is able to produce hydrogen and oxygen at competitive rates of 1.14 and 0.58 µL s-1, respectively, under ambient conditions, demonstrating its potential for practical applications.