Nucleic Acid-to-Small Molecule Converter through Amplified Hairpin DNA Circuits

Many microRNAs (miRNAs) are characteristically found in cancer cells, making miRNAs promising marker biomolecules for cancer diagnosis and therapeutics. However, it is challenging to use miRNA as a cancer signature because it is difficult to convert the nucleic acid sequence information into molecular functionality. To address this challenge, we realize nucleic acid-to-small molecule converters using hairpin DNA circuits. Harnessing a Staudinger reduction as a trigger for the conversion, we constructed hybridization chain reaction (HCR) and catalytic hairpin assembly (CHA) circuits that respond to oncogenic miR-21. Fluorophore and dye molecules were released in response to miR-21 through the HCR, providing fluorogenic and chromogenic readouts. Selective cytotoxicity in miR-21-abundant cells was realized by the CHA to release the anticancer drug SN-38. This would be the first example of selective activation of a small-molecule prodrug triggered by oncogenic miRNA in human living cells.     

Subnanomolar Detection of Oligonucleotides through Templated Fluorogenic Reaction in Hydrogels: Controlling Diffusion to Improve Sensitivity

Oligonucleotide‐templated reactions are valuable tools for nucleic acid sensing both in vitro and in vivo. They are typically carried out under conditions that make any reaction in the absence of template highly unfavorable (most commonly by using a low concentration of reactants), which has a negative impact on the detection sensitivity. Herein, we report a novel platform for fluorogenic oligonucleotide‐templated reactions between peptide nucleic acid probes embedded within permeable agarose and alginate hydrogels. We demonstrate that under conditions of restricted mobility (that is, limited diffusion), non‐specific interactions between probes are prevented, thus leading to lower background signals. When applied to nucleic acid sensing, this accounts for a significant increase in sensitivity (that is, lower limit of detection). Optical nucleic acid sensors based on fluorogenic peptide nucleic acid probes embedded in permeable, physically crosslinked, alginate beads were also engineered and proved capable of detecting DNA concentrations as low as 100 pm .     

Catalytic Molecular Imaging of MicroRNA in Living Cells by DNA‐Programmed Nanoparticle Disassembly

Molecular imaging is an essential tool for disease diagnostics and treatment. Direct imaging of low‐abundance nucleic acids in living cells remains challenging because of the relatively low sensitivity and insufficient signal‐to‐background ratio of conventional molecular imaging probes. Herein, we report a class of DNA‐templated gold nanoparticle (GNP)–quantum dot (QD) assembly‐based probes for catalytic imaging of cancer‐related microRNAs (miRNA) in living cells with signal amplification capacity. We show that a single miRNA molecule could catalyze the disassembly of multiple QDs with the GNP through a DNA‐programmed thermodynamically driven entropy gain process, yielding significantly amplified QD photoluminescence (PL) for miRNA imaging. By combining the robust PL of QDs with the catalytic amplification strategy, three orders of magnitude improvement in detection sensitivity is achieved in comparison with non‐catalytic imaging probe, which enables facile and accurate differentiation between cancer cells and normal cells by miRNA imaging in living cells.     

Coupling a universal DNA circuit with graphene sheets/polyaniline/AuNPs nanocomposites for the detection of BCR/ABL fusion gene

This article described a novel method by coupling a universal DNA circuit with graphene sheets/polyaniline/AuNPs nanocomposites (GS/PANI/AuNPs) for highly sensitive and specific detection of BCR/ABL fusion gene (bcr/abl) in chronic myeloid leukemia (CML). DNA circuit known as catalyzed hairpin assembly (CHA) is enzyme-free and can be simply operated to achieve exponential amplification, which has been widely employed in biosensing. However, application of CHA has been hindered by the need of specially redesigned sequences for each single-stranded DNA input. Herein, a transducer hairpin (HP) was designed to obtain a universal DNA circuit with favorable signal-to-background ratio. To further improve signal amplification, GS/PANI/AuNPs with excellent conductivity and enlarged effective area were introduced into this DNA circuit. Consequently, by combining the advantages of CHA and GS/PANI/AuNPs, bcr/abl could be detected in a linear range from 10 pM to 20 nM with a detection limit of 1.05 pM. Moreover, this protocol showed excellent specificity, good stability and was successfully applied for the detection of real sample, which demonstrated its great potential in clinical application.     

Allosterically Regulated Phosphatase Activity from Peptide–PNA Conjugates Folded Through Hybridization

The importance of spatial organization in short peptide catalysts is well recognized. We synthesized and screened a library of peptides flanked by peptide nucleic acids (PNAs) such that the peptide would be constrained in a hairpin loop upon hybridization. A screen for phosphatase activity led to the discovery of a catalyst with >25‐fold rate acceleration over the linear peptide. We demonstrated that the hybridization‐enforced folding of the peptide is necessary for activity, and designed a catalyst that is allosterically controlled using a complementary PNA sequence.     

A Multi‐component All‐DNA Biosensing System Controlled by a DNAzyme

We report on a programmable all‐DNA biosensing system that centers on the use of a 4‐way junction (4WJ) to transduce a DNAzyme reaction into an amplified signal output. A target acts as a primary input to activate an RNA‐cleaving DNAzyme, which then cleaves an RNA‐containing DNA substrate that is designed to be a component of a 4WJ. The formation of the 4WJ controls the release of a DNA output that becomes an input to initiate catalytic hairpin assembly (CHA), which produces a second DNA output that controls assembly of a split G‐quadruplex as a fluorescence signal generator. The 4WJ can be configured to produce either a turn‐off or turn‐on switch to control the degree of CHA, allowing target concentration to be determined in a quantitative manner. We demonstrate this approach by creating a sensor for E. coli that could detect as low as 50 E. coli cells mL^?1 within 85 min and offers an amplified bacterial detection method that does not require a protein enzyme.     

Catalytic Hairpin Assembly‐Programmed DNA Three‐Way Junction for Enzyme‐Free and Amplified Electrochemical Detection of Target DNA

DNA three‐way junctions (DNA 3WJ) have been widely used as important building blocks for the construction of DNA architectures and dynamic assemblies. Herein, we describe for the first time a catalytic hairpin assembly‐programmed DNA three‐way junction (CHA‐3WJ) strategy for the enzyme‐free and amplified electrochemical detection of target DNA. It takes full advantage of the target‐catalyzed hairpin assembly‐induced proximity effect of toehold and branch‐migration domains for the ingenious execution of the strand displacement reaction to form the DNA 3WJ on the electrode surface. A low detection limit of 0.5 pM with an excellent selectivity was achieved for target DNA detection. The developed CHA‐3WJ strategy also offers distinct advantages of simplicity in probe design and biosensor fabrication, as well as enzyme‐free operation. Thus, it opens a promising avenue for applications in bioanalysis, design of DNA‐responsive devices, and dynamic DNA assemblies.     

An Engineered Aryl Acid Adenylation Domain with an Enlarged Substrate Binding Pocket

Adenylation (A) domains act as the gatekeepers of non‐ribosomal peptide synthetases (NRPSs), ensuring the activation and thioesterification of the correct amino acid/aryl acid building blocks. Aryl acid building blocks are most commonly observed in iron‐chelating siderophores, but are not limited to them. Very little is known about the reprogramming of aryl acid A‐domains. We show that a single asparagine‐to‐glycine mutation in an aryl acid A‐domain leads to an enzyme that tolerates a wide range of non‐native aryl acids. The engineered catalyst is capable of activating non‐native aryl acids functionalized with nitro, cyano, bromo, and iodo groups, even though no enzymatic activity of wild‐type enzyme was observed toward these substrates. Co‐crystal structures with non‐hydrolysable aryl‐AMP analogues revealed the origins of this expansion of substrate promiscuity, highlighting an enlargement of the substrate binding pocket of the enzyme. Our findings may be exploited to produce diversified aryl acid containing natural products and serve as a template for further directed evolution in combinatorial biosynthesis.     

Hairpin Assembly Amplified Electrochemical Biosensor for Highly Sensitive and Specific Detection of DNA

In this report, a simple electrochemical biosensor has been developed for highly sensitive and specific detection of DNA based on hairpin assembly amplification. In the presence of target DNA, the biotin‐labelled hairpin H1 is opened by hybridizing with target DNA through complementary sequences. Then the opened hairpin H1 assembles with the hairpin H2 to displace the target DNA, generating H1‐H2 complex. The displaced target DNA could trigger the next cycle of hairpins assembly, resulting in the generation of numerous H1‐H2 complexes. Subsequently, the H1‐H2 complex hybridizes with the capture probe immobilized on the electrode. Finally, the streptavidin alkaline phosphatase (ST‐ALP) binds to biotin in the capture probe‐H1‐H2 complex and catalyzes the substrate α‐naphthol (α‐NP) to produce electrochemical signal. To make a more fascinating hairpin assembly amplification strategy in signal amplification, mismatched base sequences are designed in hairpin H2 to decrease non‐specific binding of the hairpin substrates. The developed biosensor achieves a sensitivity of 20 pM with a linear range from 25 pM to 25 nM, and shows high selectivity toward single‐base mismatch. Thus, the proposed electrochemical biosensor might have the potential for early clinical diagnosis and therapy.     

基于催化发卡自组装和 Ru(NH3)63+ 的核酸光电化学灵敏分析

基于催化发卡自组装反应（CHA）和电活性材料[Ru(NH₃)₆]Cl₃,发展了一种“信号增强”型光电化学生物传感器,实现了核酸的灵敏检测. 首先,采用逐层离子吸附法（SILAR）将CdS 固定于TiO₂/ITO 电极表面. 光电材料CdS 不仅能够将TiO₂ 的吸收范围从紫外光区拓展到可见光区,而且还能提高光电转换效率. 之后,通过Cd-S 键将捕获DNA（C-DNA）固定于CdS/ TiO₂/ITO 电极表面. 与此同时,将Au 结合的发卡DNA 探针1（Au-HP1）,发卡DNA 探针2（HP2）和目标DNA（T-DNA）混合物于溶液中进行CHA 反应,得到大量的Au-HP1:HP2 复合物. 再通过Au-HP1:HP2 复合物与C-DNA 的杂交反应将大量的双链DNA 引入到电极表面. 最后,将电活性物质Ru(NH₃)₆³⁺嵌入DNA 的磷酸骨架中,从而使得光电流大幅度的增强. 该光电生物传感器检测核酸的线性范围为10 fmol·L^-1 到 1500 fmol·L^-1,检测线为6.19 fmol·L^-1,在生物分析、新药筛选以及疾病的早期诊断等方面具有潜在的应用前景.     

Imaging Endogenous Metal Ions in Living Cells Using a DNAzyme–Catalytic Hairpin Assembly Probe

DNAzymes are a promising platform for metal ion detection, and a few DNAzyme‐based sensors have been reported to detect metal ions inside cells. However, these methods required an influx of metal ions to increase their concentrations for detection. To address this major issue, the design of a catalytic hairpin assembly (CHA) reaction to amplify the signal from photocaged Na⁺‐specific DNAzyme to detect endogenous Na⁺ inside cells is reported. Upon light activation and in the presence of Na⁺, the NaA43 DNAzyme cleaves its substrate strand and releases a product strand, which becomes an initiator that trigger the subsequent CHA amplification reaction. This strategy allows detection of endogenous Na⁺ inside cells, which has been demonstrated by both fluorescent imaging of individual cells and flow cytometry of the whole cell population. This method can be generally applied to detect other endogenous metal ions and thus contribute to deeper understanding of the role of metal ions in biological systems.     

Enzyme‐Regulated Activation of DNAzyme: A Novel Strategy for a Label‐Free Colorimetric DNA Ligase Assay and Ligase‐Based Biosensing

The DNA nick repair catalyzed by DNA ligase is significant for fundamental life processes, such as the replication, repair, and recombination of nucleic acids. Here, we have employed ligase to regulate DNAzyme activity and developed a homogeneous, colorimetric, label‐free and DNAzyme‐based strategy to detect DNA ligase activity. This novel strategy relies on the ligation‐trigged activation or production of horseradish peroxidase mimicking DNAzyme that catalyzes the generation of a color change signal; this results in a colorimetric assay of DNA ligase activity. Using T4 DNA ligase as a model, we have proposed two approaches to demonstrate the validity of the DNAzyme strategy. The first approach utilizes an allosteric hairpin‐DNAzyme probe specifically responsive to DNA ligation; this approach has a wide detection range from 0.2 to 40 U mL^?1 and a detection limit of 0.2 U mL^?1. Furthermore, the approach was adapted to probe nucleic acid phosphorylation and single nucleotide mismatch. The second approach employs a “split DNA machine” to produce numerous DNAzymes after being reassembled by DNA ligase; this greatly enhances the detection sensitivity by a signal amplification cascade to achieve a detection limit of 0.01 U mL^?1.     

Enzyme-free Recycling Amplification-based Sensitive Electrochemical Thrombin Aptasensor

In this work, an enzyme-free recycling amplification-based sensitive electrochemical thrombin aptasensor using catalytic hairpin assembly (CHA) and bisferrocene was proposed for electrochemical beacon. Thrombin triggered the CHA reaction that in turn formed a number of double-stranded complexes,which are fixed on the surface of the gold electrode through potential-assisted Au−S deposition, and a large number of labeled bisferrocene are placed close to the gold electrode to generate electrochemical signal. The linear range of the electrochemical sensor was 0.25 pM-2.5 nM for thrombin with detection limit of 0.18 pM. This sensor can be employed to monitor the thrombin in human serum samples.     

Biosynthesis of palladium nanoparticles as a heterogeneous and reusable nanocatalyst for reduction of nitroarenes and Suzuki coupling reactions

A facile and green route for the synthesis of palladium nanoparticles (Pd‐NPs) was developed utilizing non‐toxic and renewable natural green tea extract as the reducing, stabilizing and capping agent. The as‐prepared Pd‐NPs@Oak Gum catalyst was characterized using UV–visible spectroscopy, X‐ray diffraction, Fourier transform infrared spectroscopy, field emission scanning electron microscopy, transmission electron microscopy and energy dispersive X‐ray spectroscopy. The Pd‐NPs@Oak Gum catalyst could be used as an efficient and heterogeneous catalyst for Suzuki coupling reactions between phenylboronic acid and a range of aryl halides containing iodo, bromo and chloro moieties and also for the reduction of nitroarenes using sodium borohydride in an environmental friendly medium. Excellent yields of products were obtained with a wide range of substrates and the catalyst was recycled multiple times without any significant loss of its catalytic activity. Copyright © 2016 John Wiley & Sons, Ltd.     

4-氨基吡啶树脂负载钯(Ⅱ)催化Heck反应研究

将4-氨基吡啶树脂负载钯配合物（简写为4-APR-Pd(Ⅱ)）用于卤代或杂环卤代芳烃与烯烃的Heck反应可以获得满意的收率,该法具有环境友好、实用性及树脂催化剂的重复使用性能等特点。并对反应条件进行了讨论,所得产物用1H NMR、13C NMR、红外光谱及元素分析进行了表征。     

Greener approach for synthesis of monodispersed palladium nanoparticles using aqueous extract of green tea and their catalytic activity for the Suzuki–Miyaura coupling reaction and the reduction of nitroarenes

A facile and green route for the synthesis of palladium nanoparticles (NPs) was developed utilizing non‐toxic and renewable natural green tea extract as the reducing, stabilizing and capping agent. The as‐prepared Pd‐NPs@G.Tea extract was characterized using UV–visible spectroscopy, X‐ray diffraction, Fourier transform infrared spectroscopy, field‐emission scanning electron microscopy, transmission electron microscopy and energy‐dispersive X‐ray spectroscopy. The Pd‐NPs@G.Tea extract could be used as an efficient and heterogeneous catalyst for Suzuki coupling reactions between phenylboronic acid and a range of aryl halides containing iodo, bromo and chloro moieties, and also for the reduction of nitroarenes using sodium borohydride in an environmentally friendly medium. Excellent yields of products were obtained with a wide range of substrates and the catalyst was recycled multiple times without any significant loss of its catalytic activity.     

Label‐Free Detection of MicroRNA: Two‐Step Signal Enhancement with a Hairpin‐Probe‐Based Graphene Fluorescence Switch and Isothermal Amplification

A label‐free approach with multiple enhancement of the signal for microRNA detection has been introduced. The key idea of this strategy is achieved by taking advantage of a novel graphene oxide (GO)/intercalating dye based fluorescent hairpin probe (HP) and an isothermal polymerization reaction. In this paper, we used microRNA‐21 (mir‐21) as the target to examine the desirable properties of this assay. When the target, as a “trigger”, was hybridized with the HP and caused a conformation change, an efficient isothermal polymerization reaction was activated to achieve the first step of the “signal” amplification. After incubation with the platform of GO/intercalating dye, the formed complex of DNA interacted with the high‐affinity dye and then detached from the surface of the GO, a process that was accompanied by distinguishable fluorescence recovery. Further signal enhancement has been accomplished by a mass of intercalating dye inserting into the minor groove of the long duplex replication product. Due to the efficient and multiple amplification steps, this approach exerted a substantial enhancement in sensitivity and could be used for rapid and selective detection of Mir‐21 at attomole levels. Proof‐of‐concept evidence has been provided for the proposed cost‐effective strategy; thus, this strategy could expand the application of GO‐material‐based bioanalysis for nucleic acid studies.