Chemistry-An Asian Journal
·
2023
·
IF 4.1
Junyou Li,Hung-Wing Li
By combining exquisitely designed hairpins with the catalytic hairpin assembly to form tripedal DNA walkers driven by enzyme, we constructed a 3D DNA walker with accordingly complementary hairpins attached on gold nanoparticles (AuNPs) and sensitive fluorescence sensing system for the sensitive detection of target miRNA-21. The presence of miR-21 triggers the CHA among three hairpins, which lead to the formation of the tripedal DNA walkers. For the walking trajectories, FAM-labeled hairpins were attached to the surface of AuNPs, the fluorescence of which was initially quenched due to its close proximity to AuNPs. After the binding/cleaving/moving process of tripedal DNA walkers with HP4 driven by Exonuclease III (Exo III), a number of single-stranded DNAs (ssDNAs) will be released with FAM fluorescence recovered. Benefiting from the DNA walker and CHA cascade amplification, the proposed sensing strategy showed remarkable improvement in sensitivity with the LOD of 46 aM. Also, the system was practically applied in human serum samples, demonstrating satisfactory outcome. Owing to the precise design of the system, this method exhibited excellent specificity to distinguish miR-21 from its single-, double-mismatched sequences and non-complementary sequences, showing great versatility and potential for the biological analysis and early disease diagnosis.
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ANALYTICAL CHEMISTRY
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2019
·
IF 6.35
Jianguo Xu,Chao Yan,Xinxin Wang,Bangben Yao,Jianfeng Lu,Guodong Liu,Wei Chen
Facile and efficient assembly of intelligent DNA nano-objects with the ability to exert robust microRNA determination is essential for DNA nanobiotechnology and basic biomedical study. Herein, we present a novel target-triggered DNA assembly pathway for the construction of multibranched DNA nanoarchitectures by the combination of DNA concatamers with G-quadruplex wires. The DNA concatamers acting as the main body structures were assembled by hybridization chain reaction (HCR), while the G-quadruplex wires acting as the branch structures were generated by terminal deoxynucleotidyl transferase (TdT)-promoted polymerization and G-quadruplex units (GUs) based self-assembly. With a copious number of G-quadruplex replicates collected on the electrode surface, the obtained multibranched DNA nanoarchitectures were able to bind with lots of hemin, which further led to a significantly amplified electrochemical sensing signal for ultrasensitive and selective detection of miRNA-21. The detection limit was achieved as low as 0.2 fM with a wide dynamic response ranging from 10 fM to 100 nM, which is much more powerful or at least comparable to most of the reported studies. Furthermore, the electrochemical biosensor offered an excellent specificity, and even the single-base mutation against the perfectly matched target miRNA can be easily distinguished easily. Furthermore, the real biological samples were also desirably analyzed, indicating that the proposed strategy is an ideal platform for the fabrication of versatile DNA nanobiosensors.
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Theranostics
·
2018
·
IF 8.537
Shulian Bai,Bangtian Xu,Yongcan Guo,Juhui Qiu,Wen Yu,Guoming Xie
While detection of microRNA with or without signal amplification is highly informative, nanosensors with high specificity for cell-specific RNA detection are rare. Methods: In this study, a tetrahedral DNA nanostructure (TDN) with a specific function was combined with gold nanoparticles (Au-NP) possessing fluorescence quenching effects and a large surface area to fabricate a fluorescence resonance energy transfer based nanosensor (Au-TDNN). The presence of miR-21 (target) can separate the fluorescent dye-labeled detection probe on Au-TDNNs from Au-NPs, which separates the donor and acceptor, thus inducing an intensive fluorescence signal. High specificity for discerning point mutation targets was achieved by rationally designing the nucleic acid strand displacement reaction to occur spontaneously with ΔG 0 ≈ 0 based on thermodynamic parameters; under this condition, slight thermodynamic changes caused by base mismatch exert significant effects on hybridization yield. Results: Chemically synthesized DNA of three single-base-changed analogues of target, let-7d, and miR-200b were tested. A discrimination factor (DF) of 15.4 was produced by the expected detection probe on Au-NPs for proximal single-base mismatch. As the control group, the DF produced by an ordinary detection probe on Au-NPs only reached 2.4. The feasibility of the proposed strategy was also confirmed using hepatocyte cancer cells (HepG2). Conclusion: This improved nanosensor opens a new avenue for the specific and easy detection of microRNA in live cells.
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SENSORS AND ACTUATORS B-CHEMICAL
·
2017
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IF 5.401
Bingchen Li,Huanshun Yin,Yunlei Zhou,Minghui Wang,Jun Wang,Shiyun Ai
MicroRNAs play a crucial role in regulating plant growth, such as involving in the pathways of phytohormons signaling, which function in broad range of important aspects in many stages of plant development and evolution. To figure out the components part of microRNA in phytohormone signaling network, a sensitive photoelectrochemical biosensor was developed to detect miRNA-319a specifically using CuO-CuWO 4 as photoactive material and in situ generation electron donor technique. Taking the advantage of rolling circle amplification, nicking endonuclease triggered exponential amplification of target molecule, specific interaction between phosphate group and phos-tag and between biotin and avidin, the developed strategy can greatly amplify the detection signal only using trace amount of target miRNA-319a. The wide linear range was obtained from 1 fM to 0.1 nM and the detection limit was estimated to be 0.47 fM (S/N = 3). The developed method also showed good detection specificity. The effect of five phytohormones on the expression level of miRNA-319a in rice leaves was also investigated. This will be a basal principle of investigating the signaling network of phytohormones.
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PESTICIDE BIOCHEMISTRY AND PHYSIOLOGY
·
2022
·
IF 4.966
Benshui Shu,Yanzheng Lin,Guozhao Qian,Xueming Cai,Luyang Liu,Jintian Lin
As a destructive agricultural pest, Spodoptera frugiperda has spread worldwide in the past few years. Azadirachtin , an environmentally friendly and most promising compound, showed adverse effects, including mortality and growth inhibition, against S. frugiperda . While the effects of azadirachtin on the midgut of this pest remain to be determined. In this study, structural damage was observed in the larval midguts of S. frugiperda with azadirachtin exposure. RNA-seq on the larval midguts with different azadirachtin treatments was performed. Compared to the control group, a total of 3344 and 4759 differentially expressed genes (DEGs) were identified in the midguts with 0.1 and 0.5 μg/g azadirachtin exposure, respectively. Among them, the DEGs encoding detoxification enzymes/proteins, immune-related proteins, digestion and absorption-related proteins, and transcript factors were further analyzed. High-throughput sequencing was also used for the identification of differentially expressed microRNAs in different treatments. A total of 153 conserved miRNAs and 147 novel miRNAs were identified, of which 11 and 29 miRNAs were affected by 0.1 and 0.5 μg/g azadirachtin treatments, respectively. The integrated analysis found that 13 and 178 miRNA versus mRNA pairs were acquired in the samples with 0.1 and 0.5 μg/g azadirachtin treatments, respectively. The results of high-throughput sequencing were confirmed by real-time quantitative polymerase chain reaction (RT-qPCR). These results provide useful information for revealing the molecular mechanism of S. frugiperda larval midgut in response to azadirachtin.
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NEW JOURNAL OF CHEMISTRY
·
2021
·Vol. 45
·期 24
·10907-10913
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IF 3.591
Yanfang Cui,Jing Zheng,Wei Zhuang,Haiwang Wang
A novel surface-enhanced Raman scattering (SERS) platform has been developed for the highly sensitive detection of miRNA-21 by target activation depending on exonuclease-assisted signal amplification with a plasmon coupling phenomenon. In this system, a Raman dye-modified gold nanoparticle (AuNP) substrate can be covalently linked by the thiolated DNA track and DNA walker, which combine the protection probe at the 3′ terminal end to prevent reaction with the DNA track. In the presence of miRNA-21, it will combine the protect probe to the DNA walker depending on more complementary base pairing and release the DNA walker, which will combine with the adjacent DNA track. Depending on the exonuclease III (exo III) cleavage, the DNA walker can walk along the surface of AuNPs and produce the self-assembled hot spots between AuNPs, allowing a homogenous detection of the miRNA-21 with high sensitivity and reproducibility. Under optimized experimental conditions, the platform detected miRNA-21 with a wide range from 10 pM to 1.0 × 105 pM and displayed very low detection limit (4.0 pM). Hence, the novel strategy will become a promising tool for the SERS assay of miRNA-21 with high sensitivity and repeatability. Furthermore, this platform also owns great potential for cancer typing and clinical diagnostics.
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Chemical Science
·
2016
·Vol. 7
·期 7
·4184-4189
·
IF 9.144
Zhen Zhang,Yuanyuan Wang,Ningbo Zhang,Shusheng Zhang
We herein report a novel finding that nucleic acid molecular aggregates (NAMAs) self-assembled on graphene oxide nanoplates (GONPs) as a result of DNA rolling circle amplification (RCA) and a functionalized triple-helix probe (THP) in single cells. The functionalized THP containing the aptamer region for target recognition and the trigger DNA region for RCA was firstly used to activate RCA for miRNA imaging in single cells. Interestingly, NAMAs with the fluorescent labels were hybridized by both the RCA products and FAM-DNA, and could partly self-assemble on GONPs; meanwhile, NAMAs could extend from the GONPs, which led to the quenched fluorescence being renewed. Significantly, the NAMAs were successfully applied for low-abundance miRNA detection and imaging in single cells. The self-assembled NAMAs could generate prominent and agminated fluorescence-bright spots in single cancer cells, which will effectively drive cell imaging into a new era.
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SPECTROCHIMICA ACTA PART A-MOLECULAR AND BIOMOLECULAR SPECTROSCOPY
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2022
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IF 4.831
Qingyou Cai,Fanfan Wang,Jingying Ge,Zhiguo Xu,Mei Li,Hui Xu,Hua Wang
Herein, we reported the G-wire-based self-quenched fluorescence probe and its application in ultrasensitive microRNA (miRNA) detection by combining with target-activated isothermal cascade amplification. The terminal-single-fluorescein (FAM)-labeled G-rich oligonucletides self-assembled into G-wire nanostructures (G-wires) with K + and Mg 2+ . Thereafter, the G-wires brought terminal-labeled FAM into close proximity, as a result, the self-quenched signal probe formed. Besides, when there was the target miRNA, target-activated isothermal cascade amplification converted miRNA into the copious trigger DNA. After hybridization between trigger DNA and the self-quenched probe, the G-wires were splited and forced the apart of proximate FAM, and then the self-quenched probe displayed an “on” mechanism. Therefore, the approach gave a limit of detection (LOM) of 0.82 aM to miRNA-21 and could be implemented within a wide linear range of 2 aM to 2 nM. This approach was able to distinguish the single-mismatched miRNA-21, which was selective and sensitive in detecting human spiked serum samples.
研究领域:
分子生物学
·
生物化学
·
纳米技术
·
癌症诊断
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JOURNAL OF SOLID STATE ELECTROCHEMISTRY
·
2014
·Vol. 18
·期 10
·2829-2835
·
IF 2.234
Wang Mo,Yin Huanshun,Fu Zhengliang,Guo Yunlong,Wang Xinxu,Zhou Yunlei,Ai Shiyun
MicroRNAs (miRNAs), a class of small endogenous nonprotein-coding RNAs, regulate a wide range of biological processes, and their abnormal expressions are related to the growth and development of plants. Thus, a simple, rapid, and highly sensitive assay for miRNA detection is of great significance. In this work, a label-free and ultrasensitive assay for miRNA detection using protein cage nanoparticles has been developed. Apoferritin-encapsulated Cu nanoparticles (Cu-apoferritin) could be immobilized on the electrode through special reaction between amino and carboxyl. Hybridization event between the probe DNA and the target miRNA-159a is confirmed by electrochemical oxidation signal after Cu released into the detection buffer by adjusting the pH. This assay is highly selective and sensitive with a low detection limit of 3.5 fM. Moreover, the developed method can even discriminate single-base mismatched strand between the complementary targets. The effect of abscisic acid on the expression level of miRNA-159a in Arabidopsis thaliana seeds was also investigated.
研究领域:
植物学
·
遗传学
·
纳米技术
·
电化学
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STAR Protocols
·
2024
·
IF 1.3
Xiaoxiang Gao,Yinghui Qiu,Wei Liao,Chao Zhao
Summary Regulating cancer-related microRNAs (miRNAs) may become a new generation of therapeutic modalities for cancer treatment. Here, we describe a protocol based on hepatoma-22 (H22) tumor-bearing mice to screen potential targets for treating hepatocellular carcinoma (HCC). We detail the construction of H22 tumor-bearing mice and treatment with two natural compounds, Ulva lactuca L. polysaccharide (ULP) and 5-fluorouracil (5FU). We further describe the isolation of the tumor tissues for miRNA sequencing and the discovery and validation of potential miRNA gene targets against HCC. For complete details on the use and execution of this protocol, please refer to Qiu et al. 1
研究领域:
肿瘤学
·
分子生物学
·
遗传学
·
药理学
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BIOSENSORS & BIOELECTRONICS
·
2026
·
IF 11.8
Ting Huang,Ziyue Qiu,Siyuan Tan,Luyin Zhang,Jing Peng,Simin Liu,Xiaoming Lyu,Zong Dai,Jun Chen,Jin-Xiang Chen
Precise imaging of intracellular biomarkers is crucial for accurate disease diagnosis and mechanistic insight. Although confined catalytic hairpin assembly (CCHA) can accelerate reaction kinetics, its performance is frequently compromised by nonspecific amplification, resulting in high background signals and limited imaging contrast. Here, we develop a tumor-upregulated endogenous apurinic/apyrimidinic endonuclease 1 (APE1)-triggered CCHA (AP-CCHA) system based on a DNA nanowire for selective microRNA (miRNA) imaging in living tumor cells. Using miR-21 as a proof-of-concept model, the mechanistic analyses demonstrated that conventional CCHA suffers from significant nonspecific signal amplification during both in vitro assembly and storage. For the proposed AP-CCHA system, we incorporated an APE1-activatable AP-H1 probe that improves molecular stability, suppresses nonspecific amplification, and consequently enhances the signal-to-noise ratio while preserving high reaction kinetics. As a result, the AP-CCHA system delivers a 3.5-fold improvement in sensitivity compared with CCHA and achieves an 18.2 pM detection limit for miR-21. Leveraging the elevated cytoplasmic APE1 levels in tumor cells, AP-CCHA remains quiescent in normal cells but is selectively activated in cancer cells, enabling high-contrast miRNA discrimination and precise in vivo tumor imaging, and effectively minimizing false positives. By integrating confinement-enhanced kinetics with endogenous enzyme activation, this strategy enables rapid, highly sensitive, and high-contrast biomarker imaging. The AP-CCHA platform thus provides a versatile analytical tool for nucleic acid-based diagnostics with strong potential for precision therapeutics and drug development applications.
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ANALYTICAL CHEMISTRY
·
2021
·
IF 6.986
Jiwei Wang,Caiyi Zhang,Zhao Liu,Shibao Li,Ping Ma,Fenglei Gao
A multifunctional theranostic nanosystem that integrates dynamic monitoring and therapeutic functions is necessary for precision tumor medicine. Herein, an entropy-driven self-assembly nanomachine is developed that overcomes the mechanism differences of different diagnostic modes and is applied to miRNA surface-enhanced Raman scattering (SERS)–fluorescence dual-mode dynamic monitoring and synergy phototherapy. It is worth noting that the activated dual-mode theranostic nanosystem (DTN) is capable of tumor in situ fluorescence imaging and SERS absolute quantification of the target. After being internalized into tumor cells, the DTN nanosystem is activated by the DNA cascade chain displacement of the target miR-21, resulting in the secondary release of fluorophores and the assembly of core–satellite structures (CS structures). The coupling of localized surface plasmon resonances (LSPRs) in the CS structure results in the formation of numerous enhanced electric fields (hot spot) in the nanogap of the CS structure. Then the DTN nanosystem greatly improves the sensitivity and repeatability of Raman detection by converting trace targets into numerous adenines residing in the electromagnetic hot spot of the CS structure. Meanwhile, the CS structure and the loaded photosensitizer are used for synergy phototherapy under the guidance of fluorescence imaging. This proposed strategy is confirmed by in vivo and in vitro results, and it provides new ideas for tumor SERS–fluorescence dual-mode diagnosis and effective tumor therapy.
研究领域:
纳米技术
·
生物医学工程
·
癌症治疗
·
分子诊断
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