MICROCHIMICA ACTA
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2024
·Vol. 191
·期 7
·1-13
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IF 5.3
Zhao Tangtang,Xiao Ruilin,Li Yueqi,Ren Jierong,Niu Liyun,Chang Bingmei
With their regulated Boolean logic operations in vitro and in vivo, DNA logic circuits have shown great promise for target recognition and disease diagnosis. However, significant obstacles must be overcome to improve their operational efficiency and broaden their range of applications. In this study, we propose an Exo III-powered closed-loop DNA circuit (ECDC) architecture that integrates four highly efficient AND logic gates. The ECDC utilizes Exo III as the sole enzyme-activated actuator, simplifying the circuit design and ensuring optimal performance. Moreover, the use of Exo III enables a self-feedback (autocatalytic) mechanism in the dynamic switching between AND logic gates within this circulating logic circuit. After validating the signal flow and examining the impact of each AND logic gate on the regulation of the circuit, we demonstrate the intelligent determination of miR-21 using the carefully designed ECDC architecture in vitro. The proposed ECDC exhibits a linear detection range for miR-21 from 0 to 300 nM, with a limit of detection (LOD) of approximately 0.01 nM, surpassing most reported methods. It also shows excellent selectivity for miR-21 detection and holds potential for identifying and imaging live cancer cells. This study presents a practical and efficient strategy for monitoring various nucleic acid-based biomarkers in vitro and in vivo through specific sequence modifications, offering significant potential for early cancer diagnosis, bioanalysis, and prognostic clinical applications. Graphical abstract
研究领域:
分子生物学
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生物医学工程
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诊断学
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PubMed
高影响因子
MICROCHIMICA ACTA
·
2017
·Vol. 184
·期 3
·951-959
·
IF 4.58
Zhang Yuhuan,Wang Yanru,Zhu Wenxin,Wang Jing,Yue Xiaoyue,Liu Wei,Zhang Daohong,Wang Jianlong
The capability of multi-level logic operations in biological diagnosis is far from being fully realized. In particular, the simplification of logic judgments to realize rapid, on-site complex diagnoses is still a key issue in bioelectronics. The authors here describe the construction of a colorimetric multilevel DNA circuit that incorporates two IMPLY gates and a sample extraction technology (SET) with anti-BPA aptamer as a co-recognizing element and the color of gold nanoparticles as the output signal. The circuit can perform multi-bioanalysis of the plasticizers and hormone mimetics bisphenol A (BPA) and bisphenol S (BPS). The assay is based on the finding that the aptamer against BPA can recognize both BPA and BPS. This DNA logic detection system is simple, fast, sensitive and selective because of the utilization of a co-recognition element which decreased input numbers. This, in turn, cascades multiplex Boolean logic gates and simplifies the diagnostic challenge. Both BPA and BPS can be determined by photometry at 620 nm, the limit of detection being 1.5 ng⋅mL −1 for BPA and 1.3 ng⋅mL −1 for BPS. Application to (spiked) water samples shows good analytical performance in terms of recovery (95.4 to 106.8%), linear range (4.4 to 66 ng⋅mL −1 for BPA, 2.5 to 75 ng⋅mL −1 for BPS) and correlation coefficients (>0.98). In our perception, the method represents a simple route for the fabrication of colorimetric multi-level DNA circuits. It may shorten the gap between bioelectronic logic circuits and high throughput real sample analysis.
Illustration of sample extraction treatments (SET) of bisphenol A (BPA) and bisphenol S (BPS) and the three-input IMPLY1-IMPLY2 logic operation with BPA, BPS and anti-BPA aptamer as inputs.
研究领域:
生物化学
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分析化学
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生物医学工程
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高影响因子
Analytical Methods
·
2022
·Vol. 14
·期 11
·1140-1147
·
IF 3.532
Tuqiang Li,Yulan Wang,Yanan Zhang,Guobao Zhou,Lei Li
An entropy-driven DNA circuit offers an efficient means of sensitive analyte detection with signal amplification. In this article, we rationally engineered an aptamer-based entropy-driven signal-off DNA circuit for colorimetric detection of small molecules. The proposed signal-off DNA circuit is activated by target small molecule binding to drive the collapse of G-quadruplex DNAzyme, accompanied by the colour change of the detection solution from dark blue to light blue. Entropy-driven recycling hybridization significantly magnified the input signal of the target small molecule. Such an assay enables naked-eye detection of adenosine triphosphate and oxytetracycline at concentrations as low as 0.5 μM and 1 μM respectively. Moreover, when compared with the signal-on DNA circuit, the entropy-driven signal-off DNA circuit for colorimetric detection has two advantages. Firstly, unlike in the signal-on DNA circuit, the unavoidable formation of waste complexes in the absence of a target in the signal-off DNA circuit has no influence on target detection performance as its background signal is only determined by the substrate complex. Secondly, the signal-on DNA circuit cannot distinguish false-positive signals generated by invasive catalysts (e.g., HRP, serum, Fe3O4), while the signal-off DNA circuit can distinguish those signals as undesired signals. Overall, the signal-off DNA circuit affords a novel strategy for sensitive and accurate detection of small molecules.
研究领域:
生物化学
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分子生物学
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PubMed
高影响因子
BIOSENSORS & BIOELECTRONICS
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2024
·
IF 10.7
Yujing Liang,Yifei Wang,Mengdi Yu,Yuqian Jiang,Jinhua Shang,Xiaoqing Liu,Fuan Wang
Biomolecules play essential roles in regulating the orderly progression of biochemical reaction networks. DNA-based biocircuits supplement an attractive and ideal approach for the visual imaging of endogenous biomolecules, yet their sensing performance is commonly encumbered by the undesired signal leakage. To solve this issue, here we proposed a glutathione (GSH)-activated DNA circuit for achieving the spatio-selective microRNA imaging through the successive response of a GSH-specific activation procedure and a non-enzymatic catalytic signal amplification procedure. In this design, by incorporating a disulfide bond into the pre-sealed nucleic acid probe, the uncontrolled circuitry leakage could be effectively ameliorated. In target cancer cells with high-abundant GSH and miR-21, endogenous GSH recognized and cleaved the pre-installed disulfide bond within DNA probes, thereby restoring the activity of circuitry components. The miR-21 then catalyzed the specific operation of circuitry for generating an amplified readout signal. We demonstrate that this system not only enables the effective discriminations of various cell types, but also contributes to the exploration of the correlationship between GSH and miR-21. This on-site activated DNA circuit can be extended to the robust analysis and exploration of different biomolecular interactions, offering a reliable reference for the in-depth understanding of biochemical interaction networks.
研究领域:
生物化学
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分子生物学
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医学诊断
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DOI
PubMed
高影响因子
JACS Au
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2024
·
IF 8.5
Suo Lv,Qunyan Yao,Jiasheng Yi,Jingyi Si,Yifan Gao,Shao Su,Changfeng Zhu
Hepatitis B virus (HBV) infection remains a major global health concern, necessitating the development of sensitive and reliable diagnostic methods. In this study, we propose a novel approach to enhance the sensitivity of HBV DNA detection by leveraging a concentration imbalance-driven DNA circuit (CIDDC) as an operational amplifier, coupled with a hybridization-responsive DNA-templated silver nanocluster (DNA-AgNCs) nanoprobe named Q·C6-AgNCs. The CIDDC system effectively converts and amplifies the input HBV DNA into an enriched generic single-stranded DNA output, which subsequently triggers the fluorescence of the DNA-AgNCs reporter upon hybridization, generating a measurable signal for detection. By incorporating the DNA circuit, we not only achieved enhanced sensitivity with a lower detection limit of 0.11 nM but also demonstrated high specificity with single-base mismatch discriminability for HBV DNA detection. Additionally, this mix-and-detect assay format is simple, user-friendly, and isothermal. This innovative strategy holds promise for advancing molecular diagnostics and facilitating the effective management of HBV-related diseases.
研究领域:
分子生物学
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医学诊断
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纳米技术
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DOI
PubMed
高影响因子
JOURNAL OF FOOD COMPOSITION AND ANALYSIS
·
2025
·
IF 4.6
Xin Xie,Jingxi Wang,Daxiu Li,Ding Wang
Ochratoxin A (OTA) poses a great threat to food and environmental safety owing to its high toxicity. Herein, we developed a sensitive electrochemical aptasensor that integrates aptamer, enzyme-free DNA circuits, and electrochemical technology for OTA detection. In the presence of target OTA, the aptamer recognition first initiated the EDC circuit to releasing DNA (T2) from a ternary DNA complex (S-O-T2). The released T2 as the trigger to activate the CHA circuit and expose amounts of G-quadruplex sequences on modified electrode surface. Eventually, hemin was embedded in the G-quadruplex structure and generated an amplified electrochemical signal. Under optimal conditions, this developed biosensor is capable of detecting OTA ranging from 1 pg/mL to 10 ng/mL with a low detection limit of 0.135 pg/mL, which could be contributed to the design of target-triggered EDC and CHA cascade amplification. Additionally, the proposed biosensor was applied to analyze OTA in corn samples with satisfactory results, demonstrating that the proposed method has great potential in food safety and environmental monitoring.
研究领域:
生物化学
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分析化学
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食品科学
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高影响因子
ANALYTICAL CHEMISTRY
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2021
·
IF 6.986
Dan Zhu,Zihao Ma,Zichun Wang,Qingyun Wei,Xiaojian Li,Jingjing Wang,Shao Su,Xiaolei Zuo,Chunhai Fan,Jie Chao,Lianhui Wang
Accurate, specific, and inexpensive detection of multiple infectious pathogens simultaneously is a significant goal for human health and safety. Herein we present a rationally designed modular DNA circuit for point-of-care (POC) detection of a variety of infectious pathogens based on nucleic acid isothermal amplification technology and DNAzyme-mediated colorimetric readout. A modular DNA circuit was constructed with a fixed module and a flexible module and was rationally designed according to genetic targets. On this basis, the platform could detect multiple genetic targets corresponding to infectious pathogens simultaneously. Signal amplification properties of the DNA circuit and the peroxidase-like DNAzyme enable the detection limits to reach the picomolar level. By urea treatment and magnetic separation, the fixed module can be reused at least five times, which makes this assay more economical and environmentally friendly. The detection of genetic infectious pathogens should be accomplished in 2 h with naked-eye observation and may provide an efficient tool for POC analysis of multiple infectious pathogens, especially in resource-poor areas.
研究领域:
生物化学
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分子诊断
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医学工程
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DOI
PubMed
高影响因子
ANALYTICA CHIMICA ACTA
·
2022
·
IF 6.911
Dongyan Li,Huaiyue Xia,Yingying Sun,Wenjie Liu,Wen Liu,Jianna Yu,Guoxing Jing,Jian Zhang,Wenshan Li
Ochratoxin A(OTA), a highly toxic mycotoxin commonly found in food, poses a serious threat to health even at low concentrations. Developing a sensitive, accurate, simple, and cost-effective detection method is of great significance for food safety and quality control. Herein, a triple cascade amplification strategy was used to construct the colorimetric assay for the detection of OTA, where the amplification process consists of an entropy-driven DNA circuit (EDC), a catalytic hairpin assembly (CHA), and Mg 2+ -assisted DNAzyme catalysis (MNAzyme). Through the specific binding of ochratoxin A (OTA) and its aptamer , an initiator strand is released to initiate upstream EDC and then produce a new trigger unit that motivates downstream CHA to generate MNAzyme, which further cleaves the substrate strand to induce the formation of G-quadruplex/hemin DNAzyme as a signal readout. The aptasensor was shown to detect OTA, with a low detection limit of 8.7 fM and good selectivity . The developed method could be used as a highly colorimetric aptasensor for the detection of OTA in spiked rice samples.
研究领域:
食品安全
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分析化学
·
分子生物学
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PubMed
高影响因子
ANALYTICAL CHEMISTRY
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2025
·
IF 6.7
Ting Li,Tat San Lau,Junyou Li,Kaiqi Hu,Man Lung Lee,Pin You Chen,Chi Chiu Wang,Hung-Wing Li
Nonenzymatic autocatalytic DNA circuits, capable of exponential signal amplification, exhibit superior amplification efficiency compared to traditional single or cascade DNA amplification circuits, which offer only linear or quadratic signal amplification. However, autocatalytic DNA circuits are currently limited by complicated splitting designs, low autocatalytic efficiency, the need for additional probes, and a lack of universal design principles. Herein, we developed a PCR-like split-free autocatalytic amplification (SAA) DNA circuit with a simple design but extraordinary autocatalytic efficiency for effective biosensing. The SAA system could consecutively perform multiple cycles of a three-step process upon initiation, target recognition, replicating, and recycling, which is programmed to mimic the basic three reaction steps of PCR and constantly yield numerous new split-free target replicates to expedite the whole reaction, ultimately producing an exponentially amplified signal. The PCR-like sigmoidal kinetics, the ability to accurately execute the programmed instructions, and the high autocatalytic capability of the SAA system are demonstrated, which achieves the same target replication as the PCR but without the need for enzymes and precise control of temperature. The SAA circuit, characterized by exponential signal amplification, simple design, and minimal components, offers a promising approach for developing highly efficient universal DNA circuits. This enables the analysis of low-abundance biomarkers with minimal signal leakage, holding significant potential for biochemical research and clinical diagnosis.
研究领域:
分子生物学
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生物化学
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诊断学
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DOI
PubMed
高影响因子
ANALYTICAL CHEMISTRY
·
2024
·
IF 6.7
Yexin Hu,Yuqing Cui,Zhemeng Zhang,Xinyi Zhang,Xiao Ma,Zhou Qiao,Feng Zheng,Feng Feng,Wenyuan Liu,Lingfei Han
Lipid nanoparticles (LNPs) are emerging as one of the most promising drug delivery systems. The long-circulating effect of intact LNPs (i-LNPs) is the key to efficacy and toxicity in vivo. However, the significant challenge is specific and sensitive detection of i-LNPs. Herein, a dual-recognition fluorescence enzyme-linked immunosorbent assay (DR-FELISA) was developed to directly isolate and detect i-LNPs by combining dual-recognition separation with a one-step signal amplification strategy. The microplates captured and enriched i-LNPs through antibody–antigen reaction. Dual-chol probes were spontaneously introduced into the lipid bilayer of captured i-LNPs, converting the detection of i-LNPs into the detection of double-cholesterol probes. Finally, the end of the dual-chol probes initiated the localized scaffolding autocatalytic DNA circuits (SADC) system for further signal amplification. The SADC system provides a sensitive and efficient amplifier through localized network structures and self-assembled triggers. Simultaneous recognition of i-LNPs surface PEG-lipid and lipid bilayer structures significantly eliminates interference from biological samples. i-LNPs were detected with high selectivity, ranging from 0.2 to 1.25 mg/mL with a limit of detection of 0.1 mg/mL. Moreover, this method allows the isolation and quantitative analysis of different formulations of i-LNPs in serum samples with a satisfactory recovery rate ranging from 94.8 to 116.3%. Thus, the DR-FELISA method provides an advanced platform for the exclusive and sensitive detection of i-LNPs, providing new insights for the study of the quality and intracorporal process of complex formulations.
研究领域:
生物技术
·
分子生物学
·
药物递送系统
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DOI
PubMed
高影响因子
ANALYTICA CHIMICA ACTA
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2021
·
IF 6.558
Furui Jin,Danke Xu
The DNA microarray has distinctive advantages of high-throughput and less complicated operations, but tends to have a relatively low sensitivity. Catalytic hairpin assembly (CHA) is one of the most promising enzyme-free, isothermal DNA circuit for high efficient signal amplification. Here, a microarray-based catalytic hairpin assembly (mi-CHA) biosensing method has been developed to detect various miRNAs in a single test simultaneously. The target miRNA can trigger conformational transformations of hairpin-structured DNA probes on the chip surface and lead to the specific signal amplification. A significant advantage of this approach is that each duplex produced by the solid-phase CHA will be immobilized on the certain location of the chip and release fluorescent signal via the universal domain, eliminating the requirement of different fluorophores. This method has manifested a high detection sensitivity of human cancer-associated miRNAs (miR-21 and miR-155) down to 1.33 fM and promised a high specificity to distinguish single-base mismatches. Furthermore, the practicability of this method was demonstrated by analyzing target miRNAs in human serum and cancer cells. The experimental results suggest that the proposed method has high-throughput analytical potential and could be applied to many other clinical diagnosis.
研究领域:
生物技术
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分子生物学
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癌症研究
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纳米技术
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DOI
PubMed
高影响因子
FOOD CONTROL
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2025
·
IF 6.3
Xinru Ren,Weiqing Sun,Bowen Li,Yijing Xiao,Xudong Yue,Meili Yang,Qing-ao Pang,Rui Zhu,Zhiqiang Guo,Haiping Zhang,Yu Wang,Su Liu,Jiadong Huang
The detection of pathogenic bacteria plays a crucial role in ensuring food safety and public health. The integration of isothermal amplification technology with the clustered regularly interspaced short palindromic repeats (CRISPR) and CRISPR-associated proteins (Cas) system offers a versatile approach to detecting foodborne pathogens. However, this method is often constrained by the incompatibility of the reaction systems and the lack of control over CRISPR/Cas activity. Here, we demonstrated a fluorescence biosensing strategy based on linear causal-regulated and autocatalysis-driven DNA circuits (termed LC@ADC) for highly sensitive and specific detection of Salmonella Typhimurium ( S. Typhimurium ). The approach of combining hybridization chain reaction (HCR) with DNAzyme-driven CRISPR/Cas12a activation was proposed for the first time, enabling not only one-step cascade signal amplification but also controllable DNA circuits. The LC@ADC strategy is capable of quantifying concentrations of S. Typhimurium ranging from 10 to 1 × 10 5 CFU/mL, with a detection limit as low as 6.53 CFU/mL. Furthermore, the LC@ADC strategy has been successfully employed for the detection of S. Typhimurium in samples of orange juice, chicken, and lake water. Therefore, this strategy provides a novel approach for the high-performance detection of pathogenic bacteria.
研究领域:
分子生物学
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生物技术
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食品安全
·
公共卫生
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生物传感器
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微生物学
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DOI
高影响因子
危险品化学品经营许可证（带存储）