MICROCHIMICA ACTA
·
2017
·Vol. 184
·期 5
·1305-1313
·
IF 4.58
Zhou Lili,Wang Jian,Chen Zhongping,Li Junlong,Wang Ting,Zhang Zhang,Xie Guoming
MicroRNAs (miRNAs) play a considerable role in cancer occurrence and development, and have been identified as promising noninvasive biomarkers. The authors describe a voltammetric method for the determination of the cancer biomarker microRNA-21 (miRNA). It is based on a combination of a universal DNA signal transducer and isothermal target recycling amplification. A hairpin capture probe is bound to the target miRNA to form a duplex structure and to create a toehold in the transducer for initiating the target recycling amplification reaction. In contrast to traditional capture probes, a mismatched site is introduced to improve its ability to capture the target. In order to reduce the complex design procedures of the sequence and widen the applicability of this method, a signal transducer is introduced. Under optimal conditions, response to target miRNA is linear in the 0.5 to 2000 pM concentration range, with a 56 fM. detection limit (at an S/N ratio of 3). In order to characterize the process of target recycling and the stepwise modification of the electrode, real-time fluorescence, agarose gel electrophoresis, cyclic voltammetry, electrochemical impedance spectroscopy and chronocoulometry were used. The results indicate that this isothermal target recycling amplification results in an electrochemical biosensing scheme with wide potential for sensing other bioanalytes.
Schematic illustration of the electrochemical biosensing platform for miRNA-21 detection based on isothermal target recycling amplification and DNA signal transducer triggered strategy.
研究领域:
生物化学
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分析化学
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生物传感器
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癌症研究
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SENSORS AND ACTUATORS B-CHEMICAL
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2022
·
IF 9.221
Yanting Feng,Zewei Luo,Juan Wu,Zhijun Huang,Lu He,Yaqiang Feng,Xian Li,Xudong Zhang,Yonghui Tian,Yongxin Li,Yixiang Duan
Present DNA logic platforms mainly focused on distinguishing a specific kind of cancer cell from several other types of cell lines, while limited efforts have been paid to high-throughput recognition of cancer cells. A new DNA logic platform coupled with multivariate statistical analysis was developed to classify seven kinds of cancer cells. Four confined DNA circuits containing localized catalytic hairpin assembly (LCHA) and apurinic/apyrimidinic endonuclease 1 (APE1)-assisted circuits were conjugated to a protein of streptavidin (SA) for DNA logic platform. The mismatch minimizes the circuit leakage of the confined DNA circuits by inhibiting the incorrectly intramolecular structure switch. Benefitting from the spatial-confined effect, the DNA logic platform as a modified AND logic gate sensitively responded to the dual intracellular biomarkers, thereby generating strong dual fluorescent output signals in living cells. Based on the fluorescent cell imaging, multidimensional data collected from 50 individual cells were concatenated as a dataset for multivariate statistical analysis. Principal component analysis (PCA) shows distinct clustering among the seven kinds of cancer cell lines. A random forest algorithm obtained the specificity and sensitivity of 100%. Therefore, the DNA logic platform coupling with multivariate statistical analysis shows promising potential for cancer diagnosis and treatment.
研究领域:
生物技术
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癌症生物学
·
分子生物学
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生物信息学
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ACS Synthetic Biology
·
2023
·
IF 4.7
Peng Shen,Xiaojun Qu,Qinyu Ge,Ting Huang,Qingjiang Sun,Zuhong Lu
DNA is an attractive medium for long-term data storage because of its density, ease of copying, sustainability, and longevity. Recent advances have focused on the development of new encoding algorithms, automation, and sequencing technologies. Despite progress in these subareas, the most challenging hurdle in the deployment of DNA storage remains the reliability of preservation and the repeatability of reading. Herein, we report the construction of a magnetic bead spherical nucleic acid (MB-SNA) composite microstructure and its use as a cost-effective platform for reliable DNA preservation and repeated reading. MB-SNA has an inner core of silica@γ-Fe2O3@silica microbeads and an outer spherical shell of double-stranded DNA (dsDNA) with a density as high as 34 pmol/cm2. For MB-SNA, each strand of dsDNA stored a piece of data, and the high-density packing of dsDNA achieved high-capacity storage. MB-SNA was advantageous in terms of reliable preservation over free DNA. By accelerated aging tests, the data of MB-SNA is demonstrated to be readable after 0.23 million years of preservation at −18 °C and 50% relative humidity. Moreover, MB-SNA facilitated repeated reading by facile PCR-magnetic separation. After 10 cycles of PCR access, the retention rate of dsDNA for MB-SNA is demonstrated to be as high as 93%, and the accuracy of sequencing is more than 98%. In addition, MB-SNA makes cost-effective DNA storage feasible. By serial dilution, the physical limit for MB-SNA to achieve accurate reading is probed to be as low as two microstructures.
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ELECTROCHIMICA ACTA
·
2019
·
IF 5.383
Xia-Xia Liang,Lei Qian,Rong-Fu Huang
Endogenous cell metabolism and chemical reactions can induce oxidative DNA damage, which is involved in the development of different diseases. In this work, a label-free electrochemiluminescence (ECL) assay was proposed for the sensitive detection of oxidative DNA damage in an assembled DNA film. We employed the formamidopyrimidine-DNA glycosylase (Fpg) to convert DNA oxidative nucleobases to strand break, allowing to detect the DNA damage inducing minimal change to the helical structure of DNA. A “light-switch” DNA intercalator, [Ru(bpy) 2 (dppz)] 2+ (bpy = 2, 2 ′ -bipyridine, dppz = dipyrido[3, 2-a:2 ′ , 3 ′ -c]phenazine) was introduced as an ECL signal reporter to detect the DNA strand breaks. The damaged DNA film on the reduced graphene oxide and gold nanoparticles (r-GO@Au) modified ITO electrode bound less ECL indicator than the intact film and accompanied by a drop in ECL intensity, which were also confirmed by gel electrophoresis and fluorescence measurements. As a result, a Fe 2+ -mediated Fenton reaction with as low as 10 nM Fe 2+ and 40 nM H 2 O 2 induced DNA damage can be detected, 100-fold lower than the concentration measured without Fpg. To demonstrate its universality, the successful detection of DNA damage induced by Rose Bengal under irradiation was also achieved. The proposed strategy shows its potential practicality for the sensitive and rapid assessment of the genotoxicity of environmental pollutants .
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JOURNAL OF ELECTROANALYTICAL CHEMISTRY
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2018
·
IF 3.235
Hong Zhang,Zhaopeng Song,Feilong Pan,Fan He
A novel and enzyme-free electrochemical sensor was designed for multiplexed DNA detection based on a surface-confined DNA assembly enabled target recycling amplification. In this designed system, two hairpin DNA probes (hairpin 1 and hairpin 2) were immobilized on the surface of gold nanoparticles/graphene/nafion modified glassy carbon electrode (AuNPs/Gr/Nf/GCE). In the presence of two DNA targets, the hairpin structures of hairpin 1 and hairpin 2 opened through the complementary hybridization, resulting in the formation of hairpin 1: target DNA 1 and hairpin 2: target DNA 2. When they met methylene blue (MB)-labeled hairpin 3 (hairpin 3-MB) and ferrocene (Fc)-labeled hairpin 4 (hairpin 4-Fc), DNA cyclic amplification was activated, and the DNA targets were released and could be reused for the next recycling. Meanwhile, coupled with the utilization of positively charged gold nanoparticles ((+)AuNPs), multiplexed DNA detection was realized in the concentration range from 10 fM to 1.5 pM with the detection limits of 3.6 fM and 2.5 fM for target DNA 1 and target DNA 2, respectively. Moreover, satisfactory results were obtained when detecting DNA targets in human serum samples, suggesting that this proposed sensing platform is promising for the applications in complex biological samples.
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Biosensors-Basel
·
2022
·Vol. 12
·期 7
·449
·
IF 5.743
Yuxing Yang,Yang Qing,Xudong Hao,Chenxin Fang,Ping Ouyang,Haiyu Li,Zhencui Wang,Yazhen Liao,Haobin Fang,Jie Du
High-risk human papillomavirus (HPV) infection is an important cause of cervical cancer formation; therefore, being able to detect high-risk HPV (e.g., HPV-16) is important for the early treatment and prevention of cervical cancer. In this study, a combination of a 3-aminopropyltriethoxysilane (APTES) modified gold electrode and a super sandwich structure was creatively developed, resulting in the development of a biosensor that is both sensitive and stable for the detection of HPV-16. The electrochemical biosensor possesses a lower detection limit compared with previous studies with an LOD of 5.475 × 10−16mol/L and it possesses a wide linear range from 1.0 × 10−13mol/L to 1.0 × 10−6mol/L (R2= 0.9923) for the target DNA. The experimental data show that the sensor has good stability, and there is no significant decrease in the current response value after 7 days in the low-temperature environment. In addition, the sensor proved to be a powerful clinical tool for disease diagnosis because it showed good interference resistance in complex human serum samples.Keywords:cervical cancer;electrochemical detection;3-aminopropyltriethoxysilane;super sandwich structure
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Chemical Science
·
2026
·
IF 8.1
Xinyu Luan,Han Zhang,Zhe Li,Miao Ma,Junrui Zhang,Fang Liu,Junqiu Zhai,Tiangang Luan
Profiling the spatiotemporal dynamics of DNA demethylases is critical for deciphering the mechanisms of epigenetic regulation and genomic maintenance. However, existing fluorescent strategies often suffer from false-positive signals in living cells, primarily arising from non-specific nuclease degradation or instability of the complex amplification components. Herein, we present a generalisable "demethylation-activated" fluorescent light-up DNA aptamer (FLAP) strategy for high-contrast imaging of DNA alkylation repair in living cells. Our design relies on a precise "caging" strategy: site-specific methyl lesions (e.g., O6-meG) are engineered into the ligand-binding domain of the Bibb Lettuce aptamer, which disrupts its folding and suppresses fluorescence. Upon specific enzymatic repair, the aptamer structure is restored, triggering a robust fluorescence "turn-on" signal. This mechanism effectively minimises false-positive signals. The optimised probe detects MGMT activity with high sensitivity (LOD: 1.64 nM) and enables direct visualisation of active demethylation processes in MCF-7 cells, revealing distinct responses to inhibitors. Highlighting the modularity of the platform, we extended the design to detect AlkBH2 (LOD: 0.81 nM) simply by substituting the lesion with 1-methyladenine (1-meA). This work establishes a versatile and programmable framework for converting transient DNA repair events into quantifiable optical signals, providing a powerful tool for exploring epigenetic dynamics and cancer pharmacology.
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MICROCHEMICAL JOURNAL
·
2026
·
IF 5.2
Manlin Luo,Xiehui Peng,Fangfang Sheng,Yao Zhao,Hailiang Qin,Yuqing Zhang,Keke Wang,Yi Wu,Shuxia Xu
GelRed-photosensitized DNA cleavage enabled Hg 2+ detection. • T-Hg 2+ -T coordination triggered dsDNA assembly and GR intercalation. • The biosensor showed a linear range of 0.01–100 nM and an LOD of 1.30 pM. • Spiked water samples gave recoveries of 83.89–119.43%. A label-free GelRed-photosensitized electrochemical DNA biosensor was developed for Hg 2+ detection in water based on light-induced DNA cleavage. The sensing strategy integrates Hg 2+ -specific T-Hg 2+ -T coordination, GelRed (GR) intercalation, photosensitized oxidation, and impedance-based electrochemical readout. In the presence of Hg 2+ , two thymine-rich single-stranded DNA probes assemble into a double-stranded DNA structure through T-Hg 2+ -T coordination, allowing the nucleic acid dye GR to intercalate into the double-stranded DNA (dsDNA). Upon green-light irradiation, the dsDNA-GR complex acts as a photosensitizing system to generate singlet oxygen ( 1 O 2 ), which induces oxidative cleavage of the DNA and consequently changes the interfacial R ct . Under optimized conditions, R ct showed a linear relationship with the logarithm of Hg 2+ concentration, described by R ct (Ω) = −907 log C (Hg 2+ ) + 5312. The biosensor exhibited a linear range of 0.01–100 nM and a low limit of detection (LOD) of 1.30 pM. In spiked environmental water samples, recoveries of 83.89–119.43% were obtained with relative standard deviations of 3.49–9.32%, and the results were further evaluated by comparison with atomic fluorescence spectrometry. This work provides a GelRed-photosensitized DNA-cleavage strategy for sensitive and label-free electrochemical monitoring of Hg 2+ in aquatic environments. A label-free photocatalytic electrochemical DNA biosensor was developed for the detection of Hg 2+ in water. Download: Download high-res image (126KB) Download: Download full-size image
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SENSORS AND ACTUATORS B-CHEMICAL
·
2026
·
IF 8.3
Yu Zou,Xu Zhang,Chen Yue Lin,Shu Jun Zhen,Lei Zhan,Cheng Zhi Huang
Home-Förster resonance energy transfer (Homo-FRET) has been widely utilized in artificial light-harvesting systems to construct antenna structures with enhanced energy-capture efficiency. Although these systems typically exhibit remarkable antenna effects and signal amplification capabilities, their application in detection systems remains limited. Herein, we reported a rationally designed homo-FRET mediated three-donor/one-acceptor (3D-A) antenna nanostructure assembled on a rigid DNA tetrahedron scaffold for the quantitative detection of Hepatitis C virus (HCV) DNA. Robust homo-FRET interactions among the three donors significantly amplified the hetero-FRET efficiency to the single acceptor, generating an enhanced antenna effect. Upon target recognition, the system provided a ratiometric readout, where the fluorescence intensity ratio between Cy5 and Cy3 increased proportionally with HCV DNA concentration. The proposed 3D-A nanoprobe exhibited a linear response range from 1 to 100 nM with a detection limit of 65 pM. Furthermore, by simply altering the target-binding sequence, this system offered a high versatile platform for universal DNA detection detection.
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BIOSENSORS & BIOELECTRONICS
·
2026
·
IF 11.8
Chuang Wang,Yue Peng,Yuanyuan Miao,Xinyuan Sun,Qianlei Zhang,Zhaokun Zheng,Wenting Cheng,Jinlong Li
Aberrant DNA methylation has emerged as a critical epigenetic biomarker closely associated with bacterial pathogenicity and human tumorigenesis. In this study, a highly sensitive and label-free electrochemical biosensor has been developed for the detection of Dam MTase activity. 3′-aminated hairpin DNA probes (HP1) containing Dam MTase-specific recognition sites are immobilized onto the surface of a gold electrode. In the presence of Dam MTase, HP1 is methylated and subsequently cleaved by Dpn I, thereby exposing free 3′-hydroxyl groups. These hydroxyl groups serve as primers and are extended by terminal deoxynucleotidyl transferase (TdT) to generate long poly-thymine (polyT) tails. As an electrochemical redox indicator with numerous positive charges, ruthenium hexaammine trichloride (RuHex) can be captured by negatively charged DNA extension products. Accordingly, a remarkably enhanced electrochemical signal is produced, and the signal response is proportional to methyltransferase activity. This biosensor exhibits a good linear relationship in the range of 0.1 U/mL to 20 U/mL, and the limit of detection (LOD) is as low as 0.57 U/mL. Furthermore, its application value has been verified through the successful screening of existing MTase inhibitors (5-fluorouracil and gentamicin), indicating its potential application prospects in clinical diagnosis and antibacterial drug screening.
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MOLECULAR CELL
·
2025
·
IF 16.6
Lu-ning Qin,Ting Wu,Xue-ting Zhen,Yun-long Zhao,Jie-shi Zhou,Shan-bin Cheng,Kai-wen Wang,Shuai Qiao,Ding-zhi Huang,Heng Zhang,Tao Sun
The link between extrachromosomal DNA (ecDNA) and tumors has been well established, and its role in cancer is of increasing interest. While ecDNA is thought to originate from genomic instability, the molecular mechanisms driving DNA end ligation during ecDNA formation and the regulatory factors controlling its selective gene packaging remain unresolved. Here, using the multi-layer perceptron model, a series of imaging strategies in human cancer cells, and clinical chip verification, we demonstrate that ecDNA biogenesis depends on transcription factor Yin Yang 1 (YY1)-mediated DNA looping coupled with religation catalyzed by DNA ligase 3 (Lig3), a mechanism that extends existing models. Notably, PARylation-dependent acidic microenvironments mediated by the Lig3-YY1 complex play a critical role in the formation of Z-DNA, which potentially facilitates the fusion-religation process to drive ecDNA biogenesis. Furthermore, our findings establish PARP inhibitors as specific agents for ecDNA-targeted strategies in cancer therapy.
研究领域:
分子生物学
·
遗传学
·
癌症生物学
·
生物信息学
·
细胞生物学
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ACS Applied Materials & Interfaces
·
2026
·
IF 7.8
Fang Yin,Yuchun Guo,Jiangtao Ren,Erkang Wang
DNA-encoded nanomaterials have been widely developed, of which the properties are dependent on the DNA sequences and structures. Herein, stimulus-responsive catalytic nanosystems are presented based on DNA-templated copper nanoclusters (DNA-CuNCs) and the DNA allosteric effect. DNA-CuNCs synthesized with one of the DNA homopolymers, poly guanine with 5 guanine bases (5G DNA), as the template reveal apparent and stable catalytic activity toward 4-nitrophenol reduction by NaBH4. The rules are disclosed regarding the inhibition effects of diverse DNA on the catalytic activity of 5G-CuNCs. Of note, through adjusting the molar ratio of poly adenine (polyA) and poly thymine (polyT) from 1:1 to 1:2, a triplex DNA structure consisting of T–A·T triplets (poly(TAT)) was generated from a duplex with T–A base pairings (poly(AT)), which enabled the catalytic activity of 5G-CuNCs restored from the inactivated states in the presence of polyA or poly(AT). Hence, catalytic properties of 5G-CuNCs are encoded by different DNA structures and regulated reversibly through fuel-driven DNA allostery between duplex poly(AT) and triplex poly(TAT), thus yielding intriguing switchable catalytic nanosystems, which are also utilized for sensing designated DNA strands or one early cancer biomarker. It is believed that our research will contribute to formulating smart nanoprobes and nanodrugs for precise detection and therapy in the future.
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