BIOSENSORS & BIOELECTRONICS
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2012
·
IF 5.602
Limei Zhu,Liqiang Luo,Zhenxin Wang
A novel protocol for development of DNA electrochemical biosensor based on thionine-graphene nanocomposite modified gold electrode was presented. The thionine-graphene nanocomposite layer with highly conductive property was characterized by scanning electron microscopy, transmission electron microscopy, cyclic voltammetry and electrochemical impedance spectroscopy. An amino-substituted oligonucleotide probe was covalently grafted onto the surface of the thionine-graphene nanocomposite by the cross-linker glutaraldehyde. The hybridization reaction on the modified electrode was monitored by differential pulse voltammetry analysis using an electroactive intercalator daunomycin as the indicator. Under optimum conditions, the proposed biosensor exhibited high sensitivity and low detection limit for detecting complementary oligonucleotide. The complementary oligonucleotide could be quantified in a wide range of 1.0 × 10 −12 to 1.0 × 10 −7 M with a good linearity ( R 2 = 0.9976) and a low detection limit of 1.26 × 10 −13 M (S/N = 3). In addition, the biosensor was highly selective to discriminate one-base or two-base mismatched sequences.
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JOURNAL OF THE ELECTROCHEMICAL SOCIETY
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2023
·Vol. 170
·期 11
·117513
·
IF 3.9
Qing-Zheng Zhang,Chun-Bo Su,San-Jun Shi,Yue Gao,Rong-Fu Huang
Because the cytotoxic DNA methylated bases are chemically inert and small in size, limited biosensing strategies especially with high sensitivity were established to detect DNA methylation damage. In this work, a label-free electrochemical assay was proposed for the sensitive detection of DNA methylation damage in dsDNA film on indium tin oxide electrode. The human alkyladenine DNA glycosylase was employed to recognize and selectively remove DNA methylated bases, generating apurinic site. Subsequently, exonuclease III not only further converted the methylation sites into strand breaks, but also progressively removed nucleotides from the 3' to 5' end starting from the apurinic sites. These processes could maximum amplify DNA methylation damage, also confirmed by gel electrophoresis and fluorescence measurements. The damaged DNA film bound much less electrochemical indicator, Ru(bpy)2(dppz)2+, and accompanied by an anodic current drop. As a result, DNA methylation damage produced with as low as 10 μM of methyl methanesulfonate can be detected, which was 100-fold lower than the previously reported photoelectrochemical sensing strategy. Other DNA base modification products showed much less decrease of oxidation current, demonstrating its good selectivity. This strategy can be utilized to sensitively and rapidly assess the genotoxicity of environmental pollutants.
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ACS Sensors
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2020
·
IF 7.333
Fei Li,Siyu Wang,Huanshun Yin,Yan Chen,Yunlei Zhou,Jing Huang,Shiyun Ai
5-Formylcytosine (5fC) is a rare base found in mammalian DNA, which is thought to be involved in the demethylation of DNA. As a stable epigenetic modification, 5fC participates in gene regulation and cell differentiation, and plays an important role in the growth and development of plants. However, the abundance of 5fC is only as low as 0.002–0.02% of cytosine. Therefore, to further understand the functions of 5fC, a rapid, highly sensitive, and efficient method is needed for detecting 5fC. Herein, a novel photoelectrochemical (PEC) biosensor was constructed for 5fC detection, where a MoS2/WS2 nanosheet heterojunction was employed as a photoactive material, amino-functionalized Fe3O4 and SMCC were used as a linker, 4-amino-3-hydrazino-5-mercapto-1,2,4-triazole was adopted as 5fC recognition reagent, and black TiO2 (B-TiO2) was used as a signal amplification unit. Under the optimal experimental conditions, this PEC biosensor showed a wide linear range of 0.01–200 nM and a low detection limit of 2.7 pM (S/N = 3). Due to the specific covalent reaction between −NH2 and −CHO, the biosensor presented high detection sensitivity, even discriminating 5fC with 5-methylcytosine and 5-hydroxymethylcytosine. The biosensor was then applied to investigate the effect of heavy metal Cd2+ on 5fC content in the root, stem, and leaves of maize seedlings.
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MICROCHIMICA ACTA
·
2016
·Vol. 183
·期 11
·2965-2971
·
IF 4.831
Meng Yan,Hun Xu,Zhang Yue,Luo Xiliang
A toehold-aided DNA recycling amplification technology was developed based on the combination of toehold-aided DNA recycling and the hemin/G-quadruplex label. The dsDNA formed between aptamer and DNA1 was first immobilized on magnetic beads. On addition of target analyte (exemplified here for riboflavin), the aptamer-riboflavin complex is formed and DNA1 is released by the beads. After magnetic separation, the supernatant containing the released DNA1 is added to a solution containing the hairpin capture DNA on magnetic beads. DNA1 will hybridize with the hairpin capture DNA via toehold binding and branch migration. This process will open the hairpin structure, and an external toehold is formed in the newly formed dsDNA. On addition of reporter DNA containing the G-quadruplex, it will interact with the formed dsDNA via toehold binding and branch migration, resulting in the releasing of DNA1 and capturing of reporter DNA on the magnetic beads. The released DNA1 will bind to another hairpin capture DNA which can start another round of DNA1 recycling. Chemiluminescence (CL) is generated by the G-quadruplex-hemin-luminol CL reaction system. Under optimal conditions, the calibration plot is linear in the 0.1 to 700 nM riboflavin concentration range, with a 30 pM detection limit (at a signal-to-noise ratio of 3). The method was successfully applied to the quantitation of riboflavin in spiked urine samples.
Toehold-aided DNA recycling coupled with hemin G-quadruplex for target detection.
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JOURNAL OF CRYSTAL GROWTH
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2024
·
IF 1.7
Sibo Zhao,Dan Xiu,Min Zhang,Yao Wang,Miao Qiu,Christopher D. Snow,Yanxin Wang,Laurence A. Belfiore,Jianguo Tang
In this study, a highly sensitive anticancer drug sensor was synthesized using DNA crystals loaded with luminescent Ln 3+ (Eu 3+ /Tb 3+ ) complexes. The sensors exhibited a pronounced color transformation property due to the differential quenching of Eu 3+ and Tb 3+ emissions upon drug interactions. These luminescent hybrid DNA crystals present a significant advancement in sensing anticancer drugs like curcumin, transitioning from monitoring fluorescence intensity changes to a visually discernable color change. This new approach eliminates the need for specialized instrumentation. Owing to the intrinsic biocompatibility of materials composed of DNA, this hybrid sensor has the potential to sense drugs within the human body. Hybrid crystals loaded with a single complex will lose their fluorescence properties due to drug quenching; however, crystals loaded with mixed complexes emit distinct fluorescent colors, such as yellow-green and orange-red, at different drug concentrations. This color transformation allows for the direct determination of drug concentration based on crystal color, making the sensing process more simple and easily observable.
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JOURNAL OF MOLECULAR STRUCTURE
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2011
·
IF 1.599
Xian-Lan Hong,Hong Li,Cui-Hong Peng
A new Ru(II) complex [Ru(dmb) 2 (pdta)](ClO 4 ) 2 ( 1 ) (dmb = 4,4′-dimethyl-2,2′-bipyridine, pdta = 3-(pyridine-2-yl)-as-triazino [5,6-f]-acenaphthylene) was synthesized and characterized by elemental analysis (EA), ES–MS, 1 H NMR, UV–Vis and CV. The DNA-binding properties of complex 1 were investigated by absorption titration, thermal denaturation , viscosity measurement and photoactivated cleavage. The DNA-binding constant was determined to be 2.37 ± 0.14 × 10 5 M −1 ( s = 1.90 ± 0.04) by electronic absorption titration, indicating that complex 1 interacts with DNA through intercalative mode. The redox peak potentials of this complex in CV were rationally assigned with the frontier molecular orbital stereographs resulting from the density functional theory (DFT) calculation. The photoactivated cleavage and cleavage mechanism of plasmid pBR322 DNA in the presence of complex 1 and various inhibitors were studied. The experiment for detecting the formation of singlet oxygen photo-sensitized by complex 1 was carried out, and the antioxidant activity of the Ru-complex and the ligand pdta against hydroxyl radical was also investigated.
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JOURNAL OF MOLECULAR MODELING
·
2015
·Vol. 21
·期 11
·1-7
·
IF 1.736
Zhao Dongxin,Lu Kui
Breast cancer susceptibility gene 2 (BRCA2)—a human tumor suppressor gene—is related to various malignancies such as breast and ovarian cancer. This gene can induce the key protein RAD51 recombinase, which is involved in homologous recombination with single-stranded DNA in the human body and can regulate RAD51 to complete the repair of damaged double-stranded DNA. Eight highly conserved BRC repeat motifs in BRCA2 protein serve as sites for the interaction between BRCA2 and RAD51. BRCA2 regulates RAD51 through these motifs. However, the mechanism of this interaction still requires further research. In this study, the BRC4 motif that demonstrated strong interaction with RAD51 was selected as template peptide. On the basis of known data regarding the crystal structure of the BRC4-RAD51(191–220) complex, a series of BRC4 mutants was designed using PyMOL software based on the sequence of BRC4, and polypeptides were synthesized by the Fmoc solid-phase method. After purification by reversed-phase high-performance liquid chromatography, the purity of the polypeptides reached >95 %. The primary determination of circular dichroism spectra showed that the polypeptides exhibited slight changes in secondary structure, which indicated that mutation on the non-conserved sites in BRC4 probably affected the interaction with BRC4. These findings will facilitate research on the interaction between targeting peptides and BRC4 mutants, as well the basic rules covering this interaction.
研究领域:
分子生物学
·
结构生物学
·
肿瘤学
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ANALYTICA CHIMICA ACTA
·
2021
·
IF 6.558
Guoyan Zhao,Yongmei Liu,Jie Du,Huizi Zhang,Hanqing Feng,Xiaoquan Lu
Extracellular ATP (eATP) is an important biological signal transduction molecule. Although a variety of detection methods have been extensively used in ATP sensing and analysis, accurate detection of eATP remains difficult due to its extremely low concentration and spatiotemporal distribution. Here, an eATP measurement strategy based on tetrahedral DNA (T-DNA)-modified electrode sensing platform and hybridization chain reaction (HCR) combined with G-quadruplex/Hemin (G4/Hemin) DNAzyme dual signal amplification is proposed. In this strategy, ATP aptamer and RNA-cleaving DNAzyme were combined to form a split aptazyme . In the presence of ATP, this aptazyme hydrolyzes the cleaving substrate strand with high selectivity , releasing cleaved ssDNA , which are captured by the T-DNA assembled on the electrode surface, triggering an HCR on the electrode surface to form numerous linker sequences of the HCR dsDNA product. When [email protected] (G4) spherical nucleic acid enzymes (SNAzymes) with other linkers are used as nanocatalyst tags, they are captured by HCR dsDNA through sticky linkers present on the electrode surface. An amplified electrochemical redox current signal is generated through SNAzyme-mediated catalysis of H 2 O 2 , enabling easy detection of picomole amounts of ATP. Using this strategy, eATP levels released by tobacco suspension cells were accurately measured and the distribution and concentration of eATP released on the surface of an Arabidopsis leaf was determined.
研究领域:
植物学
·
分子生物学
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SCIENCE OF THE TOTAL ENVIRONMENT
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2021
·
IF 7.963
Haiyan Wang,Yiming Xie,Yujia Wang,Guosong Lai
The abuse of kanamycin (Kana) in many fields has led to increasing antibiotic pollution problems and serious threats to public health. Therefore, determining how to develop methods to realize the convenient detection of antibiotics in complicated environmental matrices is highly desirable. In this study, we utilized a target biorecognition-triggered hybridization chain reaction (HCR) assembly of a G-quadruplex DNAzyme (G-DNAzyme)-decorated nanotree to develop a novel homogeneous colorimetric biosensing method for the convenient and ultrasensitive detection of Kana antibiotic residues in real samples. Through the designed aptamer-recognition reaction, an Mg 2+ -dependent DNAzyme (MNAzyme) strand can be liberated. Thus, its catalyzed cleavage of the hairpin substrates anchored at a DNA nanowire will cause the assembled formation of an HCR-initiator; this process can be greatly amplified by the exonuclease III-assisted target recycling and the MNAzyme-catalyzed release of another MNAzyme strand. Based on the DNA-nanowire-accelerated HCR assembly of many G-DNAzyme-decorated DNA duplexes on the two sides of the nanowire, a DNA nanotree decorated by numerous G-DNAzymes will form to realize the ultrasensitive colorimetric signal output. Under the optimal conditions, this method exhibited a wide five-order-of-magnitude linear range and a very low detection limit of 28 fg mL −1 . In addition, excellent selectivity, repeatability, and reliability were also demonstrated for this homogeneous bioassay method. These unique features along with its automatic manipulation and low assay cost show promise for practical applications.
研究领域:
分析化学
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生物传感器
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环境科学
·
分子生物学
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INTERNATIONAL JOURNAL OF RADIATION BIOLOGY
·
2024
·
IF 2.1
Lingyu Zhang,Lina Cai,Yashi Cai,Weiyi Ke,Linqian Zhou,Yuhua Yang,Weixu Huang,Jianming Zou,Huifeng Chen
Purpose To investigate the role of moderate doses of ionizing radiation-induced cellular senescence in mouse lung tissue and whole-body inflammation levels.Material and methods Forty-two C57BL/6J mice were randomly divided into the control group, the 1, 3, and 7 days after 2 Gy irradiation group, and the 1, 3, and 7 days after 4 Gy irradiation group, with six mice in each group. The histopathology, cellular senescence, oxidative-antioxidant, DNA damage repair, and inflammation-related indicators of irradiated mice were examined.Results Compared with the control group, the histopathological scores, the positive area of senescence-associated-β-galactosidase (SA-β-Gal) staining, and the mRNA levels of senescence-related genes in the lung tissues in all dose groups increased on 1, 3, and 7 days after irradiation. In peripheral blood, erythrocytes, leukocytes, platelets, hemoglobin, 8-hydroxydeoxyguanosine (8-OHdG), C-reactive protein, and other indicators showed a different trend in all dose groups. The levels of malondialdehyde(MDA), superoxide dismutase (SOD), glutathione (GSH), and 8-OHdG in the lung tissue showed different trends after 2 Gy and 4 Gy irradiation. The 8-Oxoguanine DNA glycosylase 1 (hOGG1) and O-6-methylguanine-DNA methyltransferase (MGMT) mRNA levels showed a trend of increasing and then decreasing. The levels of whole-body inflammation were significantly correlated with the levels of indicators related to cellular senescence and damage repair in the lung tissue of mice.Conclusions The moderate doses of ionizing radiation induce oxidative stress, and DNA damage and increase DNA repair gene expression in mouse lung tissue. The lung tissue cellular senescence correlates with the level of whole-body inflammation.
研究领域:
放射生物学
·
分子生物学
·
免疫学
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ACS Sensors
·
2021
·
IF 7.711
Fubo Ma,Shuanghong Yan,Jinyue Zhang,Yu Wang,Liying Wang,Yuqin Wang,Shanyu Zhang,Xiaoyu Du,Panke Zhang,Hong-Yuan Chen,Shuo Huang
Cisplatin, which selectively binds to N7 atoms of purines to inhibit normal replication and transcription, is a widely applied chemotherapeutic drug in the treatment of cancer. Though direct identification of cisplatin lesions on DNA is of great significance, existing sequencing methods have issues such as complications of preamplification or enrichment-induced false-positive reports. Direct identification of cisplatin lesions by nanopore sequencing (NPS) is in principle feasible. However, relevant investigations have never been reported. By constructing model sequences (83 nucleotides in length) containing a sole cisplatin lesion, identification of corresponding lesions by NPS is achieved with <10 ng of input sequencing library. Moreover, characteristic high-frequency noises caused by cisplatin lesions are consistently observed during NPS, clearly identifiable in corresponding high-pass filtered traces. This feature is, however, never observed in any other combinations of natural DNA bases and could be taken as a reference to identify cisplatin lesions on DNA. Further investigations demonstrate that cisplatin stalls the replication of phi29 DNA polymerase, which appears as a ∼5 pA level fluctuation in the single-molecule resolution. These results have confirmed the feasibility of NPS to identify cisplatin lesions at the genomic level and may provide new insights into understanding the molecular mechanism of platinum-based drugs.
研究领域:
分子生物学
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癌症研究
·
基因组学
·
化学生物学
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ANALYTICAL CHEMISTRY
·
2026
·
IF 7.3
Yanjun Wang,Wenlu Meng,Ruoyu Yao,Zhiyao Lu,Chunyan Liu,Yulian Wang,Lei Dong
Silicon (Si) participates in diverse biological processes, yet its specific roles remain elusive because of the lack of tools for visualizing silicon in living organisms. In biological contexts, silicon predominantly occurs as silicates with varying polymerization states and structural heterogeneity, posing fundamental challenges for recognition and imaging using existing chemical or analytical methods. Here, we introduce a molecular recognition strategy that leverages single-stranded DNA aptamers selected through a three-dimensional silicified hydrogel screening system, yielding high-affinity binders with nanomolar dissociation constants. We validated these aptamers using electrophoretic mobility shift assays (EMSA) and microscale thermophoresis (MST), and molecular docking revealed the sequence-structure motifs governing silicate recognition. Using these aptamers, we engineered two fluorescent sensors that map intracellular silicate distributions with high specificity. To our knowledge, these are the first aptamers that selectively recognize silicates with distinct polymerization states, providing a powerful tool for real-time visualization of silicon in living cells. This approach opens new avenues for biological imaging and for elucidating the functional roles of biogenic silicon in living organisms.
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