SPECTROCHIMICA ACTA PART A-MOLECULAR AND BIOMOLECULAR SPECTROSCOPY
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2014
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IF 2.129
Jinhua Zhu,Lanlan Chen,Yingying Dong,Jiazhong Li,Xiuhua Liu
In this work, the interaction of 5-Hydroxymethyl-2-furfural (5-HMF) with calf thymus DNA (ctDNA) under simulated physiological conditions (Tris–HCl buffer of pH 7.40), was explored by UV absorption spectroscopy, fluorescence spectroscopy and molecular modeling method, using ethidium bromide (EB) as a fluorescence probe of DNA. The fluorescence quenching mechanism of EB–ctDNA by 5-HMF was confirmed to be a static quenching, which derived from the formation of a new complex. The binding constants of 5-HMF with DNA in the presence of EB were calculated to be 2.17 × 10 3 , 4.24 × 10 3 and 6.95 × 10 3 L mol −1 at 300, 305 and 310 K, respectively. The calculated thermodynamic parameters, enthalpy change Δ H and entropy change Δ S , suggested that both hydrophobic interactions and hydrogen bonds played a predominant role in the binding of 5-HMF to DNA. According to the UV absorption spectroscopy and melting temperature ( T m ) curve results, the binding mode of 5-HMF with DNA was indicative of a non-intercalative binding, which was supposed to be a groove binding. The molecular modeling results showed that 5-HMF could bind into the hydrophobic region of ctDNA and supported the conclusions obtained from the above experiments.
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高影响因子
BIOSENSORS & BIOELECTRONICS
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2015
·
IF 6.409
Xiuzhong Wang,Ting Hou,Shanshan Dong,Xiaojuan Liu,Feng Li
Pesticides are of great importance in agricultural and biological fields, but pesticide residues may harm the environment and human health. A highly sensitive fluorescent biosensor for the detection of carbamate pesticide has been developed based on acetylcholinesterase (AChE)-catalyzed hydrolysis product triggered Hg 2+ release coupled with subsequent nicking enzyme-induced cleavage of a duplex DNA for cycling amplification. In this protocol, two DNA probes, an unmodified single-stranded helper DNA probe 1 (HP1) and a quencher–fluorophore probe (QFP) are ingeniously designed. HP1 can be folded into hairpin configuration through T–Hg 2+ –T base pair formation. QFP, labeled with FAM and BHQ1 at its two terminals, contains the recognition sequence and the cleavage site of the nicking enzyme . In the presence of carbamate pesticide, the activity of AChE is inhibited, and the amount of the product containing the thiol group generated by the hydrolysis reaction of acetylthiocholine chloride (ACh) decreases, resulting in the release of a low concentration of Hg 2+ . The number of HP1 that can be selectively unfolded would be reduced and the subsequent nicking enzyme-assisted cleavage processes would be affected, resulting in decreased fluorescence signals. The fluorescence intensity further decreases with the increase of the pesticide concentration. Therefore, the pesticide content can be easily obtained by monitoring the fluorescence signal change, which is inversely proportional to the logarithm of the pesticide concentration. The detection limit of aldicarb , the model analyte , is 3.3 μg L −1 , which is much lower than the Chinese National Standards or those previously reported. The as-proposed method has also been applied to detect carbamate pesticide residues in fresh ginger and artificial lake water samples with satisfactory results, which demonstrates that the method has great potential for practical application in biological or food safety field.
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高影响因子
Theranostics
·
2017
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IF 8.766
Feifei Xu,Weixian Zhou,Jianxiang Cao,Qingqing Xu,Dechen Jiang,Yun Chen
The distorted and unique expression of microRNAs (miRNAs) in cancer makes them an attractive source of biomarker. There is much evidence indicating that a panel of miRNAs, termed “miRNA fingerprints”, is more specific and informative than an individual miRNA as biomarker. Thus, multiplex assays for simultaneous quantification of multiple miRNAs could be more potent in clinical practice. However, current available assays normally require pre-enrichment, amplification and labeling steps, and most of them are semi-quantitative or lack of multiplexing capability. In this study, we developed a quasi-targeted proteomics assay for multiplexed miRNA quantification by a combination of DNA-peptide probes and liquid chromatography-tandem mass spectrometry (LC-MS/MS). Specifically, the signal of target miRNAs (i.e., miR-21, miR-let7a, miR-200c, miR-125a and miR-15b) was converted into the mass response of reporter peptides by hybridization of miRNAs with DNA-peptide probes and subsequent tryptic digestion to release the peptides. After a careful optimization of conditions related to binding, conjugation, hybridization and multiple reaction monitoring (MRM) detection, the assay was validated for each miRNA and the limit of quantification (LOQ) for all the miRNAs can achieve 1 pM. Moreover, crosstalk between DNA-peptide probes in multiplex assay was sophisticatedly evaluated. Using this quasi-targeted proteomics assay, the level of target miRNAs was determined in 3 human breast cell lines and 36 matched pairs of breast tissue samples. Finally, simplex assay and qRT-PCR were also performed for a comparison. This approach grafts the strategy of targeted proteomics into miRNA quantification and may offer a new way for multiplexed miRNA profiling.
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JOURNAL OF ELECTROANALYTICAL CHEMISTRY
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2017
·
IF 3.012
Jianzhi Huang,Guoqing Yue,Jie Yang,Silan Bai,Qiong Hu,Lishi Wang
In this work, we provided a logical idea to design, synthesis and application of a high-performance electrochemical biosensor based on carboxylic multi-walled carbon nanotubes/tetrahexahedral platinum nanocrystals nanocomposites , which can realize high-performance simultaneous determination for guanine and adenine in DNA . The morphology evolution of platinum nanoparticles from nanospheres to tetrahexahedral nanocrystals was also briefly studied in our work. The carboxylic multi-walled carbon nanotubes/tetrahexahedral platinum nanocrystals nanocomposites biosensor showed excellent synergistic effects in electrocatalytic oxidation of guanine and adenine in DNA, compared with other reported sensors, our proposed nanocomposites biosensor showed wider linear range of 0.05–100 μmol dm − 3 and 0.05–100 μmol dm − 3 with lower detection limit of 0.01 μmol dm − 3 (S/N = 3) and 0.01 μmol dm − 3 (S/N = 3) for guanine and adenine respectively. And it also exhibited excellent selectivity, stability and reproducibility. Moreover, the proposed biosensor was successfully applied in real DNA samples determination, which has great significance in application of the bioscience and clinical diagnosis.
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ANALYTICAL AND BIOANALYTICAL CHEMISTRY
·
2016
·Vol. 409
·期 6
·1615-1625
·
IF 3.125
Wang Lang-Hong,Zhang Zhi-Hong,Zeng Xin-An,Gong De-Ming,Wang Man-Sheng
Thymol (2-isopropyl-5-methylphenol) is a natural ingredient used as flavor or preservative agent in food products. The antibacterial mechanism of thymol against Gram-positive, Staphylococcus aureus was investigated in this work. A total of 15 membrane fatty acids were identified in S. aureus cells by gas chromatography–mass spectrometry. Exposure to thymol at low concentrations induced obvious alterations in membrane fatty acid composition, such as decreasing the proportion of branched 12-methyltetradecanoic acid and 14-methylhexadecanoic acid (from 22.4 and 17.3% to 7.9 and 10.3%, respectively). Membrane permeability assay and morphological image showed that thymol at higher concentrations disrupted S. aureus cell membrane integrity, which may decrease cell viability. Moreover, the interaction of thymol with genomic DNA was also investigated using multi-spectroscopic techniques, docking and atomic force microscopy. The results indicated that thymol bound to the minor groove of DNA with binding constant ( K
a ) value of (1.22 ± 0.14) × 10 4 M −1 , and this binding interaction induced a mild destabilization in the DNA secondary structure, and made DNA molecules to be aggregated.
Thymol exerts its antibacterial effect throught destruction of bacterial cell membrane and binding directly to genomic DNA
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SENSORS AND ACTUATORS B-CHEMICAL
·
2016
·
IF 4.758
Yaomin Yang,Xiaojuan Liu,Min Wu,Xiuzhong Wang,Ting Hou,Feng Li
Pesticides are of significant importance in agricultural fields, but the pesticide residues are considered to be strong hazards to the environment and human health. Motivated by the urgent demand for sensitive pesticide assay, this study addresses the need by reporting a new electrochemical biosensing platform for pesticide detection, which is relied on acetylcholinesterase (AChE)-catalyzed hydrolysis product-triggered Hg 2+ release coupled with subsequent hybridization chain reaction (HCR) for signal amplification. The hydrolysis product thiocholine (TCh) can interact with Hg 2+ embedded in the stem of hairpin structured helper DNA probe to switch its conformation to single-stranded DNA (ssDNA). The ssDNA then triggers the HCR between two hairpin probes and yields long double-stranded DNA, which can capture numerous methylene blue molecules, thus generating a remarkably amplified electrochemical signal. In the presence of pesticides, AChE activity is inhibited and the amount of generated TCh decreases, eventually resulting in the decrease of electrochemical signal. It has been found that the as-proposed approach shows a linear relationship between the peak current and the logarithm of the pesticide concentration. A directly measured detection limit of 10 μg/L is achieved by using aldicarb as a model analyte. Furthermore, this method exhibits good applicability for aldicarb detection in real samples. It is also versatile for the detection of other carbamate and organophosphate pesticides that have inhibition effect on AChE activity. Therefore, the proposed method shows great potential for practical application in food safety fields and will provide alternative approaches for the detection of pesticide residues.
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SPECTROCHIMICA ACTA PART A-MOLECULAR AND BIOMOLECULAR SPECTROSCOPY
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2018
·
IF 2.88
Fei Qu,Zeqiu Chen,Jinmao You,Cuihua Song
Human telomere DNA plays a vital role in genome integrity control and carcinogenesis as an indication for extensive cell proliferation. Herein, silver nanoclusters (Ag NCs) templated by polymer and unmodified gold nanoparticles (Au NPs) are designed as a new colorimetric platform for sensitively differentiating telomere DNA with different lengths, monitoring G-quadruplex and dsDNA. Ag NCs can produce the aggregation of Au NPs, so the color of Au NPs changes to blue and the absorption peak moves to 700 nm. While the telomere DNA can protect Au NPs from aggregation, the color turns to red again and the absorption band blue shift. Benefiting from the obvious color change, we can differentiate the length of telomere DNA by naked eyes. As the length of telomere DNA is longer, the variation of color becomes more noticeable. The detection limits of telomere DNA containing 10, 22, 40, 64 bases are estimated to be 1.41, 1.21, 0.23 and 0.22 nM, respectively. On the other hand, when telomere DNA forms G-quadruplex in the presence of K + , or dsDNA with complementary sequence, both G-quadruplex and dsDNA can protect Au NPs better than the unfolded telomere DNA. Hence, a new colorimetric platform for monitoring structure conversion of DNA is established by Ag NCs-Au NPs system, and to prove this type of application, a selective K + sensor is developed.
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MICROCHEMICAL JOURNAL
·
2024
·
IF 4.9
Chaoqun Fei,Shulan Qi,Jiahuan Zhang,Shi Zhou,Yingxue Guo,Yanli Zhao,Jiazheng Jin,Jinlian Li,Ximing Cui,Dongmei Wu
As industrialization accelerates, there is an increasing need to find a quick, easy, and affordable method to assess the potential DNA damage caused by newly developed chemicals. Electrochemical voltammetry using intracellular purine bases as markers shows promise for detecting DNA damage. However, it is unclear whether drugs with different DNA damage mechanisms will impact purine metabolism in cells and consequently disturb the electrochemical indicators of DNA damage. In this paper, the electrochemical behaviors of HepG2 cells exposed to the direct DNA-damaging agent (MNNG), the indirect DNA-damaging agent (CPT11), and the non-DNA-damaging agent (KCl) were studied. The findings showed that the electrochemical signals of cells increased with the rising concentration of DNA-damaging drugs. A time-dependent effect was observed, with a lower threshold dose for 4 h compared to 1 h. However, the non-DNA-damaging agent did not induce an increase in the cellular electrochemical signal. Despite the higher cytotoxicity of CPT11, MNNG triggered DNA damage at a lower dose, as detected by electrochemical indicators. The results of the electrochemical indicators assessment of DNA damage correlated significantly with those of the γH2AX focus and alkaline comet assays, with r > 0.98 and P < 0.01. Particularly, there was a stronger correlation with the alkaline comet assay. Furthermore, electrochemical voltammetry detected DNA damage at a lower threshold compared to other assessment methods, demonstrating a higher sensitivity to DNA damage. These findings suggest that by using purine bases as markers, electrochemical voltammetry enables precise assessment of DNA damage caused by various mechanisms.
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CHEMICAL ENGINEERING JOURNAL
·
2024
·
IF 13.3
Jiayuan Zheng,Jinhua Li,Tianci Lin,Zhanpeng Ren,Fucheng Wang,Zhonghao Shi,Haiyang Yu,Wei Jiang,Wei Tang
Staphylococcus aureus ( S. aureus ) is one of the leading causes of foodborne illnesses worldwide, posing a significant risk to food quality and safety. However, conventional detection methods often require complex amplification and labeling procedures, which are time consuming and expensive. In this study, an extremely sensitive electrochemical biosensor using a solution-gated graphene transistor (SGGT) was constructed for the amplification-free and label-free rapid detection of S. aureus by utilizing specific single-stranded DNA (ssDNA) to modify the gold (Au) sensing gate. This modified ssDNA was designed to hybridize with the target S. aureus DNA sequence. Interface engineering of the ssDNA-modified sensing gate via optimization of specific target and probe sequences was proposed to improve its hybridization efficiency. This enabled the sensitive quantitative detection of S. aureus DNA. The resulting biosensor exhibited excellent specificity in distinguishing non-complementary, 3-base/9-base DNA mismatch targets of S. aureus DNA and the specific DNA sequences of other common pathogenic bacteria. It also enabled the rapid detection of extracted target DNA sequences in solution (within 27 min) and had a low limit of detection (LoD) of 10 −17 M over a wide linear detection range (10 −17 –10 −8 M). Furthermore, the newly-developed biosensor facilitated the real-time and on-site detection of the S. aureus genome (ATCC 6538) with LoD of 10 −17 M (10 3 CFU/mL) in a portable smart-sensing system. This suggests a promising future for the development of rapid, label-free, and amplification-free detection of foodborne illnesses using low-cost, highly sensitive SGGT DNA biosensors with appropriate functionalization and interface engineering of the sensing electrode.
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JOURNAL OF ELECTROANALYTICAL CHEMISTRY
·
2011
·
IF 2.733
Xianggang Liu,Yinghua Peng,Xiangjin Qu,Shiyun Ai,Ruixia Han,Xiangbin Zhu
A novel bio-composite film which contains multi-walled carbon nanotube (MWNT)-chitosan (Chit)/poly(amidoamine) (PAMAM) nanocomposite along with the incorporation of DNA modified Au electrode as a biosensor for determination of dopamine(DA) and uric acid (UA) under coexistence of ascorbic acid (AA) was fabricated by layer-by-layer modification. Electrochemical impedance spectroscopy (EIS) and Cyclic Voltametry (CV) were used to characterize the electrochemical properties of the modified electrodes. The biosensor was applied to detect DA and UA in the presence of AA. It not only exhibited strong catalytic activity toward the oxidation of DA and UA but also separated the originally overlapped signals of UA, DA and AA oxidation at the bare electrode into three well-defined peaks. The peak separation between AA and DA, AA and UA was 179 mV and 288 mV, respectively. In the presence of 1.0 mM AA, two linear relationships were obtained for DA over the concentration range from 0.2 to 10 μM ( R = 0.9984) and 10–100 μM ( R = 0.9957) with a detection limit of 0.03 μM ( s / n = 3). The anodic peak current of UA was also a linear relationship in the concentration range 0.5–100 μM ( R = 0.9971) with a detection limit of 0.07 μΜ. Moreover, the modified electrode surface has very good reproducibility and stability.
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ANALYTICAL CHEMISTRY
·
2024
·
IF 6.7
Jing Li,Minhui Chen,Qi Jiang,Wei Zhang,Yiting Lan,Md. Maruf Ahmed,Cheng Ma,Jin Huang,Qin Xu
To tackle the predicament of the traditional turn-off mechanism, exploring an activated turn-on system remains an intriguing and crucial objective in biosensing fields. Herein, a dark DNA Ag nanocluster (NC) with hairpin-structured DNA containing a six-base cytosine loop (6C loop) as a template is atypically synthesized. Intriguingly, the dark DNA Ag NCs can be lit to display strong red-emission nanoclusters. Building upon these exciting findings, an unprecedented and upgraded turn-on biosensing system [entropy-driven catalysis circuit (EDCC)-Ag NCs/graphene oxide (GO)] has been created, which employs an EDCC to precisely manipulate the conformational transition of DNA Ag NCs on the GO surface from adsorption to desorption. Benefiting from the effective quenching of GO and signal amplification capability of the EDCC, the newly developed EDCC–Ag NCs/GO biosensing system displays a high signal-to-background (S/B) ratio (26-fold) and sensitivity (limit of detection as low as 0.4 pM). Meanwhile, it has good specificity, excellent stability, and reliability in both buffer and biological samples. To the best of our knowledge, it is the first example that adopts an EDCC to precisely modulate the configuration transformation of DNA Ag NCs on the GO surface to obtain a biosensor with low background, strong fluorescence, high contrast, and sensitivity. This exciting finding may provide a new route to fabricate a novel turn-on biosensor based on hairpin-templated DNA Ag NCs in the optical imaging and bioanalytical fields.
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高影响因子
Nanoscience and Nanotechnology Letters
·
2019
·Vol. 11
·期 8
·1104-1115
·
IF 0
Bhatti Huma,Jawed Rohil,Liu Hang,Ali Irshad,Zhu Libo,Liu Quanjun
Biological nanopores have been proved as impressive nano-devices capable of holding the detection sensitivity from a nanoparticle to a single macromolecule. Protein pores are efficiently reproducible with assured channel geometry and their propensity to be engineered easily make them
convenient in nanopore sensing techniques. Among various porin-proteins, MspA porin of Mycobacterium smegmatis is quite ideal for nanopore DNA sequencing. However, the traversing speed of singlestranded DNA (ssDNA) through both the mutants of MspA (M1MspA and M2MspA) is too fast to
be analyzed. Therefore, we utilized a new mutant of MspA, termed as M3MspA which was previously purified in our laboratory. We, for the first time, demonstrated that translocation of ssDNA is achieved at a minimum voltage-threshold of 40 mV at pH 8.0. This new mutant of MspA exhibits a crystal-clear
discrimination between two homopolymers, poly dA50 and poly dC50 with duration time up to few milliseconds and well-resolved signature current-amplitudes were obtained for both sides (3′ or 5′) of the polymer entered the pore, without any modification to ssDNA.
Significantly, M3MspA determines a precise length of a hetero-homopolymer, poly(dA50dC50) by producing a dwell time congruent to the sum of the time spent by their component-homopolymers, separately. On account of their specificity and sensitivity towards translocating
polynucleotides, we suggest that this new mutant of MspA would be a sophisticated bio-nanopore in further enlightening the translocation dynamics caused by diverse conformations of a same biomolecule. On top of that, it would also be helpful in nanopore DNA sequencing.
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