ANALYTICA CHIMICA ACTA
·
2024
·
IF 5.7
Manting Li,Haikun Luo,Zhao Wang,Qian Mo,Shanshan Zhong,Yu-ang Mao,Shuting Li,Xinchun Li
Background Assembling framework nucleic acid (FNA) nanoarchitectures and tuning luminescent quantum dots (QDs) for fluorescence assays represent a versatile strategy in analytical territory. Rationally, FNA constructs could offer a preferential orientation to efficiently recognize the target and improve detection sensitivity, meanwhile, regulating size-dependent multicolor emissions of QDs in one analytical setting for ratiometric fluorescence assay would greatly simplify operation procedures. Nonetheless, such FNA/QDs-based ratiometric fluorescence nanoprobes remain rarely explored. Results We designed a sensitive and signal amplification-free fluorescence aptasensor for lead ions (Pb 2+ ) that potentially cause extensive contamination to environment, cosmetic, food and pharmaceuticals. Red and green emission CdTe quantum dots (rQDs and gQDs) were facilely prepared. Moreover, silica nanosphere encapsulating rQDs served as quantitative internal reference and scaffold to anchor a predesigned FNA and DNA sandwich containing Pb 2+ binding aptamer and gQD modified DNA signal reporter. On binding of Pb 2+ , the gQD-DNA signal reporter was set free, resulting in fluorescence quenching at graphene oxide (GO) interface. Owing to the rigid structure of FNA, the fluorescence signal reporter orderly arranged at the silica nanosphere could sensitively respond to Pb 2+ stimulation. The dose-dependent fluorescence signal-off mode enabled ratiometric analysis of Pb 2+ without cumbersome signal amplification. Linear relationship was established between fluorescence intensity ratio ( I 555 / I 720 ) and Pb 2+ concentration from 10 nM to 2 μM, with detection limit of 1.7 nM (0.43 ppb), well addressing the need for Pb 2+ routine monitoring. The designed nanoprobe was applied to detection of Pb 2+ in soil, cosmetic, milk, drug, and serum samples, with the sensitivity comparable to conventional ICP-MS technique. Significance Given the programmable design of FNA and efficient recognition of target, flexible tuning of QDs emission, and signal amplification-free strategy, the present fluorescence nanoprobe could be a technical criterion for other heavy metal ions detection in a straightforward manner.
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JOURNAL OF HAZARDOUS MATERIALS
·
2025
·
IF 11.3
Lei Miao,Tian Ma,Jiaxi Qi,Yaohui Deng,Yaqi Hong,Xiaoxiao Gong,Hailian Zang,Yi Cheng,Chunyan Li
17β-Estradiol (17β-E2), a persistent endocrine-disrupting compound, threatens ecosystem health through bioaccumulation. While bioaugmentation offers promise for environmental remediation, mechanistic insights into interspecies interactions between exogenous and indigenous degraders remain underexplored. Here, a synthetic microbial consortium (EL) was constructed by combining Rhodococcus erythropolis D310–1 and Microbacterium oxydans ML-6, which reduced the 17β-E2 degradation half-life by 53.65 % compared with that of the noninoculated control while suppressing the accumulation of the toxic intermediate estrone (E1). Temporal 16S rRNA gene amplicon sequencing profiling with co-occurrence network analysis revealed that the consortium EL dynamically reinforced ecological synergies with indigenous functional microbiota, accelerating contaminant mineralization. DNA-stable isotope probing (DNA-SIP) coupled with metagenomics identified Rhodanobacter , Mycobacterium , Rhodococcus , Sphingomonas , and Microbacterium spp. as active 17β-E2 assimilators. Furthermore, high-performance liquid chromatography coupled with quadrupole time flight mass spectrometry (HPLC QTOF MS) was used to predict three complementary degradation pathways in the assembled genomes, revealing related functional enzymes and addressing functional partitioning between exogenous inoculants and indigenous degraders. Two novel gene clusters responsible for 17β-E2 biodegradation were evaluated. This study pioneers DNA-SIP and metagenomics to track 13 C-labelled 17β-E2 fate within bioaugmented soil microbiota, resolving intrakingdom bacteria collaborations that drive 17β-E2 biodegradation in soil. The identification of cross-consortium metabolic handoffs provides a blueprint for engineering syntrophic partnerships targeting steroidal estrogens (SEs) pollutants.
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Antioxidants
·
2025
·Vol. 14
·期 11
·1381
·
IF 6.6
Yongjie Zhang,Tingjun Fan
Background: Dry eye disease (DED), characterized by tear film hyperosmolarity, can lead to corneal epithelial damage. The mechanisms linking hyperosmotic stress to human corneal epithelial cell (HCEPC) damage are not fully understood. Methods: A DED model was established by exposing HCEPCs to sustained hyperosmotic stress (400 mOsm/L) over multiple passages in vitro. Senescence was assessed using senescence-associated-β-galactosidase (SA-β-gal) staining, 5-ethynyl-2′-deoxyuridine (EdU) assays, p16INK4Aand senescence-associated secretory phenotypes (SASP) analysis. Mechanisms were investigated by measuring reactive oxygen species (ROS), mitochondrial function, energy metabolism, DNA damage, and inflammatory signaling. The role of autophagy was probed pharmacologically. Results: Hyperosmotic stress induced HCEPC senescence, driven by mitochondrial dysfunction, oxidative stress, DNA damage, bioenergetic crisis, and compromised autophagy (especially mitophagy). Autophagy and mitophagy play a key role in regulating senescence progression. Enhancing autophagy with LYN-1604 ameliorated oxidative stress, improved energy homeostasis, and attenuated senescence. Inhibiting autophagy exacerbated these states. Conclusion: Hyperosmolarity promotes HCEPC senescence via mitochondrial dysfunction and oxidative damage. Autophagy serves a critical protective role, and its enhancement represents a promising therapeutic strategy for DED.
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ANALYTICAL AND BIOANALYTICAL CHEMISTRY
·
2017
·Vol. 409
·期 28
·6677-6688
·
IF 3.431
Hu Yufang,Zhang Qingqing,Xu Lihua,Wang Jiao,Rao Jiajia,Guo Zhiyong,Wang Sui
Electrochemical methods allow fast and inexpensive analysis of enzymatic activity. Here, a simple and yet efficient “signal-on” electrochemical assay for sensitive, label-free detection of DNA-related enzyme activity was established on the basis of terminal deoxynucleotidyl transferase (TdT)-mediated extension strategy. TdT, which is a template-independent DNA polymerase, can catalyze the sequential addition of deoxythymidine triphosphate (dTTP) at the 3’-OH terminus of single-stranded DNA (ssDNA); then, the TdT-yield T-rich DNA nanowires can be employed as the synthetic template of copper nanoclusters (CuNCs). Grown DNA nanowires-templated CuNCs (noted as DNA-CuNCs) were attached onto graphene oxide (GO) surface and exhibited unique electrocatalytic activity to H 2 O 2 reduction. Under optimal conditions, the proposed biosensor was utilized for quantitatively monitoring TdT activity, with the observed LOD of 0.1 U/mL. It also displayed high selectivity to TdT with excellent stability, and offered a facile, convenient electrochemical method for TdT-relevant inhibitors screening. Moreover, the proposed sensor was successfully used for BamHI activity detection, in which a new 3′-OH terminal was exposed by the digestion of a phosphate group. Ultimately, it has good prospects in DNA-related enzyme-based biochemical studies, disease diagnosis, and drug discovery.
Extraordinary TdT-generated DNA-CuNCs are synthesized and act as a novel electrochemical sensing platform for sensitive detection of TdT and BamHI activity in biological environments.
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Frontiers in Microbiology
·
2025
·
IF 4.5
Yuqi Zhen,Quzhen Baima,Shipeng Yang,Yu Cao,XiuPing Meng
Enterococcus faecalis (E. faecalis) is commonly associated with persistent periapical infections. Even after multiple courses of root canal therapy, the infection is difficult to eradicate due to its drug resistance and adaptability. However, root canal treatment will remove nutrients from the root canal and make the remaining E. faecalis near starvation. Iron is an essential element for the growth and metabolism of E. faecalis, but previous studies were mostly based on bacterial nutrient sufficient conditions. Therefore, in this study, the starvation state was used as the breakthrough point to explore the mechanism of iron on the biofilm formation of E. faecalis, so as to be more suitable for clinical practice. In this study, we first constructed a starving E. faecalis model. Subsequently, we found that iron supply promoted biofilm formation in starved E. faecalis, with more eDNA in the biofilm. Iron starvation induced by the iron competitive inhibitor gallium nitrate reduced biofilm formation but increased the proportion of eDNA. In contrast, high iron levels in the environment counteracted this inhibition of biofilm formation. Following DNase I treatment, both the eDNA content and viable bacteria within the biofilm of the iron-supply group exhibited a statistically significant reduction. These results suggest that iron supply may regulate the proliferation of active bacteria by regulating eDNA release, thereby promoting biofilm formation of starved E. faecalis and providing a new perspective on its survival strategy under stress.
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FASEB JOURNAL
·
2022
·Vol. 36
·期 5
·e22266
·
IF 5.834
Huiqing Hu,Ruxing Zhao,Qin He,Chen Cui,Jia Song,Xinghong Guo,Nan Zang,Mengmeng Yang,Ying Zou,Jingwen Yang,Jinquan Li,Liming Wang,Longqing Xia,Lingshu Wang,Falian He,Xinguo Hou,Fei Yan,Li Chen
Type 2 diabetes mellitus (T2DM) is an age-related disease characterized by impaired pancreatic β cell function and insulin resistance. Recent studies have shown that the accumulation of senescent β cells under metabolic stress conditions leads to the progression of T2DM, while senolysis can improve the prognosis. However, the specific mechanism of β cell senescence is still unclear. In this study, we found that the increased load of senescence pancreatic β cells in both older mice and obese mice induced by high-fat diet (HFD) (DIO mice) was accompanied by activation of the Cyclic GMP-AMP synthase (cGAS) - stimulator of interferon genes (STING) pathway and using cGAS or STING small interfering RNA or STING inhibitor C176 to downregulate this pathway reduced the senescence-associated secretion profile (SASP) and senescence of Min6 cells treated with palmitic acid or hydrogen peroxide. C176 intervention in DIO mice also significantly reduced the inflammation and senescence of the islets, thereby protecting the function of pancreatic β cell and glucose metabolism. Our study further revealed that mitochondrial DNA (mtDNA) leakage under metabolic stress conditions was critical for the activation of the cGAS-STING pathway, which can be reversed by the mtDNA depleting agent ethidium bromide. Consistently, mtDNA leakage was more severe in older mice and was accelerated by a chronic HFD. In conclusion, we demonstrate that cytoplasmic mtDNA activates the cGAS-STING pathway to mediate SASP during the accelerated senescence of pancreatic β-cells induced by metabolic stress, and this process can be downregulated by the STING inhibitor C176.
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NEW JOURNAL OF CHEMISTRY
·
2017
·Vol. 41
·期 15
·7613-7620
·
IF 3.269
Qianqian Pei,Yu Wang,Su Liu,Yifei Qin,Xueqi Leng,Xuejun Cui,Jiadong Huang
In this study, a novel electrochemical biosensor based on exonuclease III (Exo III)-aided autonomous cascade signal amplification for ultrasensitive and highly specific detection of Salmonella typhimurium (S. typhimurium) has been reported. Herein, two duplex DNA probes were ingeniously designed. An Ap–Pr duplex probe was constructed as a recognition element by hybridizing an S. typhimurium aptamer (Ap) with a primer (Pr). A P–S duplex probe has been designed to contain a protruding DNA fragment at 5′-termini that has an identical sequence with Pr (the secondary Pr), a complementary duplex DNA that is used for blocking a signal-triggered probe (S), and an overhung nucleic acid segment at 3′-end that can anneal with Pr and form double-stranded DNA with a blunt 3′-terminus, thus initiating Exo III-aided amplification reaction. Upon sensing of the target S. typhimurium, the specific recognition of S. typhimurium and aptamer releases Pr, which anneals with the P–S duplex and triggers the Exo III cleavage reaction, accompanied by release of Pr, S, and secondary Pr. After this, the released Pr and secondary Pr anneal with other P–S duplex, which in turn triggers the Exo III-assisted cycling cleavage. Thus, large amounts of S are liberated, which hybrids with S* (DNA probe complementary to S); thereby, 5′-methylene blue (MB)-labelled DNA probe (MBP) folds into a hairpin structure with 5′-terminus close to electrode surface for efficient electronic transfer. Moreover, the S–S* hybrid duplex is specifically hydrolyzed by Exo III to liberate S, which accordingly results in the cycling cleavage of S*. Therefore, numerous MBP transform into a hairpin structure with electroactive MB close to the electrode surface; this generates significantly amplified electrochemical signal towards S. typhimurium detection. The present developed strategy exhibited high sensitivity towards S. typhimurium with a detection limit of 2.8 × 10 cfu mL−1. Furthermore, the proposed autonomous cascade signal amplification strategy can be easily extended for detection towards a wide spectrum of analytes including nucleic acid, proteins, and small molecules possessing their corresponding aptamers. Therefore, the developed Exo III-aided autonomous cascade signal amplification strategy might indeed provide a facile and universal tool for bioanalysis and clinical diagnosis.
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SENSORS AND ACTUATORS B-CHEMICAL
·
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.
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ANALYST
·
2020
·Vol. 145
·期 8
·2975-2981
·
IF 3.978
Rufeng Zhang,Jie Zhang,Xiaonan Qu,Shasha Li,Yihan Zhao,Su Liu,Yu Wang,Jiadong Huang,Jinghua Yu
DNA walkers, one of the artificial molecular machines which are constructed via smart synthetic DNA, have attracted rapidly growing attention from researchers in the biosensing field. In this work, we design an Exonuclease III (Exo III)-aided target-aptamer binding recycling (ETBR) activated bipedal DNA machine for highly sensitive electrochemical detection of antibiotics. To the best of our knowledge, this is the first time that a bipedal DNA machine has been applied in electrochemical sensing for antibiotics. On the one hand, the bipedal DNA walker exceeds the conventional single swing arm DNA walker in terms of walking efficiency and stability. On the other hand, the ETBR strategy, along with efficient strand displacement amplification via stepwise movement of a bipedal DNA walker significantly promotes the signal amplification efficiency. Under optimal conditions, this bipedal DNA machine possesses a detection limit of 7.1 fM within a linear detection range from 10 fM to 100 pM. Moreover, this electrochemical biosensor is expected to detect a wide variety of analytes using the corresponding target recognition probes. Thus, our proposed strategy offers a highly efficient, stable and practical platform for small molecule analysis.
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Chemical Science
·
2019
·Vol. 10
·期 30
·7290-7298
·
IF 9.556
Daoqing Fan,Juan Wang,Erkang Wang,Shaojun Dong
Although DNA computing has exhibited a magical power across diverse areas, current DNA logic gates with different functions are always separately operated and can only produce hard-to-visualize output. The fussy/obligatory gates' redesign/reconstruction and the non-intuitive output cause the wastage of time and costs, low efficiency and practicality. Herein, inspired by the ancient Roman mythical God Janus, for the first time, we propose the concept of “DNA Janus Logic Pair” (DJLP) to classify the DNA logic gates with contrary functions into “Positive + Negative” gates (DJLP = Pos + Neg). Based on the biocatalytic property of G-quadruplex DNAzyme (G4zyme) and the luminescence quenching ability of oxidized 3,3′,5,5′-tetramethylbenzidine (OxTMB) towards the upconversion (UC) particles, we fabricated a universal amphichromatic platform that kills two birds with one stone for operating a versatile DJLP library. Different from the previous DNA logic systems, the “Pos + Neg” gates of each DJLP in this study were concomitantly achieved via the same one-time DNA reaction, which avoided the gates' redesign/reoperation and reduced the operating costs/time of the DNA gates by at least half. Besides, both the amphichromatic outputs (Visual-blue and UC luminescent-green) can be visualized under harmless-NIR, thus bringing greatly enhanced practicality to the method. Moreover, we constructed various concatenated logic circuits via logically modulating the G4zyme's biocatalytic property with glutathione, thus enabling the largely improved computing complexity. Furthermore, taking the circuit “YES-INH-1-2 decoder” as the “computing core”, we designed an “antioxidant indicator” with ratiometric logical responses that could recognize the presence of antioxidants smartly (output changed from “10” to “01”), which provided a typical prototype for potential intelligent bio-applications.
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MICROCHIMICA ACTA
·
2020
·Vol. 187
·期 2
·1-9
·
IF 6.232
Li Mei,Xu Xiong,Zhou ZhongGao,Xu GuoHai,Xie YongRong,Cai QingYou
A method is described for the determination of microRNAs via two-stage signal enhancement. This is attained by combining hairpin (HP) assisted cascade isothermal amplification with light-up DNA-Ag nanoclusters. A rationally designed dual-functional HP is used, and microRNA-21 is chosen as a model analyte. At the first stage, upon the hybridization of the microRNA-21 with HP, microRNA recycling via polymerase-displacement reaction and a circulative nicking-replication process are achieved. This generates numerous G-abundant overhang DNA sequences. In the second stage, the above-released G-abundant overhang DNA sequences hybridize with the dark green Ag NCs, and this results in the appearance of bright red fluorescence. Thanks to the two signal enhancement processes, a linear dependence between the fluorescence intensity at 616 nm and the concentration of microRNA-21 is obtained in the range from 1 pM to 20 pM with a detection limit of 0.7 pM. The strategy clearly discriminates between perfectly-matched and mismatched targets. The method was applied to the determination of microRNA-21 in a spiked serum sample.
Schematic representation of microRNA detection by integrating hairpin assisted cascade isothermal amplification with light-up DNA Ag nanoclusters. With microRNA, G-abundant overhang DNA sequences from amplification reaction hybridize with dark green Ag nanoclusters to produce a concentration-dependent bright red fluorescence
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Scientific Reports
·
2016
·Vol. 6
·期 1
·1-8
·
IF 5.228
Lan Jianming,Liu Yingxin,Li Li,Wen Fadi,Wu Fang,Han Zhizhong,Sun Weiming,Li Chunyan,Chen Jinghua
High-sensitivity detection of trace amounts of c-erbB-2 oncogene was reported to be equal to or surpass the ability of CA 15-3 for early diagnosis and/or follow-up recurrent screening of breast cancer. Therefore, in the current study, by using upconversion nanoparticles (UCNPs), rare earth-doped NaYF 4 :Yb 3+ /Er 3+ as the luminescent labels, a upconversion luminescent (UCL) biosensor based on dual-signal amplification of exonuclease III (ExoIII)-assisted target cycles and long-range self-assembly DNA concatamers was developed for the detection of c-erbB-2 oncogene. The proposed biosensor exhibited ultrasensitive detection with limit as low as 40 aM, which may express the potential of being used in trace analysis of c-erbB-2 oncogene and early diagnosis of breast cancer.
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