CURRENT MICROBIOLOGY
·
2025
·Vol. 83
·期 2
·112
·
IF 2.6
Gao Peng,Lu Xie-Feng,Yao Ling,Xu Yuan-Jia,Zhang Shu-Yi,Liu Guo-Hong,Zhou Shun-Gui
Two novel aerobic, rod-shaped, motile bacterial strains, designated as strains sgz302251 T and sgz5001026 T , were both isolated from paddy soils. 16S rRNA gene sequences analysis revealed that strain sgz302251 T exhibited 98.3% similarity with its closest reference strain Paenibacillus vietnamensis N4 T , while strain sgz5001026 T had the highest similarity of 97.5% to Ectobacillus polymachus KACC 18242 T . The average nucleotide identity (ANI) and digital DNA-DNA hybridization (dDDH) values between strains sgz302251 T , sgz5001026 T and their closest reference strains were 86.0% and 21.2%, 84.9% and 22.9%, respectively. The genomic DNA G + C contents of sgz302251 T and sgz5001026 T were 63.4% and 68.8%, respectively. Strain sgz302251 T grew at 20–37 °C (optimum 30 °C), pH 5.0–9.0 (optimum 6.5–7.5) and tolerated 0–1.0% NaCl (optimum 0.5%, w/v), while strain sgz5001026 T grew at 4–45 °C (optimum 37 °C), pH 5.0–9.0 (optimum 6.0) and 0–0.5% NaCl (optimum 0%). The quinone in both strains was MK-7 and major polar lipids were diphosphatidylglycerol (DPG), phosphatidylethanolamine (PE) and phosphatidylglycerol (PG). The main fatty acids (> 5%) of strain sgz302251 T were anteiso-C 15:0 , anteiso-C 17:0 , and C 16:0 , whereas strain sgz5001026 T included anteiso-C 15:0 , iso-C 15:0 , iso-C 16:0 and iso-C 14:0 . Based on the above evidence, the proposed names of the two novel species are Paenibacillus praedii sp. nov. (type strain sgz302251 T = MCCC 1K09633 T = KCTC 43808 T ), Ectobacillus soli sp. nov. (type strain sgz5001026 T = MCCC 1K09373 T = KCTC 25903 T ), respectively.
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高影响因子
BIOSENSORS & BIOELECTRONICS
·
2023
·
IF 12.6
Chunyan Wang,Yaxing Zhang,Chang Liu,Siyu Gou,Shanjin Hu,Weiwei Guo
Point-of-care testing (POCT) platforms for microRNA (miRNA) detection have attracted considerable attention in recent years, due to the increasingly important role of miRNA as biomarkers for the diagnosis of many diseases, such as cancers. However, several limitations such as the requirement of enzyme-related amplification system, expensive preservation cost, sophisticated analysis instruments and tedious operations of conventional miRNA biosensing devices severely hinder their widespread applications. In this work, a portable and smart colorimetric analysis platform was developed by employing the ultrathin DNA-gold nanoparticle (AuNP) hybrid hydrogel film as the signaling unit and the enzyme-free entropy-driven dynamic DNA network (EDN) as the signal converter and amplification unit. By programming the DNA sequences of the EDN, the EDN could respond to a specific miRNA, with miRNA-155 or miRNA-21 as the model target, and release a converter DNA with amplified concentration to further trigger the release of AuNPs from the hydrogel film as a colorimetric signal output. To avoid the use of sophisticated spectral instruments, digital analysis based on primary three-color channel (R/G/B) was further introduced by using user-friendly camera and image processing software, and a detection limit at pM level was achieved. Moreover, by introducing H 2 O 2 -mediated AuNPs enlargement procedure in the colorimetric analysis platform, the detection limit for miRNA target could further be enhanced to fM level. The POCT platform is also portable and storable with a good storage stability for at least 45 days, suggesting its great potential in practical diagnosis applications.
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Food Analytical Methods
·
2022
·Vol. 15
·期 8
·2069-2083
·
IF 3.498
Nanfack Carole D. V.,Yang Jia,Yuan Xiao,Sun Jiadi,Sun Xiulan,Ji Jian
Deoxyribonucleic acid (DNA) extraction, which is the mainstay of molecular amplification for food pathogen detection procedure, is dependent on laboratory infrastructure, cumbersome methods, and time consumption. To tackle these dependencies, we developed an enhanced mussel-inspired cellulose card for the convenient, eco-friendly, and rapid DNA extraction from bacteria present in food. This enhanced cellulose mussel-inspired DNA adhesive card (BDA card) was successfully prepared using Na + through the self-polymerization of biopolymer polyvalent ions and 3,4-dihydroxy-l-phenylalanine (L-Dopa). We observed that, when the biopolymer surface modification of the cellulose was NaCl-doped, the DNA extraction and purification performances of the obtained BDA card were enhanced when compared to the performance of the cellulose modified with the biopolymer doped with HCl. After the surface modification, the previously modified cellulose card was characterized with the Fourier transform infrared spectroscopy (FTIR), X-ray diffraction (XRD), and scanning electron microscopy (SEM). The DNA extraction performances as well as the quality of the bacteria genomic DNA extracted were equally measured. The Na + -doped DNA adhesive cellulose card (BDA card) depicted the best bacteria genomic DNA extraction performances. When compared to commercially available bacteria genomic DNA extraction kits, the BDA card portrayed better DNA extraction performances, in a one-step extraction protocol. It allowed easy and convenient DNA extraction. The whole genomic DNA extraction process could be completed in 10 min. The concentration of the genomic DNA extracted from overnight bacteria culture was highest when extracted with the BDA card 459.39 ± 86 ng/µl as compared to Ezup and PureLink genomic DNA kits. When tested with spiked chicken, it was statistically equal to the Mag-MK food genomic DNA extraction kit. The proposed method provides a simple, efficient, eco-friendly, and convenient approach for bacteria genomic DNA extraction and purification from samples.
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BIOSENSORS & BIOELECTRONICS
·
2015
·
IF 6.409
Biyan Xu,Delun Zheng,Weiwei Qiu,Feng Gao,Shaoxiong Jiang,Qingxiang Wang
In this work, a novel electrochemical DNA biosensor has been developed based on the hybrid film of fern leaf-like α-Fe 2 O 3 microparticles and chitosan (CS). The fern leaf-like α-Fe 2 O 3 microparticles were synthesized via a facile template-free hydrothermal method, and their morphologies were characterized by X-ray diffraction, energy dispersive spectrometry, scanning electron microscope, and transmission electron microscope. Electrochemical characterization assays revealed that the hybrid film modified electrode had remarkable synergistic effects of the large accessible surface area and high electrical conductivity of semiconductive Fe 2 O 3 , and the good film stability of CS. Based on the rich amino groups on CS, the CS–Fe 2 O 3 hybrid film was employed as a functional matrix for probe DNA immobilization using terephthalaldehyde (TPA) as a bifunctional arm-linker. The hybridization capacity of the developed biosensor was evaluated with electrochemical impedance spectroscopy (EIS) using [Fe(CN) 6 ] 3−/4− as the indicating probe. A wide dynamic detection range from 1.0×10 −14 to 1.0×10 −10 M with ultralow detection limit of 5.6×10 −15 M was achieved for the target DNA. The hybridization selectivity experiments further revealed that the biosensor could discriminate fully complementary sequences from one-base mismatched, three-base mismatched, and non-complementary sequences. Moreover, the biosensor showed the advantage of good regeneration ability and reproducibility.
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ANALYTICA CHIMICA ACTA
·
2015
·
IF 4.513
Xiaoyun Lin,Yongnian Ni,Serge Kokot
An electrochemical biosensor capable of indirect detection of DNA damage induced by any one of the three endocrine-disrupting compounds (EDCs) – bisphenol A (BPA), 4-nonylphenol (NP) and 4- t -octylphenol (OP), has been researched and developed. The methylene blue (MB) dye was used as the redox indicator. The glassy carbon electrode (GCE) was modified by the assembled dsDNA/graphene oxide-chitosan/gold nano-particles to produce a dsDNA/GO-CS/AuNPs/GCE sensor. It was characterized with the use of electrochemical impedance spectroscopy (EIS), cyclic voltammetry (CV) and scanning electron microscopy (SEM) techniques. The loading/release of the MB dye by the dsDNA/GO-CS/AuNPs film was investigated, and the results showed that the process was reversible. Based on this, the sensor was used to measure the difference between the loading capabilities of intact and damaged dsDNA in the films. The sensor was then successfully applied to detect DNA damage electrochemically. The differential pulse voltammetry (DPV) peak current ratio for MB, observed before and after DNA damage, increased linearly in the presence the BPA, NP or OP compounds; the treatment range was 10–60 min, and the respective damage rates were 0.0069, 0.0044 and 0.0031 min −1 , respectively. These results were confirmed by the binding constants: 2.09 × 10 6 M −1 (BPA-DNA), 1.28 × 10 6 M −1 (NP-DNA) and 9.33 × 10 5 M −1 (OP-DNA), all of which were obtained with the use of differential pulse stripping voltammetry (DPSV).
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高影响因子
SENSORS AND ACTUATORS B-CHEMICAL
·
2023
·
IF 8.4
Na Dong,Yuye Li,Shuyun Meng,Shuda Liu,Yifan Liu,Dong Liu,Tianyan You
Large-sized DNA structures have been extensively explored in electrochemical sensing for abundant binding sites or large steric hindrance, yet large steric hindrance could hinder electron transfer of probes on DNA, depressing their efficiency for signal amplification. Herein, a ratiometric electrochemical aptasensor was designed to take advantage of abundant binding sites and large steric hindrance of the tetrahedral DNA nanostructure (TDN) for efficient signal amplification. The working principle is that the recognition of the target leads to a decrease in binding sites and a reduction in steric hindrance, which in turn leads to the opposite change in the two signals. Ferrocene (Fc)-labeled complementary DNA acted as a substrate, while a TDN containing aptamer was used for fumonisin B1 (FB1) recognition and methylene blue (MB) absorption. The binding of FB1 triggered the stripping of TDN, leading to a decreased current of MB (I MB ) and an increased current of Fc (I Fc ). In this way, TDN allowed the enlarged variations in I Fc and I MB by the significant change in steric hindrance and binding sites in ratiometric electrochemical sensing, respectively. Consequently, the developed aptasensor offered a linear range of 0.1–100 pg mL −1 and a detection limit of 0.087 pg mL −1 for FB1. This strategy offers a new way to fabricate high-performance sensors with large DNA structures.
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ANALYTICA CHIMICA ACTA
·
2022
·
IF 6.911
Jing Zhu,Liutao Chen
Fluorescent dye DITO-1 has almost no fluorescence in the absence of nucleic acid . G bases in single strand DNA can induce maximum fluorescent enhancement followed by the A bases when it binds the DITO-1. However, the incorporation efficiency of the dATP was higher than dGTP in terminal transferase (TdT) polymerization. As a consequence, ploy (A) n , rather than ploy (G) n via TdT polymerization had the superior photoluminance when it binded DITO-1 fluorescent dye. Here, we developed a high selective and sensitive sensing strategy for assaying TdT and T4 polynucleotide kinase activity (T4 PNK) based on the ploy (A) n -DITO-1 fluorescent probe. An increasing amounts of TdT enzyme could promote the distinct incorporation of dATP on the DNA primer and form poly (A) n ssDNA with a difference in length. A good linear relationship between the ΔF and the concentrations of TdT in a range of 0.2–50 U/mL was obtained and the detection limit was 0.05 U/mL. Based on the experimental results for TdT, we further expanded the application of this method for detection of a series of concentrations of T4 PNK. The ΔF and the logarithm concentrations of T4 PNK in the range of 0.1–10 U/mL showed a good linear response and the detection limit of 0.02 U/mL was obtained. In addition, the detection of T4 PNK in Hela cell lysate was achieved, demonstrating that the proposed method had the potential application in complex system. The ploy (A) n -DITO-1 fluorescent probe had the excellent properties of one-step readout, robustness for target detection in complex system, and easiness operation, and showed the great potential in clinical diagnostics, inhibitor screening, and drug discovery.
研究领域:
分子生物学
·
生物化学
·
分析化学
·
生物医学工程
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高影响因子
ACS Sensors
·
2019
·
IF 6.944
Liping Liu,Zhen Fang,Xiangjiang Zheng,Dongmei Xi
A straightforward yet efficient, nanopore-based strategy that enables the sensitive detection of copper(II) ion (Cu2+) and real-time monitoring of a click reaction is provided. Two single-stranded DNAs (ssDNAs) are designed to act as the preprobes, one being modified with an azide and the other an alkyne. The presence of Cu2+ induces the ligation of two ssDNAs via click reaction, leading to the formation of a forked DNA which can quantitatively generate characteristic current signatures when interacts with α-hemolysin (α-HL) nanopore. The assay facilitates a highly selective and sensitive measurement of Cu2+ without the need for labels or signal amplification. More importantly, this nanopore platform exhibits excellent performance in real-time monitoring of a copper(I) ion (Cu+)-catalyzed click reaction at the single-molecule level, by recording the current signals of the forked DNA generated by click chemistry. The proposed strategy is believed to play an important role in both nanopore sensing and characterization of chemistry reactions, especially coupling reactions.
研究领域:
纳米孔传感
·
化学反应表征
·
生物分析化学
·
分子生物学
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APPLIED AND ENVIRONMENTAL MICROBIOLOGY
·
2025
·
IF 3.7
Ronghui Liu,Jiadun Liu,Kuo Zhang,Shujun He,Qishun Feng,Jing Dai,Xinrong Guo,Yang Fu,Yi Li
In motor-assisted nanopore sensing, increasing the salt concentration improves the signal-to-noise ratio (SNR); however, helicases used as motor proteins generally fail to sustain efficient unwinding under high-salt conditions. In this study, we characterized the structure and function of AAA+ ATPase helicases from acidophiles. Bioinformatic analysis indicated that such helicases are broadly distributed among acidophilic bacteria. A representative helicase from Leptospirillum spp., designated LfDda, adopts a dimeric architecture at 3.5 Å resolution with a flexible tower domain while retaining conserved 1A and 2A domains, akin to well-studied motor (T4 Dda helicase). Biochemical assays demonstrated that the dimeric form of LfDda is functional, acting as a 5′–3′ directional helicase that can utilize various divalent metal ions as cofactors, with Mn2+ supporting the highest catalytic activity. Crosslinking of the flexible 1B and 2B domains yielded a monomeric variant capable of efficient DNA translocation at 600 mM KCl, representing a 6-fold enhancement in ionic tolerance. These findings suggest that helicases derived from extremophilic bacteria can be engineered to modulate DNA translocation behavior, providing a potential avenue for developing new motor proteins for nanopore and other DNA-unwinding applications.
研究领域:
分子生物学
·
结构生物学
·
生物物理学
·
合成生物学
·
纳米技术
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JOURNAL OF FOOD AND DRUG ANALYSIS
·
2025
·Vol. 33
·期 4
·451
·
IF 3
Zhang Yun,Wu Qiong,Gao Hui,Zhang Hua,Miao Xiang-Min
Evidence had accumulated that serotonin (5-HT), a hormone and neurotransmitter, was not only involved in a variety of different physiological and central nervous system functions but also in the development and manifestation of psychiatric diseases. Here, DNA tetrahedron-Au NPs-GO for enhanced fluorescence sensor was designed for detecting serotonin. Au NPs-GO was used as a fluorescence quencher, while fluorophore-labeled DNA tetrahedron was used as a donor, resulting in fluorescence resonance energy transfer (FRET) from the fluorophore to Au NPs-GO (signal off). With the strong binding ability of aptamer to serotonin, S5 was released from Aptamer: S5 duplex, then reacted with the tail of DNA tetrahedron (DTNs), followed by the formation of three double stranded DNA products in the tail of DTNs, bringing in signal readout responses (signal on). Consequently, a reliable, sensitive and selective sensor was obtained for one-step quantificative detection of serotonin from 50 pM to 200 nM with a detection limit of 16.8 pM. Furthermore, satisfactory stability, reproducibility, specificity and good recovery efficiency in human serum samples revealed that the proposed sensor could be served as a prospective tool for serotonin detection.
研究领域:
生物传感器
·
纳米技术
·
分析化学
·
神经化学
·
生物医学工程
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Nature Communications
·
2025
·
IF 15.7
Xinyi Wan,Haonan Fan,Zhuoning Li,Yixuan Du,Yu Liu,Weiwu Zeng,Zhongxing Sun,Juejia Shao,Junqi Jia,Yanjun Zhang,Dong Fang
DNA topology is critical for regulating transcription and maintaining cellular homeostasis. Z-DNA is a left-handed DNA helix in regions with high transcriptional activity. Its physiological function remains poorly understood. Here, we demonstrate that oncoprotein MYC induces the formation of Z-DNA by recruiting the chromatin remodeler FACT, independent of RNA Polymerase II activity. FACT facilitates Z-DNA formation by remodeling H2A/H2B dimers within intact nucleosomes. Additionally, the phosphorylation of FACT regulates its liquid-liquid phase separation, promoting its efficient recruitment to chromatin by MYC. Through a genome-wide analysis and characterization of engineered Z-DNA promoters, we found that Z-DNA directly facilitates the loading of RNA Polymerase II, thereby promoting transcriptional activity. This study elucidates the molecular mechanisms of Z-DNA dynamics and emphasizes its functional importance in transcriptional regulation, providing insights into the role of left-handed DNA structures in chromatin biology and MYC-driven cancer. Z-DNA forms at highly active genes, but its function is unclear. Here, the authors show that MYC recruits FACT to promote Z-DNA formation within nucleosomes, enabling RNA Polymerase II loading and enhancing transcription, revealing a mechanistic role for Z-DNA in MYC-driven regulation.
研究领域:
分子生物学
·
肿瘤学
·
表观遗传学
·
染色质生物学
·
转录调控
·
癌症机制
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BIOMATERIALS
·
2011
·
IF 7.883
Ruilong Sheng,Ting Luo,Yingdan Zhu,Hui Li,Jingjing Sun,Shengdian Chen,Wenyan Sun,Amin Cao
Stimuli-responsive biomaterials derived from natural products toward efficient drug/gene delivery have been attracting increasing attention in the past decade. In this work, we first designed and prepared a new series of cholesterol-disulfide lipids , namely CHOSS-N, CHOSS-N+, CHOSS-Lys and CHOSS-4N bearing cholesterol and a variety of headgroups via disulfide and carbonate bond linkages, and their molecular structures were characterized by NMR and ESI-MS. Furthermore, plasmid DNA binding affinity for these new CHOSS lipids was separately examined by ethidium bromide displacement and agarose-gel retardant assay. Average diameter sizes and surface potentials of the CHOSS/pDNA lipoplex particles prepared under various N/P charge ratios were analyzed by dynamic laser light scattering (DLS). Under 10 m m dithiothreitol (DTT), stability and disassembly of the CHOSS/pDNA lipoplex nanoparticles were investigated by agarose-gel retardant assay and atomic force microscopy (AFM). Employing a COS-7 cell line, cell viability was examined for the prepared CHOSS lipids and their pDNA lipoplexes with branched PEI-25k as the reference. Finally, COS-7 cell gene transfection efficacies with these CHOSS lipids as potential delivery vectors were investigated by luciferase and EGFP transfection assay in the absence and presence of serum, and intracellular uptake capability, trafficking and cellular localization of Cy3-labeled pEGFP-N1 DNA were studied with a flow cytometer and fluorescent microscopy with Lipofectamine™ 2000 as the control. The results demonstrated low cytotoxicity, strong pDNA binding affinity and high transgenetic efficacy for new prepared CHOSS lipids, and particularly high intracellular uptake capability and specific cellular localization of pDNA at the periphery of cell nuclei were for the first time interestingly observed for the CHOSS lipid delivery carriers. In general, these may pave a new way to utilize cholesterol, amino acids and other functional natural products to prepare efficient gene/drug delivery carriers with simple structure and low cytotoxicity.
研究领域:
生物材料学
·
分子生物学
·
药剂学
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