INTERNATIONAL JOURNAL OF BIOLOGICAL MACROMOLECULES
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2025
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IF 8.5
Jiangli Song,Hanlian Chen,Rongkai Pan,Fangyu Jin,Jie Tang,Qianqian Huang,Guohua Zhou,Xiumei Song
Understanding the interactions between small molecules and calf thymus deoxyribonucleic acid (ctDNA) is critical for certain aspects of drug discovery. In this study, three 11 H -indeno[1,2-b]quinoxalin-11-one thiosemicarbazones were synthesized and their interaction with ctDNA was examined through various spectroscopic techniques, including ultraviolet (UV) spectroscopy, fluorescence spectroscopy, and circular dichroism (CD) spectrum, and through physicochemical methods, including viscosity measurements. In addition, the effects of these thiosemicarbazone compounds 4a, 4b and 4c on several cancer cell lines were explored. The results of UV absorption, fluorescence quenching and CD experiments indicated that compounds 4a, 4b and 4c primarily bound to ctDNA by an intercalation. This mode of interaction was further corroborated by viscosity measurements. Docked poses of compound 4a revealed that it formed a crucial N position hydrogen bond with the DNA receptor. The chemical structure of compound 4a was further confirmed by X-ray crystallographic analysis. Through biological evaluation, it was found that the in vitro cytotoxicity of three compounds agreed with the order of their binding strength to ctDNA, indicating that the antitumor activity of these compounds correlated with their binding affinity to ctDNA.
研究领域:
生物化学
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药物化学
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肿瘤学
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PubMed
高影响因子
INTERNATIONAL JOURNAL OF THERMOPHYSICS
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2019
·Vol. 40
·期 12
·1-18
·
IF 0.853
Zhang Zeyu,Meng Xianyang,Zhang Ke,Wu Jiangtao
Viscosity is one of the most important properties for many scientific and technological applications, and therefore it has been the subject of an enormous effort of measurement, correlation, and interpretation. Reliable reference data can be of great help to improve viscosity accuracy, while for viscosity, the only accepted standard is the viscosity of pure water at 20 °C (the reference value recommended by ISO is 1.0016 mPa·s). With the technology and industry advancing, there is a new requirement for reference materials of viscosity covering wide temperature, pressure, and viscosity ranges in order to face the challenge that the order of magnitude of viscosity turns to 10 14 . Considering the dissatisfaction of the only standard, we put forward these candidates to meet the need of appropriate viscosity standard materials: dimethyl adipate (DMA), diethyl adipate (DEA), dipropyl adipate (DPA), and dibutyl adipate (DBA). These materials have the characteristics of easy to obtain, high purity, high thermal chemical stability, and especially larger viscosity value. In this work, the viscosity was experimentally measured by the vibrating wire viscometer over the temperature range of (283 to 363) K and at pressures up to 40 MPa. The combined expanded uncertainty of the reported viscosity is about 2 % with a confidence level of 0.95 ( k = 2). The empirical Andrade–Tait equation was used to correlate the experimental results.
研究领域:
物理化学
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材料科学
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DOI
高影响因子
ENERGY & FUELS
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2019
·
IF 3.021
Yuchuan Chen,Bohui Shi,Yang Liu,Qianli Ma,Shangfei Song,Lin Ding,Xiaofang Lv,Haihao Wu,Wei Wang,Haiyuan Yao,Jing Gong
With the tendency of the offshore petroleum industry moving to the deep-water fields, there are several challenges for the exploration and development of oil and gas with higher paraffin content in the deep-water severe environment, especially the complex flow assurance issues including the coexistence of wax precipitation and hydrate formation. The effects of wax on hydrate slurry viscosity, hydrate nucleation and growth, and hydrate dissociation were investigated in a rheometer. Results indicated that the stage characteristics of viscosity evolution during hydrate formation in waxy and wax-free emulsions were different, and two stages could be observed during the hydrate growth process in the presence of wax. Hydrate slurry viscosity increased with the wax content. The coupled hydrate–wax aggregates were difficult to be broken by the constant shearing force. The shear-thinning property of the hydrate slurry was not affected by the precipitated wax. Hydrate formation was inhibited due to the wax precipitated in the oil phase. Specifically, cyclopentane hydrate critical time and growth time increased with the wax content. The calculated hydrate volume fraction decreased with the wax content based on the suspension viscosity model. It was difficult for a water bridge to form between two hydrate particles during the hydrate-dissociation process with 3.0 and 5.0 wt % wax contents; therefore, no obvious increase in the slurry viscosity was observed when the slurry viscosity decreased during the dissociation process.
研究领域:
石油工程
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流变学
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能源材料
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多相流
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流动保障
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DOI
高影响因子
JOURNAL OF PHYSICAL CHEMISTRY B
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2022
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IF 3.466
Jianfeng Xue,Zheng Wang,Hong Zhang,Yan He
Viscoelastic characterization is of great importance for the investigation of biomolecular condensates. Single-particle-tracking-based rotational diffusion analysis of single nanorods is an effective approach for quantitative viscosity measurement. However, in the case of high background and noise with high-speed image acquisition, accurate extraction of diffusivity from the data is a challenging task. Here, we develop a novel frequency-domain-based deep learning (DL) method for single nanorod rotational tracking analysis. We synthesized Brownian rotational time-series data for training, designed a data preprocessing module to reduce the effect of noise, and extracted rotational diffusion coefficient using recurrent neural networks in the frequency domain. Compared with the traditional curve-fitting-based methods, our method shows higher accuracy and a wider detection range for viscosity measurement. We verified our method using experimental data from plasmonic imaging of single gold nanorods (AuNRs) in glycerol solution and PGL droplets. Our method can be potentially applied to the viscosity measurement of different biomolecular condensates in vitro and in vivo.
研究领域:
生物物理学
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生物技术
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机器学习
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材料科学
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DOI
PubMed
高影响因子
CHINESE JOURNAL OF STRUCTURAL CHEMISTRY
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2022
·
IF 0.847
Hui-Chao GUAN,Xiao-Tong SONG,Gui-Bao LIU,Shu-Mei YUE
Complexes [Zn(pbm)(5-hip)3] ( 1 ), [Zn(pbm)(5-nip) 3 ] ( 2 ), [Mn(pbm)(H 3 btc) 2 (H 2 O)] ( 3 ) and [Mn(pbm)(5-nip) 3 ] ( 4 ), where H 2 HIPA = 5-hydroxyisophthalic acid, H 2 nip = 5-nitroisophthalic acid, H 3 btc = trimesic acid and pbm (pyridine benzene chelate material) = 2-(2-pyridyl)benzimidazole, were identified via single-crystal XRD analyses. 1, 2 and 4 pertain to the monoclinic space group C 2/ c , while 3 belongs to the triclinic space group P ① . The interplay of CT-DNA with those complexes was delineated using ultraviolet, fluorescence, and circular dichroism (CD) spectroscopy and viscosity measurements. Complexes 1, 2, 3 and 4 interact with CT-DNA in an electrostatic or grooving mode. We wish to offer a theory-wise foundation for developing anti-tumor medicines.
研究领域:
无机化学
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生物化学
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药学
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DOI
高影响因子
POLYHEDRON
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2025
·
IF 2.6
Keliang Wan,Lifeng Tan
Double-stranded RNA determines and regulates many biological processes in cells, plays a vital role in cell information transmission and gene regulation, and is a key target for the treatment of certain diseases. Here, we synthesized and characterized two novel ruthenium(II) complexes [Ru(phen) 2 ( o -CNPIP)] 2+ (Ru 1 ) and [Ru(phen) 2 ( o -CH 3 PIP)] 2+ (Ru 2 , phen = 1,10-phenanthroline, o -CNPIP = (2-(4-cyanodipyrido)-imidazo-[4,5- f ][1,10]-phenanthroline, o -CH 3 PIP = 2-(4-methyl)-imidazo-[4,5- f ][1,10]-phenanthroline). The interaction of the two Ru (II) complexes with double-stranded RNA poly(rA)•poly(rU) under dilute solution and molecular crowding conditions was studied by various spectroscopic methods and viscosity measurements. The results of UV–vis absorption spectroscopy and steady-state emission spectroscopy studies show that Ru 1 showed stronger binding and stabilizing ability to poly(rA)•poly(rU) and the binding affinity of Ru 1 and Ru 2 to poly(rA)•poly(rU) was weakened under molecular crowding conditions. Subsequently, the results of circular dichroism spectroscopy studies, thermal denaturation measurements and viscosity measurements also confirmed the results of our UV–vis absorption spectroscopy and steady-state emission spectroscopy studies. The results also showed that the two Ru(II) complexes bind, stabilize and perturb the structure of poly(rA)•poly(rU) by intercalation under dilute solution and molecular crowding conditions. In addition, it was found that the strength of these abilities was closely related to the binding affinity of the Ru(II) complexes to poly(rA)•poly(rU) by comparing the results of these studies. Furthermore, the thermodynamic parameters for the binding of Ru(II) complexes to poly(rA)•poly(rU) under the two conditions indicate that the binding process is spontaneous, is an enthalpy-driven process, and that hydrogen bonding serves as the dominant force. The purpose of this work is to explore the substituent effect of Ru(II) complexes and the effect of solution environment on the ability of Ru(II) complexes to bind and stabilize poly(rA)•poly(rU). Some insights resulting from this work are expected to facilitate the design of highly selective double-stranded RNA binders based on Ru(II) complexes. Interestingly, the phosphorescence intensity of Ru 2 after binding to poly(rA)•poly(rU) is significantly higher than that of Ru 1 under both solution conditions, with even stronger phosphorescence emission observed under molecular crowding conditions. This indicates that Ru 2 possesses the potential to serve as a nucleic acid luminescent probe for nucleic acid imaging in biological cells. To enhance its luminescent properties and specific binding capacity, further structural modification of Ru 2 is essential, which will be one of the key focuses of our future research efforts.
研究领域:
无机化学
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生物无机化学
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核酸化学
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分子光谱学
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生物物理化学
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DOI
高影响因子
FOOD RESEARCH INTERNATIONAL
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2025
·
IF 8
Junbo Chu,Songyi Lin,Yuxin Xie,Lin Ma,Simin Zhang
Fried oysters are a traditional dish in coastal regions; however, concerns have been raised regarding the potential nutritional loss drawbacks due to the high temperatures in the frying process, which can lead to oil oxidation. This study investigates the effects of soybean dietary fiber (SDF) and citrus dietary fiber (CDF) at supplemental levels of 0.5 %, 1 %, 2 %, and 4 % on the overall quality of fried oysters. The findings indicate that compared with the control group without dietary fiber, the addition of dietary fibers effectively reduced oil absorption and improved nutritional quality. At a 2 % concentration, SDF and CDF significantly decreased thiobarbituric acid reactive substances (TBARs) by 24.24 % and 15.59 % and peroxide value (POV) by 38.30 % and 31.24 %, respectively, while also inhibiting lipid penetration. Further analysis through molecular docking simulations, viscosity measurements, and scanning electron microscopy (SEM) revealed that dietary fibers bind to the batter, forming a protective mechanical barrier around the oysters. This research endeavor seeks to provide a theoretical basis for improving the quality of fried oysters.
研究领域:
食品科学
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营养学
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食品化学
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产品关联
DOI
PubMed
高影响因子
FOOD CHEMISTRY
·
2021
·
IF 7.514
Mingming Hu,Miao Zhu,Le Xin,Guowen Zhang,Shimin Wu,Xing Hu,Deming Gong
Benzo[ a ]pyrene (BaP), a prototype of polycyclic aromatic hydrocarbons (PAHs) with potential mutagenicity, toxicity and carcinogenicity, is ubiquitous in deep-fried foods. Herein, the changes in eight specific PAHs (PAH8) concentration in sunflower oil during frying were investigated by gas chromatography-triple quadrupole-mass spectrometry (GC-QqQ-MS). PAH8 concentrations in sunflower oil were 23.92–27.82 μg kg −1 and increased with increasing frying time. The detected BaP levels were 3.64–4.00 μg kg −1 , exceeding the upper limit (2 μg kg −1 ) set by European Union (EU), though below the limiting value (10 μg kg −1 ) in China. The interaction between BaP and calf thymus DNA (ctDNA) was explored through various spectroscopic methods and molecular docking. Melting studies, denaturation experiments, ionic strength effects and viscosity measurements indicated that BaP interacted with ctDNA primarily via groove binding as evidenced by circular dichroism analysis and molecular docking. Further gel electrophoresis assays suggested that DNA was damaged at high levels of BaP.
研究领域:
食品科学
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毒理学
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分子生物学
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分析化学
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产品关联
DOI
PubMed
高影响因子
JOURNAL OF MOLECULAR LIQUIDS
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2020
·
IF 5.065
Rui Wang,Na Li,Xing Hu,Junhui Pan,Guowen Zhang,Xinan Zeng,Deming Gong
The binding characteristics of food antioxidant tert -butylhydroquinone (TBHQ) and its oxidation product tert -butylquinone (TBQ) with calf thymus DNA (ctDNA) in vitro were investigated using multispectroscopy, chemometrics , viscosity measurements, gel electrophoresis assays and molecular docking . Analysis of fluorescence spectra found that TBHQ and TBQ bound with ctDNA to form 1:1 complexes with the binding constant in the order of 10 4 L mol −1 . The concentration profiles and the pure spectra for the components (TBHQ, TBQ, ctDNA and TBHQ– or TBQ–ctDNA complex) were obtained through analyzing the expanded ultraviolet-visible absorption data matrix by multivariate curve resolution–alternating least squares algorithm, which successfully monitored the binding process of TBHQ/TBQ with ctDNA. Fluorescence displacement, viscosity and molecular docking experiments showed that TBHQ bound to ctDNA through intercalation binding, while TBQ bound to the minor groove of ctDNA. The binding of TBHQ to ctDNA induced the conversion of DNA conformation from B-form to A-form, while TBQ caused a minor perturbation on the DNA conformation. Gel electrophoresis results indicated that the combination of TBHQ and Cu(II) could induce DNA damage. This study may contribute to understanding the binding mechanisms of TBHQ and TBQ with ctDNA and further evaluate the potential toxicological effects of TBHQ as a food additive .
研究领域:
生物化学
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分子生物学
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毒理学
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食品科学
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DOI
高影响因子
JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY
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2014
·
IF 3.107
Guowen Zhang,Langhong Wang,Xiaoyue Zhou,Yu Li,Deming Gong
The binding characteristics of sodium saccharin (SSA), an artificial sweetener, with calf thymus DNA (ctDNA) were investigated by multispectroscopic techniques, chemometrics, and molecular simulation. A combined fluorescence and UV–vis spectroscopic data matrix was resolved by the multivariate curve resolution–alternating least-squares (MCR–ALS) chemometrics algorithm. The MCR–ALS analysis extracted simultaneously the concentration profiles and spectra for the three components (SSA, ctDNA, and SSA–ctDNA complex) to quantitatively monitor the SSA–ctDNA interaction, which is difficult to perform by conventional spectroscopic approach. The binding mode of SSA to ctDNA was principally through groove binding as revealed by ctDNA melting temperature studies, viscosity measurements, and iodide and salt quenching effects. Analysis of the Fourier transform infrared and circular dichroism spectra as well as molecular docking indicated that SSA preferentially bound to the guanine base of ctDNA and led to a transformation from B-like DNA structure to A-like conformation. Moreover, gel electrophoresis results suggested that SSA did not induce any significant cleavage in plasmid DNA.
研究领域:
生物化学
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分子生物学
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分析化学
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生物物理学
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DOI
PubMed
高影响因子
JOURNAL OF FLUORESCENCE
·
2017
·Vol. 27
·期 5
·1815-1828
·
IF 1.461
Xia Kaixin,Zhang Guowen,Li Song,Gong Deming
Vanillin (VAN) and ethyl vanillin (EVA) are widely used food additives as flavor enhancers, but may have a potential security risk. In this study, the properties of binding of VAN or EVA with calf thymus DNA (ctDNA) were characterized by multi-spectroscopic methods, multivariate curve resolution-alternating least-squares (MCR–ALS) algorithm and molecular simulation. The concentration profiles for the components (VAN or EVA, ctDNA and VAN–ctDNA or EVA–ctDNA complex) by the MCR–ALS analysis showed that VAN or EVA interacted with ctDNA and formed VAN–ctDNA or EVA–ctDNA complex. The groove binding of VAN or EVA to ctDNA was supported by the results from viscosity measurements, melting studies, denaturation experiments, and competitive binding investigations. Analysis of the Fourier transform infrared spectra corroborated the prediction by molecular docking that VAN and EVA preferentially bound to thymine bases region of ctDNA. The circular dichroism and DNA cleavage assays indicated that both VAN and EVA induced conformational change (from B − like DNA structure toward to A − like form), but didn’t lead to a significant damage on DNA. The fluorescence quenching of Hoechst 33,258–ctDNA complex by VAN or EVA was a static quenching, and hydrogen bonding and van der Waals forces were main forces. This study has provided insights into the mechanism of interaction between VAN or EVA with ctDNA, and may also help better understand their potential toxicity with regard to food safety.
VAN or EVA binds to A–T rich regions of ctDNA in the minor groove.
研究领域:
化学
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生物化学
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分子生物学
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食品科学
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毒理学
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产品关联
DOI
PubMed
高影响因子
危险品化学品经营许可证（带存储）