JOURNAL OF PHOTOCHEMISTRY AND PHOTOBIOLOGY B-BIOLOGY
·
2014
·
IF 2.803
Yan-Qing Wang,Hong-Mei Zhang,Jian Cao,Bo-Ping Tang
Interactions of bisphenol S, a new bisphenol analogue with bovine serum albumin and calf thymus DNA were investigated using different spectroscopic methods and molecular modeling calculation. According to the analysis of experimental and theoretical data, we concluded that hydrophobic interactions and hydrogen bonding primarily mediated the binding processes of bisphenol S with bovine serum albumin and DNA. In addition, the electrostatic force should not be excluded. Molecular modeling studies indicated that the binding site of bisphenol S to bovine serum albumin located in the subdomain IB, while bisphenol S was a groove binder of DNA. In addition, BPS did not obviously induce second structural changes of bovine serum albumin, but it induced a conformational change of calf thymus DNA.
研究领域:
生物化学
·
分子生物学
✓ 已验证
DOI
高影响因子
SPECTROCHIMICA ACTA PART A-MOLECULAR AND BIOMOLECULAR SPECTROSCOPY
·
2017
·
IF 2.536
Jie-Hua Shi,Kai-Li Zhou,Yan-Yue Lou,Dong-Qi Pan
Molecular interaction of darunavir (DRV), a HIV protease inhibitor with calf thymus deoxyribonucleic acid (ct-DNA) was studied in physiological buffer (pH 7.4) by multi-spectroscopic approaches hand in hand with viscosity measurements and molecular docking technique. The UV absorption and fluorescence results together revealed the formation of a DRV–ct-DNA complex having binding affinities of the order of 10 3 M − 1 , which was more in keeping with the groove binding. The results that DRV bound to ct-DNA via groove binding mode was further evidenced by KI quenching studies, viscosity measurements, competitive binding investigations with EB and Rhodamine B and CD spectral analysis. The effect of ionic strength indicated the negligible involvement of electrostatic interaction between DRV and ct-DNA. The thermodynamic parameters regarding the binding interaction of DRV with ct-DNA in terms of enthalpy change (Δ H 0 ) and entropy change (Δ S 0 ) were − 63.19 kJ mol − 1 and − 141.92 J mol − 1 K − 1 , indicating that hydrogen bonds and van der Waals forces played a predominant role in the binding process. Furthermore, molecular simulation studies suggested that DRV molecule was prone to bind in the A-T rich region of the minor groove of DNA.
研究领域:
生物化学
·
药物化学
·
分子生物学
✓ 已验证
产品关联
DOI
PubMed
高影响因子
SPECTROCHIMICA ACTA PART A-MOLECULAR AND BIOMOLECULAR SPECTROSCOPY
·
2020
·
IF 3.232
Na Li,Xing Hu,Junhui Pan,Ying Zhang,Deming Gong,Guowen Zhang
4–Octylphenol is an endocrine disruptor , belonging to environmental estrogens. It can be enriched in the human body through the food chain and may harm human health. Herein, we used a variety of spectroscopic techniques, molecular docking, and gel electrophoresis to study the interaction of 4–octylphenol and ctDNA . It was found that the mechanism of ctDNA quenching the endogenous fluorescence of 4–octylphenol was static quenching, and formed a complex. The negative enthalpy change (Δ H °), entropy change (Δ S °) and Gibbs free energy (Δ G °) have shown that 4–octylphenol and ctDNA spontaneously bind together under the action of hydrogen bonds and van der Waal's force . Viscosity, melting temperature and iodide quenching experiments showed that 4–octylphenol acted on the groove of ctDNA. Insignificant change in circular dichromism spectra further confirmed this binding mode. The binding sites and groups for 4–octylphenol and ctDNA interaction were identified by molecular docking. Gel electrophoresis found that 4–octylphenol at high concentrations caused DNA cleavage. Above findings may lay a theoretical foundation for understanding the toxicity mechanism of 4–octylphenol.
研究领域:
生物化学
·
毒理学
·
环境科学
✓ 已验证
DOI
PubMed
高影响因子
JOURNAL OF MOLECULAR LIQUIDS
·
2018
·
IF 4.513
Xie-Mei Dong,Yan-Yue Lou,Kai-Li Zhou,Jie-Hua Shi
Telmisartan (TMST) can block selectively and irreversibly an angiotensin II receptor type 1 (AT1), but has no effect on other receptor systems and also induce human prostate cancer cell apoptosis. In this work, domain specific association of TMST with calf thymus DNA was explored through multi-spectral methodologies and theoretical calculation. The results of absorption spectroscopy revealed that TMST interacting with ct-DNA formed the TMST–ct-DNA complex through non-covalent interaction and the association constant ( K a ) was of 2.71 × 10 3 M −1 at 298 K. Based on the thermodynamic analysis , it can be inferred that the interacting TMST with ct-DNA was an enthalpy-driven, spontaneous, and exothermic process due to the Δ G 0 < 0, Δ H 0 < 0, and |Δ H 0 |> T |Δ S 0 | under the studied temperature ranges. The domain interacting forces for interacting TMST with ct-DNA were van der Waals forces and hydrogen bonding interaction due to the Δ H 0 < 0 and Δ S 0 < 0. Meanwhile, the electrostatic and hydrophobic interactions also played a supporting function. Additionally, from experiments and theoretical calculation (molecular docking), it was also confirmed that TMST interacted to a minor groove of the C-G rich region of ct-DNA and resulted in the slight alteration in the secondary structure of ct-DNA whereas the obvious alteration in the geometry of TMST after binding to DNA, indicating that the flexibility of TMST contributed to stabilizing the TMST–ct-DNA complex.
研究领域:
药理学
·
生物化学
✓ 已验证
产品关联
DOI
高影响因子
JOURNAL OF PHOTOCHEMISTRY AND PHOTOBIOLOGY B-BIOLOGY
·
2015
·
IF 2.96
Yan-Qing Wang,Hong-Mei Zhang
Bisphenol A and its analogues have carcinogenic potentials and toxicities. However, there are lacks of studies elucidating gene toxic interactions of bisphenols with DNA. In this work, the binding modes of five bisphenol compounds with calf thymus DNA were characterized. The multi-spectroscopic experimental results indicated that the fluorescence quenching of bisphenols by calf thymus DNA point to groove binding. The ultraviolet visible and circular dichroism spectral data displayed that bisphenols partly induced conformational changes of calf thymus DNA. In addition, the binding constants of bisphenol A, diphenolic acid, bisphenol AF, bisphenol AP, bisphenol fluorine with calf thymus DNA obtained from fluorescence emission spectra were 1.09 × 10 4 , 3.65 × 10 4 , 4.46 × 10 4 , 1.69 × 10 4 , 4.49 × 10 4 L mol −1 at 298.15 K, which indicated that the multi-noncovalent binding forces were involved in the binding processes. In silico investigations indicated that DNA has the preferable binding sites binding with bisphenols by minor groove binding and electrons transfer from DNA bases to bisphenols occurred. In addition, the structural differences of these five bisphenols partly affected the binding ability of them with DNA.
研究领域:
生物化学
·
毒理学
·
环境科学
✓ 已验证
产品关联
DOI
PubMed
高影响因子
Frontiers in Toxicology
·
2021
·
IF 0
Hu Xing,Luo Xiaoqiao,Zhou Zhisheng,Wang Rui,Hu Yaqin,Zhang Guimei,Zhang Guowen
1–Naphthaleneacetic acid (NAA), having high-quality biological activity and great yield-increasing potential in agricultural production, is a broad-spectrum plant growth regulator. Although NAA is of low toxicity, it can affect the balance of the human metabolism and damage the body if it is used in high quantity for a long time. In this study, the interaction of NAA with calf thymus DNA (ctDNA) was investigated under simulated human physiological acidity (pH 7.4) using fluorescence, ultraviolet-visible absorption, and circular dichroism spectroscopy combined with viscosity measurements and molecular simulation techniques. The quenching of the endogenous fluorescence of NAA by ctDNA, observed in the fluorescence spectrum experiment, was a mixed quenching process that mainly resulted from the formation of the NAA–ctDNA complex. NAA mainly interacted with ctDNA through hydrophobic interaction, and the binding constant and quenching constant at room temperature (298 K) were 0.60 × 105 L mol−1 and 1.58 × 104 L mol−1, respectively. Moreover, the intercalation mode between NAA and ctDNA was verified in the analysis of melting point, KI measurements, and the viscosity of ctDNA. The results were confirmed by molecular simulation, and it showed that NAA was enriched near the C–G base of ctDNA. As shown in circular dichroism spectra, the positive peak intensity of ctDNA intensified along with a certain degree of redshift, while the negative peak intensity decreased after binding with NAA, suggesting that the binding of NAA induced the transformation of the secondary structure of ctDNA from B-form to A-form. These researches will help to understand the hazards of NAA to the human body more comprehensively and concretely, to better guide the use of NAA in industry and agriculture.
研究领域:
生物化学
·
分子生物学
·
药物化学
✓ 已验证
DOI
JOURNAL OF PHOTOCHEMISTRY AND PHOTOBIOLOGY B-BIOLOGY
·
2015
·
IF 2.96
Jie-Hua Shi,Ting-Ting Liu,Min Jiang,Jun Chen,Qi Wang
The binding interaction of gefitinib with calf thymus DNA (ct-DNA) under the simulated physiological pH condition was studied employing UV absorption, fluorescence, circular dichroism (CD), viscosity measurement and molecular docking methods. The experimental results revealed that gefitinib preferred to bind to the minor groove of ct-DNA with the binding constant ( K b ) of 1.29 × 10 4 L mol −1 at 298 K. Base on the signs and magnitudes of the enthalpy change (Δ H 0 = −60.4 kJ mol −1 ) and entropy change (Δ S 0 = −124.7 J mol −1 K −1 ) in the binding process and the results of molecular docking, it can be concluded that the main interaction forces between gefitinib and ct-DNA in the binding process were van der Waals force and hydrogen bonding interaction. The results of CD experiments revealed that gefitinib did not disturb native B-conformation of ct-DNA. And, the significant change in the conformation of gefitinib in gefitinib–ct-DNA complex was observed from the molecular docking results and the change was close relation with the structure of B-DNA fragments, indicating that the flexibility of gefitinib molecule also plays an important role in the formation of the stable gefitinib–ct-DNA complex.
研究领域:
生物化学
·
药物化学
·
分子生物学
✓ 已验证
产品关联
DOI
PubMed
高影响因子
JOURNAL OF BIOMOLECULAR STRUCTURE & DYNAMICS
·
2022
·
IF 5.235
Song-Bo Kou,Kai-Li Zhou,Zhen-Yi Lin,Yan-Yue Lou,Bao-Li Wang,Jie-Hua Shi,Ying-Xin Liu
The binding behavior of ritonavir (RTV), a HIV/AIDS protease inhibitor, with ct-DNA was characterized through multiple testing technologies and theoretical calculation. The findings revealed that the RTV–DNA complex was formed through the noncovalent interaction mainly including conventional hydrogen bonds and carbon hydrogen bonds as well as hydrophobic interactions (pi–alkyl interactions). The stoichiometry and binding constant of the RTV–DNA complex were 1:1 and 1.87 × 103 M−1 at 298 K, respectively, indicating that RTV has moderate affinity with ct-DNA. The findings confirmed that RTV binds to the minor groove of DNA. The outcomes of CD experiments showed that the binding with RTV changed the conformation of DNA slightly. However, the conformation of RTV had obvious changes after binding to DNA, meaning that the flexibility of RTV molecule played an important role in stabilizing the RTV–DNA complex. Meanwhile, the results of DFT calculation revealed that the RTV and DNA interaction caused the changes in the frontier molecular orbitals, dipole moment and atomic charge distribution of RTV, altering the chemical properties of RTV when it bound to DNA. Communicated by Ramaswamy H. Sarma
研究领域:
生物化学
·
药理学
·
分子生物学
✓ 已验证
产品关联
DOI
PubMed
高影响因子
JOURNAL OF MOLECULAR LIQUIDS
·
2021
·
IF 6.165
Dan Zhang,Junhui Pan,Deming Gong,Guowen Zhang
Indole-3-butyric acid (IBA) is a broad-spectrum efficient plant growth regulator. It has been widely used in crop production, but may have a potential security risk due to its residual accumulation in agricultural products. Herein, the binding mode between IBA and calf thymus DNA (ctDNA) and influence of IBA on the structure of ctDNA were explored by using spectroscopic methods, viscosity measurement, melting temperature studies coupled with computational approaches. Fluorescence titration results indicated that ctDNA induced IBA fluorescence quenching in a static manner. The measured thermodynamic parameters demonstrated that the structure of IBA-ctDNA complex was primarily stabilized by hydrogen bonds and van der Waals forces. Fluorescence experiments, viscosity analyses and circular dichroism (CD) measurements confirmed that IBA interacted with ctDNA in terms of groove mode with no significant conformational change of ctDNA. Furthermore, molecular docking showed that IBA was preferentially bound to the minor groove of ctDNA rich in A-T bases. Molecular dynamics simulation further revealed IBA and DNA forming a stable complex and IBA could slightly increase the flexibility of ctDNA base pairs. In addition, IBA did not cause significant damage to the structure of DNA. These findings may supply conducive insights into the toxicity mechanisms of IBA at the molecular level.
研究领域:
生物化学
·
分子生物学
·
毒理学
✓ 已验证
DOI
高影响因子
Foods
·
2024
·Vol. 13
·期 12
·1878
·
IF 4.7
Yushi Wei,Dan Zhang,Junhui Pan,Deming Gong,Guowen Zhang
Indole-3-propionic acid (IPA) is a plant growth regulator with good specificity and long action. IPA may be harmful to human health because of its accumulation in vegetables and fruits. Therefore, in this study, the properties of the interaction between calf thymus DNA (ctDNA) and IPA were systematically explored using multispectroscopic and computational modeling approaches. Analysis of fluorescence spectra showed that IPA binding to ctDNA to spontaneously form a complex was mainly driven by hydrogen bonds and hydrophobic interaction. DNA melting analysis, viscosity analysis, DNA cleavage study, and circular dichroism measurement revealed the groove binding of IPA to ctDNA and showed that the binding did not significantly change ctDNA confirmation. Furthermore, molecular docking found that IPA attached in the A-T rich minor groove region of the DNA. Molecular dynamics simulation showed that DNA and IPA formed a stable complex and IPA caused slight fluctuations for the residues at the binding site. Gel electrophoresis experiments showed that IPA did not significantly disrupt the DNA structure. These findings may provide useful information on the potential toxicological effects and environmental risk assessments of IPA residue in food at the molecular level.
研究领域:
生物化学
·
分子生物学
·
计算生物学
✓ 已验证
DOI
PubMed
高影响因子
LUMINESCENCE
·
2020
·Vol. 36
·期 1
·35-44
·
IF 1.855
Hui Guo,Jiawen Xie,Tancong Liao,Xun Tuo
Donepezil (DNP) is one of approved drugs to treat Alzheimer's disease (AD). However, the potential effect of DNP on DNA is still unclear. Therefore, the interaction of DNP with calf thymus DNA (DNA) was studied in vitro using spectroscopic and molecular docking methods. Steady-state and transient fluorescence experiments showed that there was a clear binding interaction between DNP and DNA, resulting from DNP fluorescence being quenched using DNA. DNP and DNA have one binding site between them, and the binding constant (K b ) was 0.78 × 10 4 L·mol −1 at 298 K. In this binding process, hydrophobic force was the main interaction force, because enthalpy change (ΔH) and entropy change (ΔS) of DNP–DNA were 67.92 kJ·mol −1 and 302.96 J·mol −1 ·K −1 , respectively. DNP bound to DNA in a groove-binding mode, which was verified using a competition displacement study and other typical spectroscopic methods. Fourier transform infrared (FTIR) spectrum results showed that DNP interacted with guanine (G) and cytosine (C) bases of DNA. The molecular docking results further supported the results of spectroscopic experiments, and suggested that both Pi-Sigma force and Pi-Alkyl force were the major hydrophobic force functioning between DNP and DNA.
研究领域:
生物化学
·
药物研究
·
分子生物学
✓ 已验证
产品关联
DOI
PubMed
高影响因子
JOURNAL OF BIOCHEMICAL AND MOLECULAR TOXICOLOGY
·
2013
·Vol. 27
·期 5
·272-278
·
IF 1.596
Hongxu Yang,Wei Song,Mingyang Jing,Rutao Liu
By utilizing multispectrosopic techniques, the toxic interaction of 2-aminoanthraquinone (2-AAQ) with calf thymus deoxyribonucleic acid (ctDNA) was investigated in vitro under simulated physiological conditions. The experimental results proved that 2-AAQ has a toxic interaction with ctDNA. The binding capacity of DNA with 2-AAQ is diminishing as the pH value of system increasing in the optimization of experimental condition. Moreover we selected pH 7.4, which is nearly physiological condition to enhance the practical significance. According to the Stern–Volmer equation, the quenching was the static quenching process. And the quenching constant can be derived from the fluorescence quenching spectrogram. Ultraviolet absorption spectra and the change in the fluorescence intensity at different ionic strengths further indicated that there was electrostatic binding between 2-AAQ and ctDNA. The circular dichroism experiment showed that the DNA conformation varied from B to A conformation. The basic group enhanced after 2-AAQ embedding. The double helix is more compact, and the DNA conformation changes. © 2013 Wiley Periodicals, Inc. J BiochemMol Toxicol 27:272-278, 2013; View this article online at wileyonlinelibrary.com . DOI 10.1002/jbt.21487
研究领域:
生物化学
·
分子毒理学
·
药物相互作用
✓ 已验证
DOI
PubMed
高影响因子
危险品化学品经营许可证（带存储）