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Arsenault-Escobar S, Fuentes-Galvez JF, Orellana C, Bollo S, Sierra-Rosales P, Miranda-Rojas S. Unveiling the tartrazine binding mode with ds-DNA by UV-visible spectroscopy, electrochemical, and QM/MM methods. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2023; 292:122400. [PMID: 36739665 DOI: 10.1016/j.saa.2023.122400] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/30/2022] [Revised: 12/31/2022] [Accepted: 01/19/2023] [Indexed: 06/18/2023]
Abstract
Here, we studied the interaction between the food colorant tartrazine (TZ) and double stranded DNA (dsDNA), using spectroscopic, electrochemical, and computational methods such as QM/MM combined with TD-DFT. Despite the UV-vis spectroscopy is widely used to study the interaction between molecules, for the case of TZ there are discrepancies in the analyses presented in the literature available, presenting both hyperchromic and hypochromic effects and consequently different rationalizations for their results. Herein we propose the combination of UV-vis experiments with the design of high-level computational models capable of reproducing the experimental behavior to finally define the proper binding mode at the molecular scale together with the rationalization of the experimental optical response due to the complex formation. To complement the UV-vis experiments, we propose the use of electrochemical measurements, to support the results obtained through UV-vis spectroscopy, as it has been successfully used for the determination of interaction modes between small molecules and biomolecules in any condition. Our UV-vis spectroscopy experiments showed only a hypochromic effect of the absorption spectra of TZ after interaction with DNA, indicative of TZ being deeply buried in the DNA structure. The effect of ionic strength in the experimental procedures led to the dissociation of TZ, thus indicating that the interaction mode was groove binding. On the other hand, the electrochemical studies showed an irreversible reduction peak of TZ, which after the interaction with DNA exhibited a positive shift in potential that can be attributed to groove binding. The binding constant for TZ-DNA was calculated as 4.45x104M-1 (UV-vis) and 5.75x104M-1 (electrochemistry), in line with other groove binder azo dyes. Finally, through the QM/MM calculations we found that the minor-groove binding mode interacting in zones rich in adenine and thymine was the model best suited to reproduce the experimental UV-vis response.
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Affiliation(s)
- S Arsenault-Escobar
- Programa Institucional de Fomento a la Investigación, Desarrollo e Innovación, Universidad Tecnológica Metropolitana, Ignacio Valdivieso 2409, P.O Box 8940577, San Joaquín, Santiago, Chile
| | - J F Fuentes-Galvez
- Programa Institucional de Fomento a la Investigación, Desarrollo e Innovación, Universidad Tecnológica Metropolitana, Ignacio Valdivieso 2409, P.O Box 8940577, San Joaquín, Santiago, Chile
| | - C Orellana
- Departamento de Química, Facultad de Ciencias, Universidad de Chile, P.O. Box 653, Las Palmeras 3425, Ñuñoa, Santiago, Chile
| | - S Bollo
- Centro de Investigación de Procesos Redox (CiPRex), Universidad de Chile. Sergio Livingstone Polhammer 1007, Independencia, Santiago, Chile; Advanced Center for Chronic Diseases (ACCDiS), Universidad de Chile. Sergio Livingstone Polhammer 1007, Independencia, Santiago, Chile
| | - P Sierra-Rosales
- Programa Institucional de Fomento a la Investigación, Desarrollo e Innovación, Universidad Tecnológica Metropolitana, Ignacio Valdivieso 2409, P.O Box 8940577, San Joaquín, Santiago, Chile.
| | - S Miranda-Rojas
- Departamento de Ciencias Químicas, Facultad de Ciencias Exactas, Universidad Andres Bello, República 275, Santiago, Chile.
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Ponkarpagam S, Vennila KN, Elango KP. Intercalation of diafenthiuron insecticide with calf thymus DNA: spectroscopic and molecular dynamics analysis. J Biomol Struct Dyn 2022:1-9. [PMID: 35848349 DOI: 10.1080/07391102.2022.2098824] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/17/2022]
Abstract
A series of biophysical experiments like UV-Vis, fluorescence, circular dichroism (CD), competitive displacement assays, voltammetric studies, viscosity measurements and denaturation effect and metadynamics simulation studies were performed to establish the mode of binding of diafenthiuron (DF) insecticide with calf thymus DNA (CT-DNA). Analysis of absorption and fluorescence spectra in Tris-HCl buffer of pH 7.4 indicates the formation of a complex between DF and CT-DNA and the binding constant of which is in the order of 104 M-1. Competitive displacement assay with ethidium bromide (EB) and Hoechst 33258 suggests that the most probable mode of binding of DF with CT-DNA may be via intercalation mode. The results of other experiments such as CD spectral studies, viscosity measurements and the effect of denaturation agent urea support the intercalation of DF with CT-DNA. Thermodynamic parameters (ΔHo, ΔSo and ΔGo) reveal that hydrogen bonds (H-bonds) or van der Waals (vdW) force is the main binding force in the spontaneous interaction between DF and CT-DNA. Molecular dynamics (MD) simulation studies confirmed the intercalation of DF into the base pairs of CT-DNA.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- S Ponkarpagam
- Department of Chemistry, Gandhigram Rural Institute (Deemed to be University), Gandhigram, India
| | - K N Vennila
- Department of Chemistry, Gandhigram Rural Institute (Deemed to be University), Gandhigram, India
| | - Kuppanagounder P Elango
- Department of Chemistry, Gandhigram Rural Institute (Deemed to be University), Gandhigram, India
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Application of Electrochemical Sensors in the Determination of Synthetic Dyes in Foods or Beverages and Their Toxicological Effects on Human Health: a Review. FOOD ANAL METHOD 2022. [DOI: 10.1007/s12161-022-02282-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022]
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Li Y, Li Y, Jia L, Li Y, Wang Y, Zhang P, Liu X. A simple sensor based on 1-butylpyridinium hexafluorophosphate@glassy carbon microspheres composites for the quantitative analysis of azo dyes. JOURNAL OF THE IRANIAN CHEMICAL SOCIETY 2022. [DOI: 10.1007/s13738-021-02375-w] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
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Hashemi-Shahraki F, Shareghi B, Farhadian S. Characterizing the binding affinity and molecular interplay between quinoline yellow and pepsin. J Mol Liq 2021. [DOI: 10.1016/j.molliq.2021.117317] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
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Spectroscopic, viscometric and computational binding study of 1 and 2 substituted anthraquinone analogs to be potential anti-cancer agents. J Mol Struct 2021. [DOI: 10.1016/j.molstruc.2020.129293] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
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PDMAEMA grafted microspheres as an efficient adsorbent for the removal of Sunset yellow from pharmaceutical preparations, beverages and waste water. Eur Polym J 2020. [DOI: 10.1016/j.eurpolymj.2020.110089] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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Wang R, Li N, Hu X, Pan J, Zhang G, Zeng X, Gong D. Characterizing the binding of tert-butylhydroquinone and its oxidation product tert-butylquinone with calf thymus DNA in vitro. J Mol Liq 2020. [DOI: 10.1016/j.molliq.2019.112338] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
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Tikhomirova AA, Tcyrulnikov NA, Wilson RM. Synthesis, characterization, DNA binding and cleaving properties of photochemically activated phenanthrene dihydrodioxin. J Photochem Photobiol A Chem 2019. [DOI: 10.1016/j.jphotochem.2019.04.014] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
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Shahabadi N, Abbasi AR, Moshtkob A, Shiri F. DNA-binding studies of a new Cu(II) complex containing reverse transcriptase inhibitor and anti-HIV drug zalcitabine. J COORD CHEM 2019. [DOI: 10.1080/00958972.2019.1620216] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
Affiliation(s)
- Nahid Shahabadi
- Department of Inorganic Chemistry, Faculty of Chemistry, Razi University, Kermanshah, Islamic Republic of Iran
- Medical Biology Research Center (MBRC), Kermanshah University of Medical Sciences, Kermanshah, Islamic Republic of Iran
| | - Amir Reza Abbasi
- Department of Inorganic Chemistry, Faculty of Chemistry, Razi University, Kermanshah, Islamic Republic of Iran
- Institute of Nano Science and Nano Technology, Razi University, Kermanshah, Islamic Republic of Iran
| | - Ayda Moshtkob
- Department of Inorganic Chemistry, Faculty of Chemistry, Razi University, Kermanshah, Islamic Republic of Iran
- Medical Biology Research Center (MBRC), Kermanshah University of Medical Sciences, Kermanshah, Islamic Republic of Iran
| | - Farshad Shiri
- Department of Inorganic Chemistry, Faculty of Chemistry, Razi University, Kermanshah, Islamic Republic of Iran
- Medical Biology Research Center (MBRC), Kermanshah University of Medical Sciences, Kermanshah, Islamic Republic of Iran
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Determination of Sunset Yellow in Foodstuffs by Surface Modification of Nonconductive Polyester of Polyvinyl Alcohol Sheet Used as Overhead Projector Film. FOOD ANAL METHOD 2019. [DOI: 10.1007/s12161-019-01532-5] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
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In vitro binding interaction of atorvastatin with calf thymus DNA: multispectroscopic, gel electrophoresis and molecular docking studies. J Pharm Biomed Anal 2018; 161:101-109. [DOI: 10.1016/j.jpba.2018.08.033] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2018] [Revised: 08/13/2018] [Accepted: 08/16/2018] [Indexed: 12/12/2022]
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Karmakar A, Mallick T, Alam MN, Das S, Batuta S, Chandra SK, Mandal D, Begum NA. Understanding of the interactions of ctDNA with an antioxidant flavone analog: Exploring the utility of the small molecule as fluorescent probe for biomacromolecule. J Mol Struct 2018. [DOI: 10.1016/j.molstruc.2018.03.113] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
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Moradi SZ, Nowroozi A, Sadrjavadi K, Moradi S, Mansouri K, Hosseinzadeh L, Shahlaei M. Direct evidences for the groove binding of the Clomifene to double stranded DNA. Int J Biol Macromol 2018; 114:40-53. [PMID: 29555513 DOI: 10.1016/j.ijbiomac.2018.03.040] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2017] [Revised: 02/10/2018] [Accepted: 03/09/2018] [Indexed: 12/25/2022]
Abstract
It has been reported that the antiestrogen Tamoxifen induces liver tumors in rats and genotoxic effects in vitro through DNA interaction. So, it can be proposed that its structural analogue, Clomifene, also can bind to DNA. To test this hypothesis, the DNA binding properties of Clomifene have been studied by absorption spectroscopy, fluorescence spectroscopy, cellular uptake, cell viability, cell proliferation and molecular modeling techniques. Evidences are provided that Clomifene could interact with DNA via minor groove interaction mode. The negative ΔG value implied that the interaction occurred between DNA and Clomifene spontaneously. Also, the positive ΔH and positive ΔS values indicated that the binding of Clomifene with DNA is mainly entropy driven and the enthalpy is unfavorable parameter. This also suggests that the hydrophobic interaction plays a major role in the binding with overall binding constant of K=5.645×107M-1 at 298K. From the results of docking, it can be concluded that Hydrogen bonds is also one of the most important interactions. The increase in entropy of system after binding might be due to the destruction of the DNA structure.
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Affiliation(s)
| | - Amin Nowroozi
- Pharmaceutical Sciences Research Center, Kermanshah University of Medical Sciences, Kermanshah, Iran
| | - Komail Sadrjavadi
- Pharmaceutical Sciences Research Center, Kermanshah University of Medical Sciences, Kermanshah, Iran
| | - Sajad Moradi
- Medical Biology Research Center, Kermanshah University of Medical Sciences, Kermanshah, Iran
| | - Kamran Mansouri
- Medical Biology Research Center, Kermanshah University of Medical Sciences, Kermanshah, Iran
| | - Leila Hosseinzadeh
- Pharmaceutical Sciences Research Center, Kermanshah University of Medical Sciences, Kermanshah, Iran
| | - Mohsen Shahlaei
- Nano Drug Delivery Research Center, Kermanshah University of Medical Sciences, Kermanshah, Iran.
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