The experimental and theoretical QM/MM study of interaction of chloridazon herbicide with ds-DNA

Ahmadi, Farhad; Jamali, Nasibeh; Jahangard-Yekta, S.; Jafari, Batool; Nouri, Somayeh; Najafi, Farid; Rahimi‐Nasrabadi, Mehdi

doi:10.1016/j.saa.2011.04.012

Cited by 38 publications

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“…Ethanol, acetone, ). 28 The ratio of the DNA absorbance intensities at 260 and 280 nm was 1.88, indicating that the DNA was free from protein. The river water samples were collected from the Tietê River and the Jacaré-Guaçu River, in the municipalities of Barra Bonita and Araraquara, respectively.…”

Section: Reagents and Instrumentationmentioning

confidence: 99%

“…26 UV-Vis spectrophotometry is a useful tool for use in preliminary investigations of the genotoxicity of chemical substances, and has been employed to evaluate the interaction of toxic compounds with DNA. [27][28][29] The aim of this work was to investigate the solubility of disperse red 1 textile dye in aqueous solutions, develop a methodology for its determination in tap and river water, and evaluate the interaction of the dye with calf thymus ds-DNA, using UV-Vis spectrophotometry.…”

Section: 2mentioning

confidence: 99%

“…The procedure was carried out according to Ahmadi et al 28 and Marty et al 44 The double reciprocal plot of 1/(A-A 0 ) versus 1/[DR1+dispersant], in which A 0 is the initial absorbance of free DNA at 260 nm and A is the recorded absorbance of DNA at different dye concentrations, was linear (r = 0.99) and the binding constant (K) calculated from the ratio of the intercept to the slope was found to be 3.11 × 10 5 L mol -1 . This value is higher than those found for several carcinogenic compounds 28 with an affinity binding in the range of 3.5 × 10 3 to 1.6 × 10 4 L mol -1 , indicating that DR1 in the presence of the dispersant has a significant effect on DNA.These spectrophotometric effects reflect changes in the conformation and structure of DNA following analyte binding. Hypochromism results from the contraction of DNA in the helical axis, as well as from conformational changes in the DNA.…”

mentioning

confidence: 99%

“…[27][28][29] The aim of this work was to investigate the solubility of disperse red 1 textile dye in aqueous solutions, develop a methodology for its determination in tap and river water, and evaluate the interaction of the dye with calf thymus ds-DNA, using UV-Vis spectrophotometry.…”

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Spectrophotometric evaluation of the behavior of disperse red 1 dye in aqueous media and its interaction with calf thymus ds-DNA

Uliana¹,

Garbellini²,

Yamanaka³

2012

J. Braz. Chem. Soc.

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A espectrofotometria UV-Vis foi utilizada para medir a solubilidade do corante disperso red 1 (DR1) em soluções aquosas, com diferentes solventes e dispersantes. O corante foi quantificado em amostras de águas, e sua interação com o ds-DNA de timo de vitelo foi investigada. Os resultados mostraram que o dispersante comercial Fongranal ® FB foi adequado para a preparação das soluções aquosas do DR1. Para a determinação de DR1 em água pura, o limite de detecção foi de 2,47 × 10 -6 mol L . Porcentagens de recuperação de 91,2 e 103% foram obtidas para as concentrações de DR1 em 3,00 × 10 -6 e 40,0 × 10 -6 mol L -1 , respectivamente. As recuperações alcançadas de DR1 em água de torneira e de rio ficaram na faixa de 85,9-113%. A interação de DR1 com o DNA de timo de vitela foi acompanhada por efeitos de hipocromismo e hipercromismo, que foram relacionados à mudanças conformacionais e lesão na dupla hélice do DNA.UV-Vis spectrophotometry was used to measure the solubility of disperse red 1 (DR1) dye in aqueous solutions, using different solvents and dispersants. The dye was quantified in water samples, and its interaction with calf thymus ds-DNA was investigated. The results showed that the commercial dispersant Fongranal ® FB was suitable for the preparation of aqueous DR1 solutions. For the determination of DR1 in purified water, the limit of detection was 2.47 × 10 -6 mol L -1, and the limit of quantification was 8.22 × 10 -6 mol L -1. Percentage recoveries of 91.2 and 103% were obtained for DR1 concentrations of 3.00 × 10 -6 and 40.0 × 10 -6 mol L -1, respectively. The recoveries achieved for DR1 present in tap and river water were in the range 85.9-113%. The interaction of DR1 with calf thymus DNA was accompanied by hypochromic and hyperchromic effects, which were related to conformational changes and damage to the DNA double helix.Keywords: disperse red 1, textile dye, solubility, ds-DNA IntroductionSynthetic dyes can be defined as intensely colored substances that, when applied to a material, give it color that exhibits some degree of permanence.1 These dyes are extensively used in the textile, food processing, and leather tanning industries, as well as in paper production and agricultural products.1 The textile dyes show considerable structural diversity, and can be classified according to either the chromophore (including azo, anthraquinone, indigoid and triphenylmethyl groups) or the method of attachment to the textile fiber (direct, basic, acidic, reactive, disperse, etc.). 1,2 An estimated 700,000 to 850,000 tons of dyes are produced worldwide each year, and 26,500 tons per year are consumed in Brazil. 3,4 An amount equivalent to approximately 20-50% of the quantity of textile dyes used is released into natural waters due to losses that occur during the process of fixing the dye to the fibers.5 Dyes are potentially harmful to the environment and human health. [6][7][8][9] According to Resolution N. 357 of the National Environment Council of Brazil (CONAMA), 10 dyes derived from anthropogenic sources should...

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Section: Reagents and Instrumentationmentioning

confidence: 99%

Section: 2mentioning

confidence: 99%

mentioning

confidence: 99%

mentioning

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Spectrophotometric evaluation of the behavior of disperse red 1 dye in aqueous media and its interaction with calf thymus ds-DNA

Uliana¹,

Garbellini²,

Yamanaka³

2012

J. Braz. Chem. Soc.

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“…The rate of substitution (derivative formation) depends on some parameters such as nucleophilicity, leaving group and dielectric constant of the solvent. Due to fairly high dielectric constant of acetonitrile it can be separate ionic species and enhance nucleophilicity [21,22]. Thus, we chose acetonitrile as the derivation solvent.…”

Section: Role Of Acetonitrile On Derivationmentioning

confidence: 99%

Separation and quantitative determination of cinacalcet metabolites in urine sample using RP-HPLC after derivation with a fluorescent labeling reagent

Farnoudian-Habibi

Jaymand

2016

Journal of Chromatography B

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Classical Reactive Molecular Dynamics Implementations: State of the Art

2012

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Reactive molecular dynamics (RMD) implementations equipped with force field approaches to simulate both the time evolution as well as chemical reactions of a broad class of materials are reviewed herein. We subdivide the RMD approaches developed during the last decade as well as older ones already reviewed in 1995 by Srivastava and Garrison and in 2000 by Brenner into two classes. The methods in the first RMD class rely on the use of a reaction cutoff distance and employ a sudden transition from the educts to the products. Due to their simplicity these methods are well suited to generate equilibrated atomistic or material‐specific coarse‐grained polymer structures. In connection with generic models they offer useful qualitative insight into polymerization reactions. The methods in the second RMD class are based on empirical reactive force fields and implement a smooth and continuous transition from the educts to the products. In this RMD class, the reactive potentials are based on many‐body or bond‐order force fields as well as on empirical standard force fields, such as CHARMM, AMBER or MM3 that are modified to become reactive. The aim with the more sophisticated implementations of the second RMD class is the investigation of the reaction kinetics and mechanisms as well as the evaluation of transition state geometries. Pure or hybrid ab initio, density functional, semi‐empirical, molecular mechanics, and Monte Carlo methods for which no time evolution of the chemical systems is achieved are excluded from the present review. So are molecular dynamics techniques coupled with quantum chemical methods for the treatment of the reactive regions, such as Car–Parinello molecular dynamics.

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The experimental and theoretical QM/MM study of interaction of chloridazon herbicide with ds-DNA

Cited by 38 publications

References 39 publications

Spectrophotometric evaluation of the behavior of disperse red 1 dye in aqueous media and its interaction with calf thymus ds-DNA

Spectrophotometric evaluation of the behavior of disperse red 1 dye in aqueous media and its interaction with calf thymus ds-DNA

Separation and quantitative determination of cinacalcet metabolites in urine sample using RP-HPLC after derivation with a fluorescent labeling reagent

Classical Reactive Molecular Dynamics Implementations: State of the Art

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