Spectroscopic studies on the interaction between carbaryl and calf thymus DNA with the use of ethidium bromide as a fluorescence probe

Groove binding mediated structural modulation and DNA cleavage by quinoline appended chalcone derivative

The present study embodies the detail DNA binding interaction of a potential bioactive quinoline appended chalcone derivative (E)-3-(anthracen-10-yl)-1-(6,8-dibromo-2-methylquinolin-3-yl)prop-2-en-1-one (ADMQ) with calf thymus DNA (ctDNA) and its consequences by UV-Vis absorption, steady state fluorescence spectroscopy, fluorescence anisotropy, circular dichromism, helix melting, agarose gel electrophoresis, molecular docking, Induced Fit Docking (IFD) and molecular dynamics (MD) simulation. The UV-Vis absorption and fluorescence study reveal that the molecule undergoes considerable interaction with the nucleic acid. The control KI quenching experiment shows the lesser accessibility of ADMQ molecule to the ionic quencher (I(-)) in presence of ctDNA as compared to the bulk aqueous phase. Insignificant change in helix melting temperature as well as in circular dichromism (CD) spectra points toward non-covalent groove binding interaction. The moderate rotational confinement of this chalcone derivative (anisotropy=0.106) trapped in the nucleic acid environment, the comparative displacement assay with well-known minor groove binder Hoechst 33258 and intercalator Ethidium Bromide establishes the minor groove binding interactions of the probe molecule. Molecular docking, IFD and MD simulation reveal that the DNA undergoes prominent morphological changes in terms of helix unwinding and bending to accommodate ADMQ in a crescent shape at an angle of 110° in a sequence specific manner. During interaction, ADMQ rigidifies and bends the sugar phosphate backbone of the nucleic acid and thereby shortens its overall length by 3.02Å. Agarose gel electrophoresis experiment with plasmid pBR 322 reveals that the groove binded ADMQ result in a concentration dependent cleavage of plasmid DNA into its supercoiled and nicked circular form. The consolidated spectroscopic research described herein provides quantitative insight into the interaction of a heterocyclic chalcone derivative with relevant target nucleic acid, which may be useful for the future research on chalcone based therapeutic agents.

Studies on interaction of norbixin with DNA: multispectroscopic and in silico analysis

The interaction of food colorant norbixin with calf thymus DNA (CTDNA) was investigated through UV-Visible spectroscopy, Fourier Transform Infrared (FTIR), Circular Dichroism (CD), Nuclear Magnetic Resonance (NMR), DNA melting studies, electrophoretic analysis, histological staining technique and molecular docking studies. The results indicated that norbixin interacted with CTDNA by partial intercalation mode. The binding constant (K) of norbixin with CTDNA was calculated to be 5.08×10(5) Mol(-1) L. FTIR and CD studies were coupled with (1)H NMR spectra revealed that norbixin intercalates partially and binds to the groove's, phosphate group, deoxyribose sugar of DNA and also induces conformational transition of B-form to A-form DNA. Agarose gel electrophoretic and histological staining technique results further prove that, norbixin specifically binds to the DNA in the cell. Moreover, molecular docking studies on the specific binding of norbixin with CTDNA have exhibited lowest conformation energy score of -3.2. Therefore, this food colorant has the ability to interact with DNA and it could emerge as a promising class of natural DNA targeted therapeutic.

Binding characteristics and protective capacity of cyanidin-3-glucoside and its aglycon to calf thymus DNA

The binding characteristics and protective capacity of cyanidin (Cy) and cyanidin-3-glucoside (C3G) to calf thymus DNA were explored for the first time. The Cy and C3G gave a bathochromic shift to the ultraviolet-visible spectra of the DNA, indicating the formation of the DNA-Cy and DNA-C3G complexes. The complexes were formed by an intercalative binding mode based on the results of the fluorescence spectra and competitive binding analysis. Meanwhile, the Cy and C3G protected the DNA from the damage induced by the hydroxyl radical. The binding capacity and protective capacity of the C3G were stronger than that of the Cy. Furthermore, the formation of the DNA-anthocyanin complexes was spontaneous when the hydrogen bond and hydrophobic force played a key role. Hence, the Cy and C3G could protect the DNA automatically from the damage induced by the hydroxyl radical.

Experimental and molecular modeling studies of the interaction of the polypyridyl Fe(II) and Fe(III) complexes with DNA and BSA

Two mononuclear iron complexes, [Fe(tppz)₂](PF₆)₂·H₂O (1) and Fe(tppz)Cl₃·2CHCl₃ (2) where tppz is (2,3,5,6-tetra(2-pyridyl)pyrazine), have been synthesized and characterized by elemental analysis, spectroscopic methods (UV-Vis and IR) and single crystal X-ray structure analysis. The interaction of (1) as the nitrate salt ([Fe(tppz)₂](NO₃)₂) with calf-thymus DNA (CT-DNA) has been monitored by UV-Vis spectroscopy, competitive fluorescence titration, circular dichroism (CD), voltammetric techniques, viscosity measurement, and gel electrophoresis. Gel electrophoresis of DNA with [Fe(tppz)₂](NO₃)₂ demonstrated that the complex also has the ability to cleave supercoiled plasmid DNA. The results have indicated that the complex binds to CT-DNA by three binding modes, viz., electrostatic, groove and partial insertion of the pyridyl rings between the base stacks of double-stranded DNA. Molecular docking of [Fe(tppz)₂](NO₃)₂ with the DNA sequence d(ACCGACGTCGGT)₂ suggests the complex fits into the major groove. The water-insoluble complex (2) can catalyze the cleavage of BSA at 40 °C. There are no reports of the catalytic effect of polypyridyl metal complexes on the BSA cleavage. Molecular docking of (2) with BSA suggests that, when the chloro ligands in the axial positions are replaced by water molecules, the BSA can interact with the Fe(III) complex more easily.

Theoretical study on the reaction mechanism of carbaryl with OH radicals

A theoretical investigation on the multiple-channel degradation mechanism of carbaryl with ·OH in the atmosphere was completed by the variational transition state theory. Eleven reaction channels have been identified using the density functional theory. The equilibrium geometries and the corresponding harmonic vibrational frequencies of the stationary points were obtained at the B3LYP/6-31++G(d,p) level. The minimum energy paths were calculated at the same level, and energetic information was further refined at the B3LYP/6-31++G(3df,2p) level. The rate constants of the 11 reaction channels were calculated by improved canonical variational transition state theory with small-curvature tunneling correction over the temperature range 200-800 K. The total rate constants are in good agreement with available experimental data and the three-parameter expression k(T) = 1.85 × 10(-21)  T (3.44)exp(1180.18/T) cm(3) molecule(-1) s(-1) was given.

The Unusual Fluorescence Quenching of Coumarin 314 by β-Cyclodextrin and the Effect of β-Cyclodextrin on its Binding with Calf Thymus DNA

This paper discusses the binding of a laser dye, Coumarin 314 with β-cyclodextrin, studied mainly by UV-visible spectroscopy, 2D rotating-frame nuclear Overhauser effect spectroscopy (ROESY), steady-state spectroscopy and time-resolved fluorescence spectroscopy. The role of β-cyclodextrin on the binding of Coumarin 314 with calf thymus DNA was investigated. Coumarin 314 shows a hyperchromic shift of absorption and a quenching of fluorescence due to binding with β-cyclodextrin. The fluorescence quenching is non-linear and the reason for the non-linearity is discussed. The unusual fluorescence quenching on Coumarin 314–β-cyclodextrin binding is rationalised from the effect of acidity on absorption, fluorescence, and molecular modelling studies. Additional proof for the mode of binding is given by 2D ROESY. The capped and exposed portions of the Coumarin 314 molecule in the Coumarin 314–β-cyclodextrin complex when binding with calf thymus DNA were visualised based on spectral and molecular modelling studies.

Spectroscopic and Modelling Analysis on the Interaction of 3'-Azidodaunorubicin Semicarbazone with ctDNA

The synthesis and characterisation of a new anthracycline, 3′-azidodaunorubicin semicarbazone (ADNRS) is reported. The interaction between ADNRS and calf thymus DNA (ctDNA) was investigated by absorption and fluorescence spectroscopy in combination with melting temperature (Tm) curves and molecular modelling in physiological buffer (pH 7.4). Evidence indicates that ADNRS binds in the groove of ctDNA and the fluorescence quenching mechanism is a static quenching type. Calculated thermodynamic parameters show that hydrophobic interactions may play a predominant role in the binding. Furthermore, molecular modelling results corroborate the spectroscopic investigations.

Spectroscopic, viscositic and molecular modeling studies on the interaction of 3'-azido-daunorubicin thiosemicarbazone with DNA

A new daunorubicin has been synthesized and structurally characterized. The interaction of native calf thymus DNA (ctDNA) with 3′-azido-daunorubicin thiosemicarbazone (ADNRT) was investigated under simulated physiological conditions by multi-spectroscopic techniques, viscometric measurements and molecular modeling study. It concluded that ADNRT could intercalate into the base pairs of ctDNA, and the fluorescence quenching by ctDNA was static quenching type. Thermodynamic parameters calculated suggested that the binding of ADNRT to ctDNA was mainly driven by hydrophobic interactions. The relative viscosity of ctDNA increased with the addition of ADNRT, which confirmed the intercalation mode. Furthermore, molecular modeling studies corroborate the above experimental results.

Study of DNA interactions with bifenthrin by spectroscopic techniques and molecular modeling

The interaction between bifenthrin (BF) and calf thymus DNA (ctDNA) in physiological buffer (pH 7.4) was investigated by UV-vis absorption, fluorescence, circular dichroism (CD), and Fourier transform infrared (FT-IR) spectroscopy, coupled with viscosity measurements and molecular docking techniques. It was found that BF molecular could intercalate into the base pairs of ctDNA as evidenced by significant increases in absorption intensity, fluorescence polarization and relative viscosity of ctDNA, decrease in iodide quenching effect, and induced CD spectral changes. The association constant of BF with ctDNA was evaluated to be in the order of 10(4) L mol(-1). Thermodynamic analysis of the binding data obtained at different temperatures suggested that the binding process was primarily driven by hydrogen bonds and van der Waals forces, as the values of the enthalpy change (ΔH) and the entropy change (ΔS) were calculated to be -31.13±1.89 kJ mol(-1) and -22.79±1.21 J mol(-1) K(-1), respectively. The results of FT-IR spectra and molecular docking showed that a specific binding mainly existed between BF and adenine and guanine bases.

Binding characteristics of salbutamol with DNA by spectral methods

Salbutamol interacting with deoxyribonucleic acid (DNA) was examined by fluorescence, UV absorption, viscosity measurements, and DNA melting techniques. The binding constants and binding sites were obtained at different temperatures by fluorescence quenching. The Stern-Volmer plots showed that the quenching of fluorescence of salbutamol by DNA was a static quenching. To probe the binding mode, various analytical methods were performed and the results were as follows: hyperchromic effect was shown in the absorption spectra of salbutamol upon addition of DNA; there was no appreciable increase in melting temperature of DNA when salbutamol was presented in DNA solution; the fluorescence intensity of salbutamol-DNA decrease with the increasing ionic strength; the relative viscosity of DNA did not change in the presence of salbutamol; the binding constant of salbutamol with double strand DNA (dsDNA) was much higher than that of it with single strand DNA (ssDNA). All these results indicated that the binding mode of salbutamol to DNA should be groove binding. The thermodynamic parameters suggested that hydrogen bond or van der Waals force might play an important role in salbutamol binding to DNA. According to the Förster energy transference theory, the binding distance between the acceptor and donor was 3.70 nm.

Studies on the toxic interaction mechanism between 2-naphthylamine and herring sperm DNA

The toxic interaction between 2-naphthylamine (2-NA) and herring sperm deoxyribonucleic acid (hs-DNA) has been thoroughly investigated by UV absorption, fluorescence, and circular dichroism (CD) spectroscopic methods. UV absorption result indicates that 2-NA may intercalate into the stack base pairs of DNA during the toxic interaction of 2-NA with DNA. A fluorescence quenching study shows that DNA quenches the intrinsic fluorescence of 2-NA via a static pathway. The studies on effects of ionic strength and anionic quenching rule out electrostatic and groove bindings as the dominant binding modes. Further studies on denatured DNA fluorescence quenching and thermal melting studies confirm that the dominant binding mode of 2-NA-DNA is intercalative binding. A CD spectral study shows that the binding interaction of 2-NA with DNA leads to the disorganization of the neat double-helical structure of hs-DNA.