Binding of DNA-binding alkaloids berberine and palmatine to tRNA and comparison to ethidium: Spectroscopic and molecular modeling studies (original) (raw)
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Journal of photochemistry and photobiology. B, Biology, 2015
Vincristine and vinblastine are potent anti-proliferative compound whose mechanism of action inside a cell is not well elucidated and the basis of their differential cellular effect is also unknown. This work focuses towards understanding the interaction of vincristine and vinblastine with tRNA using spectroscopic approach. Fourier transform infrared (FTIR) spectroscopy, Fourier transform infrared difference spectroscopy and UV-visible spectroscopy were used to study the binding parameters of tRNA-alkaloids interaction. Both the vinca alkaloids interact with tRNA through external binding with some degree of intercalation into the nitrogenous bases. The alkaloids adduct formation did not alter the A-conformation of the biopolymer and vincristine-tRNA complexes were found to be more stable than that of vinblastine-tRNA complexes. The binding constants (K) estimated for VCR-tRNA and VBS-tRNA complexation are 3 Â 10 2 M À1 and 2.5 Â 10 2 M À1 respectively, which suggests low affinity of alkaloids to tRNA. The study recognizes tRNA binding properties of vital vinca alkaloids and contributes to a better understanding of their mechanism of action and could also help in identifying the reason behind their diverse action in a cell.
Biochimica et Biophysica Acta (BBA) - General Subjects, 2007
The base dependent binding of the cytotoxic alkaloid palmatine to four synthetic polynucleotides, poly(dA).poly(dT), poly(dA-dT).poly (dA-dT), poly(dG).poly(dC) and poly(dG-dC).poly(dG-dC) was examined by competition dialysis, spectrophotometric, spectrofluorimetric, thermal melting, circular dichroic, viscometric and isothermal titration calorimetric (ITC) studies. Binding of the alkaloid to various polynucleotides was dependent upon sequences of base pairs. Binding data obtained from absorbance measurements according to neighbour exclusion model indicated that the intrinsic binding constants decreased in the order poly(dA).poly(dT) > poly(dA-dT).poly(dA-dT) > poly(dG-dC).poly(dG-dC) > poly(dG).poly(dC). This affinity was also revealed by the competition dialysis, increase of steady state fluorescence intensity, increase in fluorescence quantum yield, stabilization against thermal denaturation and perturbations in circular dichroic spectrum. Among the polynucleotides, poly(dA).poly(dT) showed positive cooperativity at binding values lower than r = 0.05. Viscosity studies revealed that in the strong binding region, the increase of contour length of DNA depended strongly on the sequence of base pairs being higher for AT polymers and induction of unwindingrewinding process of covalently closed superhelical DNA. Isothermal titration calorimetric data showed a single entropy driven binding event in the AT homo polymer while that with the hetero polymer involved two binding modes, an entropy driven strong binding followed by an enthalpy driven weak binding. These results unequivocally established that the alkaloid palmatine binds strongly to AT homo and hetero polymers by mechanism of intercalation.
The DNA Influence on Spectral Properties of the Berberine, Chelidonine and Sanguinarine Alkaloids
The problem of elucidating of the interaction mechanisms of the DNA molecules with antitumour agents is very actual now. We report about the manifestation of interaction of alkaloids of drugs amitozine and ukrain - berberine, sanguinarine, chelidonine - with the DNA molecules in optical absorption and fluorescence (FL) spectra. The absorption and fluorescence spectra of DNA, alkaloids and DNA-alkaloids water solutions were studied. From the results of experiments it follows that these alkaloids bind with the DNA macromolecules. Assumptions about possible interaction mechanisms are presented.
Journal of Biomolecular Structure & Dynamics, 2003
A comparative study on the interaction of sanguinarine and berberine with DNA and RNA triplexes and their parent duplexes was performed, by using a combination of spectrophotometric, UV thermal melting, circular dichroic and thermodynamic techniques. Formation of the DNA and RNA triplexes was confirmed from UV-melting and circular dichroic measurements. The interaction process was characterized by increase of thermal melting temperature, perturbation in circular dichroic spectrum and the typical hypochromic and bathochromic effects in the absorption spectrum. Scatchard analysis indicated that both the alkaloids bound to the triplex and duplex structures in a non-cooperative manner and the binding was stronger to triplexes than to parent duplexes. Thermal melting studies further indicated that sanguinarine stabilized the Hoogsteen base paired third strand of both DNA and RNA triplexes more tightly compared to their Watson-Crick strands, while berberine stabilized the third strand only without affecting the Watson-Crick strand. However, sanguinarine stabilized the parent duplexes while no stabilization was observed with berberine under identical conditions. Circular dichroic studies were also consistent with the observation that perturbations of DNA and RNA triplexes were more compared to their parent duplexes in presence of the alkaloids. Thermodynamic data revealed that binding of sanguinarine and berberine to triplexes (T·AxT and U·AxU) and duplexes (A·T and A·U) showed negative enthalpy changes and positive entropy changes but that of sanguinarine to C·GxC+ triplex and G·C duplex exhibited negative enthalpy and negative entropy changes. Taken together, these results suggest that both sanguinarine and berberine can bind and stabilize the DNA and RNA triplexes more strongly than their respective parent duplexes.
Binding of alkaloid harmalol to DNA: Photophysical and calorimetric approach
Journal of Photochemistry and Photobiology B: Biology, 2014
Harmalol exhibits pH dependent structural equilibrium between protonated and deprotonated forms with a pK a of 7.8 as revealed from spectroscopic titration. The compound exists as protonated (structure I) and deprotonated (structure II) form in the pH range 1-7 and 9-12, respectively. The interaction of structure I and II to calf thymus DNA has been studied by different spectroscopic and calorimetric techniques in buffer of pH 6.8 and 9.2, respectively. The results show that structure I bind strongly to DNA showing a cooperative mode with a binding constant of 4.5 Â 10 5 M À1 and a stoichiometry of 4.8 nucleotide phosphates. The alkaloid stabilized the DNA by 8°C, the binding shows 40% quenching of fluorescence intensity, perturbation in circular dichroism spectra and enthalpy driven exothermic binding with a large hydrophobic contribution to the binding free energy. Furthermore, the alkaloid shows a prominent change of specific viscosity with sonicated linear DNA and unwinding-rewinding of covalently closed pUC 18 DNA, revealing intercalative binding. The deprotonated structure (structure II), on the other hand, in the presence of large amount of DNA concentration, converts back to a structure I-DNA complexation. This transition has been presumably induced by the polyanionic phosphate backbone of DNA at high concentration.
Flavonoid–DNA binding studies and thermodynamic parameters
Spectrochimica Acta Part A-molecular and Biomolecular Spectroscopy, 2011
Interactional studies of new flavonoid derivatives (Fl) with chicken blood ds.DNA were investigated spectrophotometrically in DMSO-H 2 O (9:1 v/v) at various temperatures. Spectral parameters suggest considerable binding between the flavonoid derivatives studied and ds.DNA. The binding constant values lie in the enhanced-binding range. Thermodynamic parameters obtained from UV studies also point to strong spontaneous binding of Fl with ds.DNA. Viscometric studies complimented the UV results where a small linear increase in relative viscosity of the DNA solution was observed with added optimal flavonoid concentration. An overall mixed mode of interaction (intercalative plus groove binding) is proposed between DNA and flavonoids. Conclusively, investigated flavonoid derivatives are found to be strong DNA binders and seem to be promising drug candidates like their natural analogues.