Drug-DNA Interactions: Structures and Spectra
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Doty, P. USA , 44 , Duportail, G. Feigon, J.
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Gabbay, E. Hudecz, F. Ishida, T. Fuji, K. Johnson, B. Lerman, L.
USA , 68 , Lybrandt, T. McGhee, J. H, J. Miller, K. Palumbo, M. Quigley, G. H, and Rich, A.
USA , 77 , Rodighiero, G. Smith New York: Plenum Publ. Full text PDF Related articles.
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Abstract Complexation between a ligand molecule and a nucleic acid leads to optical changes that can be used to monitor the binding process. Citations Recent citations: M. Caccia et al. Salem et al. Shoara et al. Related articles Based on techniques. References Peacocke A. J Biochem 16 , — Wilson W.
Gale E. Plumbridge T.
Drug Dna Interactions Structures Spectra by Nakamoto Kazuo Tsuboi Masamichi Strahan
Pharmacol 27 , , All the experiments were carried out at room temperature in sodium cacodylate trihydrate 1 mM pH 7. The mole-ratio method was employed to evaluate the isophorone-DNA binding stoichiometries, keeping constant the concentration of the isophorones and varying that of DNA. Therefore, the number of base pairs of DNA bound per Isoa and b can be estimated to be around 1. This value is in good agreement with that found for the intercalator Naphthoxazole for which a stoichiometry was assigned [ 30 ].
It was not easy to determine the stoichiometry for Isoc due to the slight hypochromic effect of the band at nm. However the plot obtained is in agreement with those found for Isoa and Isob and indicates that the number of base pairs involved in the interaction with Isoc is still one. Mole ratio plot of Isoa-DNA system. The isophorone-DNA systems were also studied by fluorescence spectroscopy, keeping constant the isophorone concentration and varying that of DNA.
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The studied molecules show intense fluorescence. The emission spectra of Isoa, b and c Fig 5 are characterized by a maximum centered at , and nm, respectively. Fluorescence emission spectra of: A Isoa B Isob C Isoc All the experiments were carried out at room temperature. With increasing concentration of DNA, progressive quenching was observed for Isoa, b and c revealing a binding interaction taking place.
It is well known that the fluorescence quenching can be static, resulting from the formation of a fluorophore-quencher complex or dynamic usually ascribed to the diffusive encounter between the fluorophore and the quencher [ 33 ]. In order to distinguish and ascertain quantitatively the possible quenching mechanism the Stern-Volmer equation was used [ 33 ], [ 34 ]: 2 where F 0 and F are the fluorescence intensity in absence and presence of DNA, respectively.
Plot of the ratio of the isophorone derivatives fluorescence intensity before and after incremental addition of DNA as a function of the quencher concentration for the determination of the Stern-Volmer quenching rate constant. For dynamic quenching, the maximum diffusion collisional quenching rate of various quenchers with biopolymers is about 2. Since the values of K q were much greater than 2. In order to provide further insights in the association process the binding constants K f and the number of binding sites n involved in the Iso-DNA systems were calculated according to the following equation [ 36 ]: 3.
Determination of the binding constant and number of binding sites for the Iso-DNA systems. The calculated binding constants for the Iso-DNA systems are slightly lower than those calculated by absorption spectroscopy due to the difference in the method used [ 37 ]. However, the magnitude of the evaluated association constants still confirms the higher affinity of Isoc, with respect to Isoa and Isob, to the DNA base pairs, which is in agreement with the data derived from UV-Vis spectroscopy.
In order to verify if the studied isophorones are able to induce DNA conformational changes, circular dichroism measurements were recorded in the — nm range with the DNA concentration kept constant and varying that of the isophorones. After addition of the isophorones an ICD band is revealed in each system studied.
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In particular, bands in the — nm, — nm and — nm range appear in the Isoa, b and c-DNA system, respectively. The induced circular dichroism bands, as found in the investigation of the interaction between the anticancer drug mitoxantrone with DNA, are much smaller in intensity as compared to the positive and negative DNA bands and their variation cannot be determined due to large noise in those regions [ 40 ].
However, the presence of these bands reveals that all the isophorone derivatives are able to interact with ds-DNA. The intensity of the band at nm decreases linearly up to C isoa concentration of The changes of the CD signal indicate that Isoa interacts with the base pairs of salmon testes DNA through the aromatic rings.
For isoc the bands at and increase continuously Fig 8C giving a total change in ellipticity of 0. The conformational changes induced by both Isoa and c are indicative of an intermediate stage of B-to-A DNA transition in which the B-conformation is still predominant. A similar trend was observed in the study of the interaction between Cyanazine [ 41 ] and Psoralen [ 29 ] with calf thymus DNA in which intercalation binding had been confirmed. On the other hand, the bands at and nm decrease linearly after each addition of Isob Fig 8B with a simultaneous slight red and blue shift of the positive and negative bands, respectively, indicating the existence of an interaction with nucleic acid.
Similar conclusions were reported about the interaction of Prodigiosin with ct-DNA [ 42 ]. The data obtained from spectrophotometric measurements indicate that all the studied isophorones interact with DNA, the affinity of Isoc to DNA being the highest. The UV-Vis spectra, recorded by keeping constant the concentration of isophorones and increasing the DNA concentration, suggest that the isophorones interact with DNA mainly through a stacking interaction between the aromatic chromophore and the base pair of DNA with a stoichiometry.
The fluorescence data are consistent with the findings drawn from the UV-Vis data and confirm the interactions with DNA. Miroslawa Rozycka is highly acknowledged for the help with the CD measurements. Browse Subject Areas? Click through the PLOS taxonomy to find articles in your field. Abstract Interactions of three new isophorone derivatives, Isoa Isob and Isoc with salmon testes DNA have been investigated using UV-Vis, fluorescence and circular dichroism spectroscopic methods.
This is an open access article distributed under the terms of the Creative Commons Attribution License , which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited Data Availability: All relevant data are within the paper. Introduction A number of studies have indicated that deoxyribonucleic acid DNA can be an interesting material not only for biological aspects but also for applications in photonics and electronics [ 1 ], [ 2 ].
Materials and Methods Synthesis The synthesis of Isoa, b and c has been described previously [ 22 ]. Reagents and preparation of stock solutions Common reagent-grade chemicals were used without further purification. Fluorescence measurements A fixed concentration of each isophorone was titrated with incremental addition of DNA and the fluorescence measurements were performed keeping the excitation and emission band slit width of 5. Results and Discussion Spectrophotometric studies It has been established that the strength of binding of organic molecules drugs with DNA helix can be quantified through spectral titration [ 21 ], [ 23 — 27 ].
Download: PPT. Table 1. Average values of the binding constants for the studied systems. UV-Vis of the isophorones derivatives-DNA interactions In order to gain more information on the mode of binding between DNA and isophorones a-c, additional UV-Vis studies were carried out in which the concentration of the isophorones was kept constant 7. Fig 3. Interaction of the isophorone derivatives in presence of ds -DNA.
Determination of the binding parameters The mole-ratio method was employed to evaluate the isophorone-DNA binding stoichiometries, keeping constant the concentration of the isophorones and varying that of DNA. Fluorescence titration studies The isophorone-DNA systems were also studied by fluorescence spectroscopy, keeping constant the isophorone concentration and varying that of DNA. Fig 5. Interaction of the isophorone derivatives with DNA studied using fluorescence spectroscopy. Fig 6. Table 2.