In vitro DNA binding studies of antiretroviral drug nelfinavir using ethidium bromide as fluorescence probe

Ramana, M. M. V.; Betkar, Rahul R.; Nimkar, Amey; Ranade, Prasanna; Mundhe, Balaji; Pardeshi, Sachin D.

doi:10.1016/j.jphotobiol.2015.08.012

Cited by 39 publications

(24 citation statements)

References 35 publications

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“…Two dyes, Ethidium bromide (EB) and 4′,6-diamidino-2-phenylindole (DAPI) with distinctly differing properties could be employed. EB is well known DNA intercalating dye which displays maximum emission at 661 nm upon binding to double stranded DNA [ 20 ]. Free molecule exhibits very low fluorescence; however, fluorescence signal magnifies when bound to DNA.…”

Section: Resultsmentioning

confidence: 99%

Spectroscopic and viscometric determination of DNA-binding modes of some bioactive dibenzodioxins and phenazines

Phadte

Banerjee

Mate

et al. 2019

Biochemistry and Biophysics Reports

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Push-pull dibenzodioxins and phenazines having ‘anthracene-like’ planar structures and good charge transfer character had been previously synthesised in our laboratory. The dibenzodioxins had earlier proven their anti-proliferative nature against HeLa tumor cell lines. Since phenazines are structural analogues of the former, these molecules were evaluated in course of the current study for their cytotoxic action against HeLa cell lines and they exhibited strong anti-tumor activity. This behavior could be related to their good DNA binding property. The DNA binding modes of molecules 1 – 4 (Fig. 1) were evaluated using various experimental techniques and they interacted with DNA in a non-covalently by both intercalative as well as groove binding mechanisms. Molecule 1 follows predominantly intercalative binding mode whereas molecules 2 and 3 have nearly equal and opposite preferences for both groove binding and intercalative modes. For molecule 4 , groove binding is preferred mode of binding to DNA. A rationale for such differential binding behaviour is provided based on the subtle structural differences in our synthesised dibenzodioxins and phenazines. Elucidation of the mode of a molecule-DNA-binding event is relevant for understanding the mechanism of action of these molecules and will help promote further research into designing better DNA targeting small molecules.

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Section: Resultsmentioning

confidence: 99%

Spectroscopic and viscometric determination of DNA-binding modes of some bioactive dibenzodioxins and phenazines

Phadte

Banerjee

Mate

et al. 2019

Biochemistry and Biophysics Reports

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“…When small molecules bind independently to a set of equivalent sites on a biomolecule, the equilibrium exits between the free and bound molecules and the corresponding equation is shown below:

\log ([], ([], F_{o} - F) / F) = \log K + n \log ([], Q)

where K is the binding constant of the system and n is the number of binding sites. The values of K and n were retrieved from the intercept and slope of the plot of log [( F o ‐ F )/ F ] vs. log[ Q ] and are given in Table .…”

Section: Resultsmentioning

confidence: 99%

Intercalation of a flavonoid, silibinin into DNA base pairs: Experimental and theoretical approach

Pawar

Seetharamappa

2019

J of Molecular Recognition

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Polyphenols are secondary plant metabolites, which have received much attention because of their potential health benefits. Silibinin (SIL) is a well-known naturally occurring flavonolignan, which is extensively used in treating a wide variety of diseases as a dietary supplement as well as a prescribed drug. The mechanism of binding of SIL to calf thymus DNA (ctDNA) was investigated by employing multispectroscopic techniques, viz., absorption, fluorescence, and circular dichroism besides viscosity measurements and docking studies. Analysis of fluorescence results indicated that SIL has interacted with ctDNA and quenched its intensity through static quenching mechanism. The binding constant at room temperature was found to be 2.48×10 4 mol −1 , suggesting moderate binding affinity between SIL and ctDNA. The hypochromicity observed in the absorption spectra of ctDNA in the presence of SIL revealed the intercalation of SIL into ctDNA base pairs. Further, the intercalative mode of binding between SIL and ctDNA was confirmed by viscosity measurements and molecular docking studies. The outcome of present study helps to decipher the interaction mechanism between SIL and DNA at physiological pH, which further assists in the design of a new analogue for better therapeutic effects.

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“…The CD spectrum of free Ct‐DNA exhibits positive and negative bands at 275 and 245 nm, due to base stacking and helicity of B‐DNA . Intercalation of small molecules to DNA led the modifications in both positive and negative bands because of enrichment in base stacking and stabilization of helicity whereas groove binding or electrostatic interaction causes less or no perturbation in the base stacking and helicity bands …”

Section: Resultsmentioning

confidence: 99%

New phthalimide‐appended Schiff bases: Studies of DNA binding, molecular docking and antioxidant activities

et al. 2016

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Herein, we investigated new phthalimide-based Schiff base molecules as promising DNA-binding and free radical scavenging agents. Physicochemical properties of these molecules were demonstrated on the basis of elemental analysis, ultraviolet-visible (UV-Vis), infra-red (IR), H and C nuclear magnetic resonance (NMR) spectroscopy. All spectral data are agreed well with the proposed Schiff base framework. The DNA-binding potential of synthesized compounds were investigated by means of UV-visible, fluorescence, iodide quenching, circular dichroism, viscosity and thermal denaturation studies. The intrinsic binding constants (K ) were calculated from absorption studies were found to be 1.1 × 10 and 1.0 × 10 M for compounds 2a and 2b suggesting that compound 2a binding abilities with DNA were stronger than the compound 2b. Our studies showed that the presented compounds interact with DNA through groove binding. Molecular docking studies were carried out to predict the binding between Ct-DNA and test compounds. Interestingly, in silico predictions were corroborated with in vitro DNA-binding conclusions. Furthermore, the title compounds displayed remarkable antioxidant activity compared with reference standard.

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In vitro DNA binding studies of antiretroviral drug nelfinavir using ethidium bromide as fluorescence probe

Cited by 39 publications

References 35 publications

Spectroscopic and viscometric determination of DNA-binding modes of some bioactive dibenzodioxins and phenazines

Spectroscopic and viscometric determination of DNA-binding modes of some bioactive dibenzodioxins and phenazines

Intercalation of a flavonoid, silibinin into DNA base pairs: Experimental and theoretical approach

New phthalimide‐appended Schiff bases: Studies of DNA binding, molecular docking and antioxidant activities

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