Binding of an anionic fluorescent probe with calf thymus DNA and effect of salt on the probe–DNA binding: a spectroscopic and molecular docking investigation

Ghosh, Saptarshi; Kundu, Pronab; Paul, Bijan Kumar; Chattopadhyay, Nitin

doi:10.1039/c4ra14298e

Cited by 49 publications

(54 citation statements)

References 54 publications

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“…DNA melting is the process by which the hydrogen bonding and base stacking interactions between the strands of the double helix View Article Online are disrupted by heating, resulting in the separation of the double helix into two single strands. 32,40,50 In the present study, the melting profiles ( Fig. 50 Intercalation of probes into the DNA double helix increases the thermal stability of the helix by stabilizing the stacking interaction that causes an appreciable enhancement of the DNA melting temperature, 7,11,47 whereas, groove binding leads to an imperceptible modulation in the value of T m .…”

Section: Circular Dichroism and Helix Melting Studiesmentioning

confidence: 53%

“…11,42,47 In contrast, groove binding of the probes has an insignificant effect on the CD profile of DNA. 42,50,51 Fig. 8(A).…”

Section: Circular Dichroism and Helix Melting Studiesmentioning

confidence: 99%

“…9,40,50,53 To provide a theoretical support in relation to the mode of binding of the drug with the DNA through finding the pragmatic binding location, we have performed the docking simulation study according to the protocol described in the Experimental section. 9,40,50,53 To provide a theoretical support in relation to the mode of binding of the drug with the DNA through finding the pragmatic binding location, we have performed the docking simulation study according to the protocol described in the Experimental section.…”

Section: Molecular Docking Analysismentioning

confidence: 99%

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Exploration of the binding interaction of a potential nervous system stimulant with calf-thymus DNA and dissociation of the drug–DNA complex by detergent sequestration

Kundu

Ghosh

Chattopadhyay

2015

Phys. Chem. Chem. Phys.

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The binding interaction of a potential nervous system stimulant, 3-acetyl-4-oxo-6,7-dihydro-12H-indolo-[2,3-a]-quinolizine (AODIQ), with calf-thymus DNA (ctDNA) has been explored thoroughly. The modified photophysics of the fluorescent molecule within the microheterogeneous biomacromolecular system has been exploited to divulge the drug-DNA binding interaction. The absorption and various fluorometric measurements together with the fluorescence quenching, urea-induced denaturation study, circular dichroism and DNA-melting studies unequivocally ascertain the mode of binding of the drug with the DNA to be groove binding. Corroborating the experimental observations, molecular docking simulation projects the minor groove of the biomacromolecule to be the site of binding. Further experiments have revealed that dissociation of the drug from the drug-DNA complex can be achieved by the detergent sequestration method. Besides providing an insight into the drug-DNA interaction the work also demonstrates the surfactant-induced excretion of the drug from the biomacromolecular assembly.

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Section: Circular Dichroism and Helix Melting Studiesmentioning

confidence: 53%

“…11,42,47 In contrast, groove binding of the probes has an insignificant effect on the CD profile of DNA. 42,50,51 Fig. 8(A).…”

Section: Circular Dichroism and Helix Melting Studiesmentioning

confidence: 99%

Section: Molecular Docking Analysismentioning

confidence: 99%

See 1 more Smart Citation

Exploration of the binding interaction of a potential nervous system stimulant with calf-thymus DNA and dissociation of the drug–DNA complex by detergent sequestration

Kundu

Ghosh

Chattopadhyay

2015

Phys. Chem. Chem. Phys.

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“…To provide a theoretical support to the atypical lowering of fluorescence anisotropy in the CD‐embedded 3HF, and to perceive the mode/pattern of encapsulation, we have performed the molecular docking simulation study ,,. Figure portrays the lowest energy docked structures of 3HF−CD inclusion complexes.…”

Section: Methodsmentioning

confidence: 99%

Supramolecular Inclusion‐Assisted Disruption of Probe‐Solvent Network

Das

Chattopadhyay

2017

ChemistrySelect

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The present communication reports the disruption of probe‐solvent cluster formed by an excited state intramolecular proton transfer (ESIPT) prone molecular system and solvent water molecules because of the confinement of the probe within the cyclodextrin nano‐cavity. The disruption results in a decrease in the fluorescence anisotropy of the probe compared to its value in the aqueous medium. This is absolutely contrasting to the normal increasing trend for the fluorescence anisotropies of other fluorophores in similar constrained environments. This work substantiates the formation of probe‐solvent cluster in protic solvent and establishes the commanding role of hydrogen bonding in the solvation of the ESIPT probes.

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“…One crucial property of DNA is its ability to interact with small molecules. Interest in the recognition and characterization of this interaction has yielded valuable information on the development of therapeutic agents and control of gene expression . Many small molecules, such as metal ions, carcinogens, steroids and different classes of drugs, can interact with DNA.…”

Section: Introductionmentioning

confidence: 99%

Comprehensive analysis of the atenolol – DNA complex by viscometric, molecular docking and spectroscopic techniques

Kale

Ottoor

2018

Luminescence

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This paper discusses multi‐spectroscopic and molecular docking analysis of the interaction between atenolol (ATN) and deoxyribose nucleic acid (DNA) using alizarin (ALZ) as a spectroscopic probe. ATN is a β1‐receptor antagonist belonging to the β‐blocker class of molecules. Experimental findings that were based on different spectroscopic analysis, melting studies, viscometric analysis, 1H nuclear magnetic resonance and circular dichroism studies revealed the presence of a grove‐binding mode. The effect of ionic strength was also studied, and observations suggested that electrostatic interaction also played a minor role during interaction. Molecular docking analysis suggested that the dominant force for the grove‐binding phenomenon was hydrogen bonding between the 24‐H residue of ATN and O of the 10‐G residue, and the 40‐H residue of ATN and N of the 17‐A base residue. Competitive binding study of the ALZ−DNA complex with ATN showed that, despite an increase in the amount of ATN in the ALZ−DNA complex, the overall absorbance remained unchanged. The decrease in fluorescence in the ALZ−DNA system may be due to new non‐fluorescent ATN−DNA−ALZ complex formation.

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Binding of an anionic fluorescent probe with calf thymus DNA and effect of salt on the probe–DNA binding: a spectroscopic and molecular docking investigation

Abstract: Binding mode of biologically relevant anionic probe, ANS, with ctDNA is divulged from spectroscopic and molecular docking studies.

Cited by 49 publications

References 54 publications

Exploration of the binding interaction of a potential nervous system stimulant with calf-thymus DNA and dissociation of the drug–DNA complex by detergent sequestration

Exploration of the binding interaction of a potential nervous system stimulant with calf-thymus DNA and dissociation of the drug–DNA complex by detergent sequestration

Supramolecular Inclusion‐Assisted Disruption of Probe‐Solvent Network

Comprehensive analysis of the atenolol – DNA complex by viscometric, molecular docking and spectroscopic techniques

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