Journal ArticleDOI
Binding of DNA with Rhodamine B: Spectroscopic and molecular modeling studies
Md. Maidul Islam,Maharudra Chakraborty,Prateek Pandya,Abdulla Al Masum,Neelima Gupta,Subrata Mukhopadhyay +5 more
TLDR
In this paper, the binding of Rhodamine B to Calf thymus DNA (CT DNA) was studied using various biophysical techniques and molecular docking method and it was concluded that the binding process is favored by both negative enthalpy change and positive entropy change.About:
This article is published in Dyes and Pigments.The article was published on 2013-11-01. It has received 107 citations till now. The article focuses on the topics: Cooperative binding & Binding constant.read more
Citations
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Journal ArticleDOI
Binding interaction between sorafenib and calf thymus DNA: spectroscopic methodology, viscosity measurement and molecular docking.
TL;DR: The binding interaction of sorafenib with calf thymus DNA (ct-DNA) was studied using UV-vis absorption spectroscopic, fluorescence emission spectroscopy, circular dichroism (CD), viscosity measurement and molecular docking methods and revealed that there was obvious binding interaction between sorafanib and ct-DNA.
Journal ArticleDOI
Characterization of interaction of calf thymus DNA with gefitinib: spectroscopic methods and molecular docking.
TL;DR: The binding interaction of gefitinib with calf thymus DNA (ct-DNA) under the simulated physiological pH condition was studied employing UV absorption, fluorescence, circular dichroism (CD), viscosity measurement and molecular docking methods and it can be concluded that the main interaction forces between gef itinib and ct-DNA in the binding process were van der Waals force and hydrogen bonding interaction.
Journal ArticleDOI
A novel view of the separate and simultaneous binding effects of docetaxel and anastrozole with calf thymus DNA: Experimental and in silico approaches.
Maryam Dareini,Zeinab Amiri Tehranizadeh,Narges Marjani,Reza Taheri,Sogand Aslani-Firoozabadi,Atiye Talebi,Negar NayebZadeh Eidgahi,Mohammad Reza Saberi,Jamshidkhan Chamani +8 more
TL;DR: DO is capable of displacing EB and AO from their binding site in ctDNA; hence, it can be concluded that DO and AN are able to intercalate into the base pairs of ct DNA in binary and ternary systems.
Journal ArticleDOI
Binding properties of pendimethalin herbicide to DNA: multispectroscopic and molecular docking approaches.
TL;DR: Pendimethalin is a systemic herbicide widely used on rice, cotton, peas, wheat, potatoes, fruits, nuts and other residential and non-residential crops but concurrently exerts toxic effects on beneficial organisms like earthworms, aquatic invertebrates and other non-targeted animals including humans.
Journal ArticleDOI
Unravelling the interaction of pirenzepine, a gastrointestinal disorder drug, with calf thymus DNA: An in vitro and molecular modelling study.
Yusra Rahman,Shumaila Afrin,Mohammed Amir Husain,Tarique Sarwar,Abad Ali,Shamsuzzaman,Mohammad Tabish +6 more
TL;DR: Thermodynamic parameters obtained from isothermal titration calorimetric studies suggest that the interaction of pirenzepine with Ct-DNA is enthalpically driven, and the role of electrostatic interaction in the binding of pirensepine to Ct- DNA cannot be precluded.
References
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Journal ArticleDOI
AutoDock Vina: Improving the speed and accuracy of docking with a new scoring function, efficient optimization, and multithreading
Oleg Trott,Arthur J. Olson +1 more
TL;DR: AutoDock Vina achieves an approximately two orders of magnitude speed‐up compared with the molecular docking software previously developed in the lab, while also significantly improving the accuracy of the binding mode predictions, judging by tests on the training set used in AutoDock 4 development.
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Thermodynamic analysis of ion effects on the binding and conformational equilibria of proteins and nucleic acids: the roles of ion association or release, screening, and ion effects on water activity.
TL;DR: The purpose of this review is to examine the various effects of low- molecular-weight electrolytes on the associations and interactions of proteins and nucleic acids through general electrostatic effects rather than chemical effects of particular ions.
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Ligand docking and binding site analysis with PyMOL and Autodock/Vina.
Daniel Seeliger,Bert L. de Groot +1 more
TL;DR: An interface between the popular molecular graphics system PyMOL and the molecular docking suites Autodock and Vina is presented and it is demonstrated how the combination of docking and visualization can aid structure-based drug design efforts.
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Molecular recognition of DNA by small molecules.
TL;DR: A pivotal path forward would be to understand in a predictive mechanistic sense how to create ensembles of weak bonds between synthetic ligands and biological macromolecules in water, the solvent of life.
Journal ArticleDOI
Urea and Guanidine Hydrochloride Denaturation of Ribonuclease, Lysozyme, α-Chymotrypsin, and b-Lactoglobulin
Raymond F. Greene,C. Nick Pace +1 more
TL;DR: Estimates of ΔGapp in the absence of denaturant suggest that several recent estimates of ΔGh2oapp are too high by 3 to 10 Cal per mole, and suggest that the mechanism of unfolding is the same in the presence of the two denaturants.
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