Evidence for Dual Site Binding of Nile Blue A toward DNA: Spectroscopic, Thermodynamic, and Molecular Modeling Studies | Zendy

Mukti Mohammad | Zendy; Harun Al Rasid Gazi | Zendy; Kumud Pandav | Zendy; Prateek Pandya | Zendy; Md. Maidul Islam | Zendy

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Evidence for Dual Site Binding of Nile Blue A toward DNA: Spectroscopic, Thermodynamic, and Molecular Modeling Studies

Author(s) -

Mukti Mohammad,

Harun Al Rasid Gazi,

Kumud Pandav,

Prateek Pandya,

Md. Maidul Islam

Publication year - 2021

Publication title -

acs omega

Language(s) - English

Resource type - Journals

SCImago Journal Rank - 0.779

H-Index - 40

ISSN - 2470-1343

DOI - 10.1021/acsomega.0c04775

Subject(s) - intercalation (chemistry) , enthalpy , minor groove , dna , binding energy , chemistry , entropy (arrow of time) , molecular model , crystallography , helix (gastropod) , binding site , nile delta , biophysics , thermodynamics , stereochemistry , biochemistry , inorganic chemistry , biology , ecology , physics , ancient history , history , snail , nuclear physics

Binding of Nile Blue (NB) with calf thymus DNA has been studied using molecular modeling, spectroscopic, and thermodynamic techniques. Our study revealed that NB binds to the DNA helix by two types of modes (groove binding and intercalation) simultaneously. The thermodynamic study showed that the overall binding free energy is a combination of several negative and positive free energy changes. The binding was favored by negative enthalpy and positive entropy changes (due to the release of water from the DNA helix). The docking study validated all experimental evidence and showed that NB binds to a DNA minor groove at low concentrations and switches to intercalation mode at higher concentrations.

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