Prof. Pradipta Bandyopadhyay

School of Computational and Integrative Sciences

Jawaharlal Nehru University

New Delhi, 110067

E-mail: praban07[at]gmail.com

 

Brief Bio-sketch:

Prof. Pradipta Bandyopadhyay has obtained his Master's degree in Chemistry from IIT Kanpur and PhD degree from Graduate University of Advanced Studies, Japan. He subsequently worked at the Iowa State University, University of California, San Francisco, IIT Guwahati before joining Jawaharlal Nehru University. His research interests are in equilibrium statistical mechanics, computer simulation to understand chemical and biological problems.

STRUCTURE AND THERMODYNAMICS OF WATER AROUND A DNA IN A CROWDED ENVIRONMENT

Crowded molecular environment can affect the structure, thermodynamics, and dynamics of macromolecules. In the current study, we have studied a system having a short DNA, water, and ethylene glycol (EG) as a crowder. Along with the properties of the DNA, we have focused on the behavior of EG, salt ions, and water with the increase of concentration of EG. We have probed the behavior of water and crowder using molecular dynamics (MD) simulation and by calculating localized thermodynamic properties. Competition between EG and water in the first solvation shell of DNA is clearly found from the analysis. The density of Na⁺ (Cl^-) near DNA increases (decreases) as the concentration of EG is increased. The density of Cl^- near Na⁺, somehow non-intuitively, increases with increase of EG concentration. It was also found that the average localized free energy per water in the first solvation shell of DNA increases with the increase in the EG concentration. A comprehensive picture of interaction among the different species of the system has come out from this work.

 

References:

[1] A. Jaiswal, R. Srivastava, P. Pandey, P. Bandyopadhyay, PLOS ONE (2018).