Force Biased Molecular Dynamics Simulation Study of Effect of Dendrimer Generation on Interaction with DNA

Nandy, Bidisha and Maiti, Prabal K and Bunker, Alex (2013) Force Biased Molecular Dynamics Simulation Study of Effect of Dendrimer Generation on Interaction with DNA. In: JOURNAL OF CHEMICAL THEORY AND COMPUTATION, 9 (1). pp. 722-729.

	PDF jol_che_com_9-1_722_2013.pdf - Published Version Restricted to Registered users only Download (588kB) | Request a copy
	PDF ct300678r_si_001.pdf - Published Supplemental Material Restricted to Registered users only Download (338kB) | Request a copy

Abstract

We have studied the effect of dendrimer generation on the interaction between dsDNA and the PAMAM dendrimer using force biased simulation of dsDNA with three generations of dendrimer: G3, G4, and G5. Our results for the potential of mean force (PMF) and the dendrimer asphericity along the binding pathway, combined with visualization of the simulations, demonstrate that dendrimer generation has a pronounced impact on the interaction. The PMF increases linearly with increasing generation of the dendrimer. While, in agreement with previous results, we see an increase in the extent to which the dendrimer bends the dsDNA with increasing dendrimer generation, we also see that the deformation of the dendrimer is greater with smaller generation of the dendrimer. The larger dendrimer forces the dsDNA to conform to its structure, while the smaller dendrimer is forced to conform to the structure of the dsDNA. Monitoring the number of bound cations at different values of force bias distance shows the expected effect of ions being expelled when the dendrimer binds dsDNA.

Item Type:	Journal Article
Publication:	JOURNAL OF CHEMICAL THEORY AND COMPUTATION
Publisher:	AMER CHEMICAL SOC
Additional Information:	Copyright for this article belongs to AMER CHEMICAL SOC, WASHINGTON,
Department/Centre:	Division of Physical & Mathematical Sciences > Physics
Date Deposited:	06 Mar 2013 11:08
Last Modified:	06 Mar 2013 11:08
URI:	http://eprints.iisc.ac.in/id/eprint/45957

Actions (login required)

View Item