On the Possibility of Facilitated Diffusion of Dendrimers Along DNA.

ABSTRACT: We investigate the electrostatics, energetics, and dynamics of dendrimer-DNA interactions that mimic protein-DNA complexes as a means to design facilitated mechanisms by which dendrimers can slide and search DNA for targets. By using all-atom molecular dynamics simulations, we calculated the free energy profiles of dendrimer-binding around the DNA via umbrella sampling. We also calculated electrostatic interaction maps in comparison to proteins, as well as the dynamical changes induced by DNA-dendrimer interactions via NMR-measurable order parameters. Our results show that for dendrimers to go around DNA, there is a free-energy barrier of 8.5 kcal/mol from the DNA major groove to DNA minor groove, with a minimum in the major groove. This barrier height makes it unlikely for an all-amine de

SUBMITTER: Ficici E 

PROVIDER: S-EPMC5468365 | biostudies-literature | 2015 Jun

REPOSITORIES: biostudies-literature