1 research outputs found
Force Biased Molecular Dynamics Simulation Study of Effect of Dendrimer Generation on Interaction with DNA
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