Figure 6
From: Specific effects of antitumor active norspermidine on the structure and function of DNA
Simulation model for rigid SPD and NSPD in (a) and typical snapshots in the simulation for SPD and NSPD interacting with double-stranded DNA in (b) and (c), when the strength of electrostatic interaction Γ = 1.36 nm. For the numerical simulation in (b), pairs of charged spheres to mimic phosphate groups are placed in a soft cylinder of length H (=3.4 nm) and radius RDNA (=1.0 nm) under a periodic boundary condition. The pictures in (c) represent the atomistic detail of the coarse-grained model. Hydrogen atoms are omitted for clarity. The positions of the three ammoniums in SPD and NSPD are indicated by #. In our model, a polyamine is allowed to partially penetrate into the DNA interior, which mimics minor and major grooves. The adjacent pairs of negatively charged moieties in the DNA model are separated by 0.34 nm.
