• octahedral geometry;
  • DNA nano-structures;
  • molecular dynamics simulation;
  • single strand linkers;
  • DNA structural parameters;
  • principal component analysis


The structural/dynamical properties of three truncated octahedral DNA nano-cages composed by identical double helices but single strand linkers with different composition, namely 7 thymidines, 7 adenines, and 7 alternated thymidines and adenines, have been investigated through classical molecular dynamics simulations. Trajectories have been analyzed to investigate the role of the linkers in defining nano-cages stability and flexibility, including possible influence on the internal cages motions. The data indicate that the cages behavior is almost identical and that the structural/dynamical parameters measured along the trajectories are not particularly affected by the presence of different bases. These results demonstrate that the constraints imposed by the nano-structure geometry are the main factor in modulating these properties. © 2014 Wiley Periodicals, Inc. Biopolymers 101: 992–999, 2014.