Simulative Analysis of a Family of DNA Tetrahedrons Produced by Changing the Twisting Number of Each Double Helix

In this paper, three tetrahedral nanocages, composed of six DNA double helix edges with all having the twist number 1, 2 or 3, have been characterized using classical molecular dynamics simulation to measure the specific structural and conformational features produced by only changing the twisting number of each double helix. The simulation result indicates that three tetrahedral cages are relatively stable and are maintained along the entire trajectory. Each double helix is more inclined to behave as a whole in the 2TD and 3TD cages than in the 1TD cage according to the cross-correlation maps for three nanocages, and also their local motions are more easily induced by the conformational variability of the thymidine linkers due to the increased flexibility of each helix. Hence, the double helices become the important factors on the structural stability of total cages with the DNA twisting number, and also give the signification contributions to the sizes of these cages conferring the larger spaces of the 2TD and 3TD cages than the 1TD cage. Our result provides an insight into which roles the double helix edges play in assembling DNA polyhedron, and also contribute to improving the loading capacity of DNA tetrahedron in drug delivery.