DNA NanoSystems Simulations

Tod Pascal, California Institute of Technology

We use molecular dynamics (MD) simulations to obtain a comprehensive understanding of relationship between structure, topology, and stability of various Paranemic crossover (PX) molecules, synthesized recently by Seeman and coworkers at NYU. These studies included all atoms of the PX structures plus an explicit description of solvent and ions. This is the first MD simulation of such complex DNA motifs. The average dynamics structures over the last 1 ns of 3 ns long simulation preserve the Watson-Crick hydrogen bonding as well as helical structure. We have also computed the strain energy for the formation of PX molecules with reference to B-DNA molecules of the same length and sequence. Various helicoidal parameters indicate that PX65 has the values for helical twist and other helical parameters that are close to the values expected for normal B-DNA of similar length and sequence. All these findings indicate that PX65 is structurally more stable compared to other PX motifs in accordance with the experimental findings. Such studies should aid the design of optimized DNA structures for use in nanoscale components and devices.

Abstract Author(s): Tod Pascal, Prabal Maiti, Jiyoung Heo, Nagarajan Vaidehi, William A Goddard III