Molecular Dynamics Simulations of Self-Assembled DNA Nanostructures

Elucidation of the molecular-level mechanisms by which DNA single strands self-assemble into nanostructures might provide new informative guidelines in the engineering of novel biomaterials. Our studies examine the role of DNA sequences and the environmental conditions on the morphology and mechanical properties of DNA assemblies by performing molecular dynamics simulations. In this work, a newly developed coarse-grained model that bridges the gaps between atomistic models and extremely simplified models by capturing geometric and energetic details yet it is sufficiently simple to allow simulations of the spontaneous self-assembly of many DNA strands simultaneously. First, the dependence of the persistence length as a function of the ionic strength is examined. In addition, the melting temperature of double-stranded DNA is examined as a function of sequence, ionic strength, and chain length. Our results from single-molecule simulations agree qualitatively with experimental data. To examine the kinetic mechanisms involved in DNA self-assembly, we perform constant-temperature simulations to observe the whole process starting from random configurations of many single-strands of DNA. In particular, we investigate the self-assembly of homogenous and random sequences to determine the kinetic mechanisms of nanostructure formation. The findings of this research will guide experimentalists to identify systems of novel biomaterials with advantageous morphological properties.