  In analogy with classic rigidity problems of networks and frames, the elastic
properties of hydrogels made of DNA nanostars (DNAns) are expected to strongly
depend on the precise geometry of their building blocks. However, it is
currently not possible to determine DNAns shape experimentally. Computational
coarse-grained models that can retain the correct geometry of DNA nanostars and
account for the bulk properties observed in recent experiments could provide
missing insights. In this study, we perform metadynamics simulations to obtain
the preferred configuration of three-armed DNA nanostars simulated with the
oxDNA model. Based on these results we introduce a coarse-grained computational
model of nanostars that can self assemble into complex three dimensional
percolating networks. We compare two systems with different designs, in which
either planar or non-planar nanostars are used. Structural and network analysis
reveal completely different features for the two cases, leading to two
contrasting elastic properties. The mobility of molecules is larger in the
non-planar case, which is consistent with a lower viscosity measured from
Green-Kubo simulations in equilibrium. To the best of our knowledge, this is
the first work connecting the geometry of DNAns with the bulk rheological
properties of DNA hydrogels and may inform the design of future DNA based
materials.
