DNA origami is a cost-effective method of controlling matter at the nanoscale that folds a long DNA strand using a custom set of complementary strands. Experimental characterization of DNA origami is essential for accurate design, but has been limited to rather low-resolution techniques. One exception is the high-resolution cryo-electron microscopy (cryo EM) reconstruction of the "pointer" object from the Dietz group.
The need for atomically-detailed computational structure prediction led us to study the pointer object using molecular dynamics simulation (see publication).
We found that it is possible to obtain high-quality structures from the idealized configuration using orders of magnitude fewer resources by ommiting solvent and using an elastic-network of restraints to guide the simulation.
You can explore these simulations through MDshowcase on NanoHUB.
This service produces NAMD configuration files needed for an elastic-network guided DNA origami structure prediction simulation.
Note that you will have to run the simulations on your own workstation, which can be a time consuming process (overnight to several days), espcially for large systems.
It may not be possible to simulate a structure that is initially very far from equilibrium (e.g. having very long bonds in the caDNAno design) out-of-the-box.
To gauge how long the simulation might need to run on your hardware, we recommend testing the protocol with a very simple design. The simulation will likely need to run ~2 ns. For a given number of processors, the walltime to run a simulation scales almost linearly with the number of atoms in the system.
Chris Maffeo (firstname.lastname@example.org).