De Novo Reconstruction of DNA Origami Structures through Atomistic Molecular Dynamics Simulation

Christopher Maffeo, Jejoong Yoo, and Aleksei Aksimentiev
Nucleic Acids Research 44(7) 3013-3019 (2016)
DOI:10.1093/nar/gkw155  BibTex


Our recent improvements to atomic force fields led us to ask: Is MD accurate enough to predict DNA origami structure? The pointer structure, studied via cryo-electron microscopy (cryo-EM), is currently the best-characterized DNA origami object. We found during a 200 ns simulation of an atomistic model of the pointer starting in idealized conformation, the DNA origami object rapidly approached a conformation consistent with the cryo-EM reconstruction.

The all-atom model of the origami object was large (~6 M atoms), and the simulations were performed over months on hundreds of supercomputer nodes. This limits the utility of the method for routine structure prediction, an important goal in the field of nanotechnology. Hence, we developed an alternative approach that neglects solvent and long-range electrostatics, utilizes an elastic network of restraints to stabilize the DNA, and uses additional restraints to spread the DNA helices away from origami crossovers.

The elastic-network guided simulation worked extremely well. In just 2 nanoseconds of simulation, the DNA conformation approached a conformation consistent with the cryo-EM reconstruction (see trajectory on nanoHUB). Such a short simulation can be performed on a workstation. To validate the all-atom simulation protocol, the elastic-network guided structure was submerged in solvent and simulated for ~150 ns. The structure was seen to be stable.

MD simulation accurately captures subtle structural features of DNA origami. For example, the characteristic chickenwire pattern observed in experiment emerges in our simulations. Unusual motifs, such as the left-handed psuedo-helix are realistically modeled. Hence, if atomically-detailed structure prediction is needed, MD simulation is the method of choice. Setup your own origami structure prediction simulation here!


The DNA origami method has brought nanometer-precision fabrication to molecular biology labs, offering myriads of potential applications in the fields of synthetic biology, biomolecular medicine, molecular computation, etc. Advancing the method further requires controlling self-assembly down to the atomic scale. Here we demonstrate a computational method that allows the equilibrium structure of a large, complex DNA origami object to be determined to atomic resolution. Through direct comparison with the results of cryo-electron microscopy, we demonstrate de novo reconstruction of a 4.7 megadalton pointer structure by means of fully atomistic molecular dynamics simulations. Furthermore, we show that elastic network-guided simulations performed without solvent can yield similar accuracy at a fraction of the computational cost, making this method an attractive approach for prototyping and validation of self-assembled DNA nanostructures.

The "pointer" object was simulated via all-atom MD for 200 ns, starting from an idealized configuration of straight DNA helices. The DNA helices were seen to spread apart quickly as a global twist developed. The root-mean-squared-deviation from the psuedo-atomic structure derived from cryo-electron microscopy was seen to decrease monotonically, approaching 1 nm.

We developed a simple protocol that provides atomically-detailed structure prediction at a small fraction of the cost of all-atom MD simulation. Solvent is neglected in the simulation, while the DNA helices are stabiliized via an elastic network of restraints. Since there are no ions to screen electrostatic interactions, long-range electrostatic interactions are truncated. We know from previous studies that DNA helices in square lattice origami in typical solvent rest about 3 nm apart away from crossovers. Without long-range electrostatics to push the helices apart, we add intra-helical harmonic bonds to spread the helices. In less than 2 nanoseconds of simulation using the above protocol, we obtain a better structure than in 200 nanoseconds of all-atom MD simulation.

Comparison between the simulated (blue) and cryo-EM derived (red) structures of the pointer object. An isosurface (white) of the electron density reconstructed from cryo-EM measurements is shown in the beginning of the movie. The simulated structure is represented by the conformation obtained at the end of the 1.7 ns elastic network-guided simulation. The movie emphasizes regions of the pointer structure that were of particular interest to the cryo-EM reconstruction study.