A defining feature of DNA nanotechnology is the broad range of length and time scales involved in device manufacturing and actuation, from the fluctuation of individual base pairs over angstroms and picoseconds to the self-assembly of large supramolecular DNA structures spanning microns and hours. This necessitates the use of diverse and specialized modeling tools to capture the full range of behaviors exhibited by the structures. In this presentation, we will discuss three areas of self-assembly and organization in DNA nanotechnology and how we have dealt with modeling challenges at their respective scales. First, we will discuss the development of a coarse-grained model that enables DNA’s dynamic behavior to be captured on a timescale sufficient to directly observe DNA nanostructure self-assembly. The critical feature of this model is a switchable forcefield used to induce the transition between single-stranded and double-stranded DNA, allowing us to overcome the modeling barriers which had until now limited the tractability of this type of study. Second, we will discuss a computationally derived strategy to induce the precise placement of heterogeneous DNA origami species onto inorganic substrates. Previous work has led to the ability to place a single type of DNA origami onto silica substrates with absolute and arbitrary positioning using an e-beam lithography-based templating technique. We address the natural evolution of this concept: the precise placement of heterogeneous DNA origami onto silica substrates. We have developed a technique which uses steric brushes and ordered introduction of species to constrain the energy landscape of self-assembly and allow two species of DNA origami to be placed onto silica substrates with arbitrary patterning. Finally, we will discuss the reversible ordering of large DNA assemblies. We envision large arrays of DNA origami rotor devices which interact with each other at their edges and can become highly ordered due to their collective interactions, similar to the Ising lattice. We developed a model for the energetic behavior of these rotor arrays and simulated their organizational behavior, where we found that most systems of this type exhibit the Schottky anomaly, a low-temperature specific heat peak and order-disorder transition arising in systems with a limited number of discrete energy levels.

Modeling DNA origami self assembly and organization at long length and time scales

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ACS Fall 2022

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