Optimizing DNA Nanotechnology through Coarse-Grained Modeling: A Two-Footed DNA Walker

Abstract

DNA has enormous potential as a programmable material for creating artificial nanoscale structures and devices. For more complex systems, however, rational design and optimization can become difficult. We have recently proposed a coarse-grained model of DNA that captures the basic thermodynamic, structural and mechanical changes associated with the fundamental process in much of DNA nanotechnology, the formation of duplexes from single strands.In this article we demonstrate that the model can provide powerful insight into the operation of complex nanotechnological systems through a detailed investigation of a two-footed DNA

Coarse-graining DNA for simulations of DNA nanotechnology

“…83 One of the features of our model is that it allows the freeenergy landscapes associated with various assembly processes to be computed. 23,28,29,66,[83][84][85][86][87] For example, Fig. 3(a) depicts the free-energy profile for the hybridization of a 15-base-pair duplex, where the number of base pairs has been used as the order parameter.…”

“…It can also be important to have a good description of the extensibility of ssDNA, since sometimes the operation of nanodevices involves externally applied or internally generated tension. 28,29 Fourthly, it must be feasible to simulate the long time scales associated with diffusion of strands in solution and with significant conformational rearrangements. These consideration rule out many possible models.…”

“…OxDNA, the coarse-grained model created in our groups in Oxford, was developed with such nanotechnological applications explicitly in mind, and it is our contention that it is currently the most well-suited model for simulating DNA nanotechnology; it is also the model that has been applied to the most DNA nanotechnology systems. 23,28,29 Therefore, for the rest of the article we focus on this model. Nevertheless, we note that if one is only interested in the structural properties of DNA nanotechnology systems, other simulation approaches can potentially be used.…”

Direct Simulation of the Self-Assembly of a Small DNA Origami

“…This behaviour is what we expect based on prior studies of hybridization in oxDNA. 38 In addition, correct binding of a 16-base-pair region is effectively irreversible at this temperature on our time scales.…”

“…oxDNA has proven to be a robust and predictive model of DNA, 37 and is being applied to an increasing number of DNA nanotechnology systems. [38][39][40] Importantly for this study, it captures the biophysics of DNA likely to be relevant for origami self-assembly, such as hybridization, 41 displacement, 42,43 and the conformational properties of single-stranded DNA.…”