DNA nanostructures are used for both surface-based and solution-based applications. For surface-based applications, unique design considerations need to be studied. Different shapes will maximize contact area with the surface, and surface interactions can affect the structure of the nanostructure. For example, a tubular DNA nanostructure can unroll when interacting with mica due to its propensity to adsorb onto the surface1. For nanostructures functioning in solution, it's important to recognize that typical high-resolution imaging methods (AFM and TEM) all image nanostructures on a surface. Therefore, MD simulations like oxDNA are useful for inferring equilibrium structure in solution.
References
- Wei, B. et al. Design Space for Complex DNA Structures. J. Am. Chem. Soc. 135, 18080–18088 (2013).