Improving the precision and function of encapsulating three-dimensional (3D) DNA nanostructures via curved geometries could have transformative impacts on areas such as molecular transport, drug delivery, and nanofabrication. However, the addition of non-rasterized curvature escalates design complexity without algorithmic regularity, and these challenges have limited the ad hoc development and usage of previously unknown shapes. In this work, we develop and automate the application of a set of previously unknown design principles that now includes a multilayer design for closed and curved DNA nanostructures to resolve past obstacles in shape selection, yield, mechanical rigidity, and accessibility. We design, analyze, and experimentally demonstrate a set of diverse 3D curved nanoarchitectures, showing planar asymmetry and examining partial multilayer designs. Our automated design tool implements a combined algorithmic and numerical approximation strategy for scaffold routing and crossover placement, which may enable wider applications of general DNA nanostructure design for nonregular or oblique shapes.
We present here the combination of experimental and computational modeling tools for the design and characterization of protein−DNA hybrid nanostructures. Our work incorporates several features in the design of these nanostructures: (1) modeling of the protein−DNA linker identity and length; (2) optimizing the design of protein−DNA cages to account for mechanical stresses; (3) probing the incorporation efficiency of protein−DNA conjugates into DNA nanostructures. The modeling tools were experimentally validated using structural characterization methods like cryo-TEM and AFM. Our method can be used for fitting low-resolution electron density maps when structural insights cannot be deciphered from experiments, as well as enable insilico validation of nanostructured systems before their experimental realization. These tools will facilitate the design of complex hybrid protein−DNA nanostructures that seamlessly integrate the two different biomolecules.
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