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This method provides the nucleic acid sequences required to form a specific geometric form. A user inputs the geometric parameters of the desired structure and may also optionally define the physical size or template sequence of the object. This strategy can produce any geometric surface, provided that it can be rendered using polyhedral surface meshes. File formats containing specifications of the target object are converted into a set of arrays, providing input to a scaffold routing and staple design procedure. A polyhedral mesh is created and used to make a graph of the targeted structure to which equations are applied to determine scaffold routing. Ultimately, positions and orientations of each nucleotide are modeled to predict the 3D structure with full control over DNA sequence. Single-stranded DNA production using asymmetric PCR is also covered for enzymatic production of the endotoxin-free DNA scaffold needed to achieve self-assembly structured DNA nanoparticles. This approach produces high fidelity nanoparticles that are stable under physiological salt concentrations, with the ability to incorporate modified nucleotides for biological stability and immune cell activation, which are important features for in vivo delivery applications.