DNA nanostructures are a class of self-assembling nanomaterials with a wide range of potential applications in biomedicine and nanotechnology. DNA nanotechnology originated in the 1980s with the construction of simple DNA polyhedra guided by human intuition or basic algorithmic approaches, which later evolved into platforms for applications such as molecular diagnostics and drug delivery. Today, the field is dominated by DNA origami constructs, to such an extent that the original algorithms used to design non-origami nanostructures have been lost. In this work, we describe Arktos: an algorithm developed to design simple DNA polyhedra without the use of DNA origami. Arktos designs DNA sequences predicted to fold into a desired structure, using simulated annealing to optimize strand binding energies and minimize misfolded configurations. As a proof-of-concept, we used Arktos to design a simple DNA tetrahedron. The generated oligonucleotide sequences were synthesized and experimentally validated via PAGE, indicating that they fold into the desired structure. These results demonstrate the feasibility of using Arktos to design simple DNA polyhedra, providing a foundation for future extensions.
Pradeep et al. (Fri,) studied this question.