AlphaFold\n3 – Aided Design of DNA Motifs To\nAssemble into Triangles

Self-assembly\nof biomolecules provides a powerful tool for a wide\nrange of applications in nanomedicine, biosensing and imaging, vaccines,\ncomputation, nanophotonics, etc. The key is to rationally design building\nblocks and the intermolecule interactions. Along this line, structural\nDNA nanotechnology has rapidly developed by limiting DNA secondary\nstructures to primarily well-established, B-form DNA duplexes, which\ncan be readily and reliably predicted. As the field evolves, more\nsophisticated structural elements must be introduced. While increasing\nthe structural complexity, they bring challenges to predicting DNA\nnanostructures. In the past, a brutal and tedious error-and-trial\napproach has often been used to solve this problem. Here, we report\na case study of applying AlphaFold 3 to model the structural elements\nto facilitate DNA nanostructure design. This protocol is expected\nto be generally applicable and greatly facilitates the further development\nof structural DNA nanotechnology.