Rapid Prototyping of Wireframe Scaffolded DNA Origami using ATHENA

Abstract

Wireframe DNA origami assemblies can now be programmed automatically from the "top-down" using simple wireframe target geometries, or meshes, in 2D and 3D geometries using either rigid, six-helix bundle (6HB) or more compliant, two-helix bundle (2HB or DX) edges. While these assemblies have numerous applications in nanoscale materials fabrication due to their nanoscale spatial addressability and high degree of customization, no easy-to-use graphical user interface software yet exists to deploy these algorithmic approaches within a single, stand-alone interface. Here, we present ATHENA, an open-source software package with a graphical user interface that automatically renders single-stranded DNA scaffold routing and staple strand sequences for any target wireframe DNA origami in 2D or 3D using 2HB or 6HB edges. ATHENA enables external editing of sequences using the popular tool caDNAno, demonstrated here using asymmetric nanoscale positioning of gold nanoparticles, as well as atomic-level models for molecular dynamics, coarse-grained dynamics, or other computational chemistry simulation approaches. We anticipate ATHENA will significantly reduce the barrier for non-specialists to perform wireframe DNA origami sequence design and fabrication for custom applications in materials science, nanotechnology, therapeutics, and other areas.