Journal
NUCLEIC ACIDS RESEARCH
Volume 49, Issue 18, Pages 10265-10274Publisher
OXFORD UNIV PRESS
DOI: 10.1093/nar/gkab762
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Funding
- National Science Foundation [CCF-1956054, CCF1564025, CBET-1729397]
- Office of Naval Research [N00014-17-12609, N00014-13-1-0664, N00014-16-1-2506]
- Army ICB Subaward [KK1954]
- Alexander von Humboldt Foundation through a Feodor-Lynen Research Fellowship
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ATHENA is an open-source software that automatically renders single-stranded DNA scaffold routing and staple strand sequences for any target wireframe DNA origami, expanding the possibilities of designing 3D DNA-based assemblies. The software also allows external editing of sequences and provides atomic-level models for molecular dynamics, coarse-grained dynamics with oxDNA, and other computational chemistry simulation approaches.
Wireframe DNA origami assemblies can now be programmed automatically from the top-down using simple wireframe target geometries, or meshes, in 2D and 3D, using either rigid, six-helix bundle (6HB) or more compliant, two-helix bundle (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, standalone interface. Further, top-down sequence design of 3D DX-based objects previously enabled by DAEDALUS was limited to discrete edge lengths and uniform vertex angles, limiting the scope of objects that can be designed. Here, we introduce the open-source software package ATHENA with a graphical user interface that automatically renders single-stranded DNA scaffold routing and staple strand sequences for any target wireframe DNA origami using DX or 6HB edges, including irregular, asymmetric DX-based polyhedra with variable edge lengths and vertices demonstrated experimentally, which significantly expands the set of possible 3D DNA-based assemblies that can be designed. ATHENA also enables external editing of sequences using caDNAno, demonstrated using asymmetric nanoscale positioning of gold nanoparticles, as well as providing atomic-level models for molecular dynamics, coarse-grained dynamics with oxDNA, and other computational chemistry simulation approaches.
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