Rapid prototyping of arbitrary 2D and 3D wireframe DNA origami
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, 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.
Document Details
- Document Type
- Pub Defense Publication
- Publication Date
- Sep 11, 2021
- Source ID
- 10.1093/nar/gkab762
Entities
People
- Hyungmin Jun
- Mark Bathe
- Molly F. Parsons
- Shanshan Li
- Steve Jackson
- Torsten John
- Wah Chiu
- William P Bricker
- Xiao Wang
Organizations
- Alexander von Humboldt Foundation
- Jeonbuk National University
- Massachusetts Institute of Technology
- National Science Foundation
- Office of Naval Research
- Stanford University