NanoFrame: A web-based DNA wireframe design tool for 3D structures

TL;DR

NanoFrame is a user-friendly, web-based tool that simplifies the design of 3D DNA nanostructures, supporting complex shapes with algorithms for routing and editing sequences.

Contribution

It introduces a web platform with novel algorithms for DNA wireframe design, addressing usability and compatibility issues in existing software.

Findings

Supports various 3D shapes including cuboids and Platonic forms

Enables editing and saving of DNA sequences online

Simplifies the design process for complex DNA nanostructures

Abstract

The rapid development of the DNA nanotechnology field has been facilitated by advances in CAD software. However, as more complex concepts arose, the lag between the needs and software capabilities appeared. Further derailed by manual installation and software incompatibility across different platforms and often tedious library management issues, the software has become hard-to-use for many. Here we present NanoFrame, a web-based DNA wireframe design tool for making 3D nanostructures from a single scaffold. Within this software, we devised algorithms for DNA routing, staple breaking, and wireframe cage opening which, while modeled for cuboid structure, can be generalized to a variety of platonic and Archimedean shapes. In addition, NanoFrame provides a platform for editing auto-generated staple sequences and saving work online.