Department of Computer Science: MSc Thesis Presentations

DNAforge 2.0: A Modular Design Tool for Nucleic Acid Wireframe Nanostructures

Author: Kaisla Nyblom
Supervisor: Pekka Orponen

Abstract: Nucleic acid origami refers to nanostructures formed by folding DNA or RNA strands into defined shapes. Their design requires software tools that are used to route the nucleic acid strand(s) and determine the base sequences necessary to form the desired shape. While there exist several such tools, these tools often have a limited number of routing design methods. To address this, this thesis studied how DNAforge, a design tool for nucleic acid wireframe nanostructures, could be made more extensible and versatile in response to the field’s growing demand for diverse design methods.

The practical work of this thesis focused on extending DNAforge by introducing plugin support and adding two new design methods to the tool: structures with six-helix bundled edges and a hybrid RNA–DNA structure. The use of plugins allows third-party developers to create their own design methods and modify existing ones, and use them directly on the DNAforge platform. In addition, the two new added design methods increase the overall functionality of the tool.

As a result of these additions, the tool can now be customized to fit individual users' needs, and is more useful to a larger group of users. Overall, the plugin support and extended features enhance DNAforge’s usability and extensibility, making it a more valuable design tool in the nucleic acid nanotechnology community.