A General Design Method for Scaffold-Free DNA Wireframe Nanostructures
Publication Date
1-1-2024
Document Type
Conference Proceeding
Publication Title
Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)
Volume
14776 LNCS
DOI
10.1007/978-3-031-63742-1_13
First Page
178
Last Page
189
Abstract
In the area of DNA nanotechnology, approaches to composing wireframe nanostructures exclusively from short oligonucleotides, without a coordinating long scaffold strand, have been proposed by Goodman et al. (2004) and Wang et al. (2019). We present a general design method that extends these special cases to arbitrary wireframes, in the sense of graphs linearly embedded in 2D or 3D space. The method works in linear time in the size of the given wireframe model and is already available for use in the online design tool DNAforge. We also interpret the method in terms of topological graph embeddings, which opens up further research opportunities in developing this design approach.
Keywords
cycle covers, DNA origami, DNA wireframes, scaffold-free nanostructure design, strong anti-parallel traces, topological graph embeddings
Department
Biomedical Engineering
Recommended Citation
Antti Elonen, Abdulmelik Mohammed, and Pekka Orponen. "A General Design Method for Scaffold-Free DNA Wireframe Nanostructures" Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics) (2024): 178-189. https://doi.org/10.1007/978-3-031-63742-1_13
