Algorithmic Design of 3D RNA Wireframe Meshes

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Flores_Ryynänen_Tommi_2025.pdf (2.49 MB)

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Kemian tekniikan korkeakoulu | Bachelor's thesis
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Date

2025-05-09

Department

Major/Subject

Chemical Engineering

Mcode

CHEM3054

Degree programme

Aalto Bachelor's Programme in Science and Technology

Language

en

Pages

27+13

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Abstract

RNA nanotechnology is an emerging field in science and engineering. It has potential applications in medicine, biosensing, and synthetic biology. A key development in this field is the design of 3D RNA wireframes, which utilises algorithms to program a self-assembling RNA strand. This thesis provides a comparative review on two currently employed methodologies, focusing on their algorithmic techniques and biological feasibility. The first study employs minimum spanning tree routing with kissing loops as connectors. It provides experimental results to corroborate theoretical findings. Results of the method indicate the concerns with scalability and kissing loops. The second method builds on the theory of minimum spanning trees, while attempting to limit the number of kissing loops by employing methods from topological graph theory. While the second study does not provide experimental results, it displays sound theoretical methodology. This thesis bridges the two methods and brings forth questions that could be addressed in the field.

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Supervisor

Hummel, Michael

Thesis advisor

Orponen, Pekka

Keywords

RNA, wireframe, nanostructures, RNA nanotechnology, topological graph theory, RNA strand routing

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https://urn.fi/URN:NBN:fi:aalto-202506245204

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[kand] Kemian tekniikan korkeakoulu / CHEM