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A General Design Method for Scaffold-Free DNA Wireframe Nanostructures

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Unconventional Computation and Natural Computation (UCNC 2024)

Part of the book series: Lecture Notes in Computer Science ((LNCS,volume 14776))

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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.

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Authors and Affiliations

  1. Department of Computer Science, Aalto University, Espoo, Finland

    Antti Elonen & Pekka Orponen

  2. Department of Biomedical Engineering, San José State University, San Jose, USA

    Abdulmelik Mohammed

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  1. Antti Elonen
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  2. Abdulmelik Mohammed
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  3. Pekka Orponen
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Correspondence to Pekka Orponen .

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Editors and Affiliations

  1. Ajou University, Suwon, Korea (Republic of)

    Da-Jung Cho

  2. Pohang University of Science and Technology, Pohang, Korea (Republic of)

    Jongmin Kim

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Elonen, A., Mohammed, A., Orponen, P. (2024). A General Design Method for Scaffold-Free DNA Wireframe Nanostructures. In: Cho, DJ., Kim, J. (eds) Unconventional Computation and Natural Computation. UCNC 2024. Lecture Notes in Computer Science, vol 14776. Springer, Cham. https://doi.org/10.1007/978-3-031-63742-1_13

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  • DOI: https://doi.org/10.1007/978-3-031-63742-1_13

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  • Online ISBN: 978-3-031-63742-1

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