A General Design Method for Scaffold-Free DNA Wireframe Nanostructures

Antti Elonen; Abdulmelik Mohammed; Pekka Orponen

doi:10.1007/978-3-031-63742-1_13

A General Design Method for Scaffold-Free DNA Wireframe Nanostructures

Antti Elonen, Abdulmelik Mohammed, Pekka Orponen^*

^*Tämän työn vastaava kirjoittaja

San Jose State University

Tutkimustuotos: Artikkeli kirjassa/konferenssijulkaisussa › Conference article in proceedings › Scientific › vertaisarvioitu

Abstrakti

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.

Alkuperäiskieli	Englanti
Otsikko	Unconventional Computation and Natural Computation - 21st International Conference, UCNC 2024, Proceedings
Toimittajat	Da-Jung Cho, Jongmin Kim
Kustantaja	Springer
Sivut	178-189
Sivumäärä	12
ISBN (elektroninen)	978-3-031-63742-1
ISBN (painettu)	978-3-031-63741-4
DOI - pysyväislinkit	https://doi.org/10.1007/978-3-031-63742-1_13
Tila	Julkaistu - 2024
OKM-julkaisutyyppi	A4 Artikkeli konferenssijulkaisussa
Tapahtuma	International Conference on Unconventional Computation and Natural Computation - Pohang, Etelä-Korea Kesto: 17 kesäk. 2024 → 21 kesäk. 2024 Konferenssinumero: 21

Julkaisusarja

Nimi	Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)
Kustantaja	Springer
Vuosikerta	14776 LNCS
ISSN (painettu)	0302-9743
ISSN (elektroninen)	1611-3349

Conference

Conference	International Conference on Unconventional Computation and Natural Computation
Lyhennettä	UCNC
Maa/Alue	Etelä-Korea
Kaupunki	Pohang
Ajanjakso	17/06/2024 → 21/06/2024

Pääsy asiakirjaan

10.1007/978-3-031-63742-1_13

Muut tiedostot ja linkit

Linkki julkaisuun Scopuksessa

Siteeraa tätä

Elonen, A., Mohammed, A., & Orponen, P. (2024). A General Design Method for Scaffold-Free DNA Wireframe Nanostructures. teoksessa D.-J. Cho, & J. Kim (Toimittajat), Unconventional Computation and Natural Computation - 21st International Conference, UCNC 2024, Proceedings (Sivut 178-189). (Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics); Vuosikerta 14776 LNCS). Springer. https://doi.org/10.1007/978-3-031-63742-1_13

Elonen, Antti ; Mohammed, Abdulmelik ; Orponen, Pekka. / A General Design Method for Scaffold-Free DNA Wireframe Nanostructures. Unconventional Computation and Natural Computation - 21st International Conference, UCNC 2024, Proceedings. Toimittaja / Da-Jung Cho ; Jongmin Kim. Springer, 2024. Sivut 178-189 (Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)).

@inproceedings{7ade0c5d1ba7435ba22f1f9c67c660e0,

title = "A General Design Method for Scaffold-Free DNA Wireframe Nanostructures",

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",

author = "Antti Elonen and Abdulmelik Mohammed and Pekka Orponen",

note = "Publisher Copyright: {\textcopyright} The Author(s), under exclusive license to Springer Nature Switzerland AG 2024.; International Conference on Unconventional Computation and Natural Computation, UCNC ; Conference date: 17-06-2024 Through 21-06-2024",

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doi = "10.1007/978-3-031-63742-1_13",

language = "English",

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series = "Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)",

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editor = "Da-Jung Cho and Jongmin Kim",

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Elonen, A, Mohammed, A & Orponen, P 2024, A General Design Method for Scaffold-Free DNA Wireframe Nanostructures. julkaisussa D-J Cho & J Kim (toim), Unconventional Computation and Natural Computation - 21st International Conference, UCNC 2024, Proceedings. Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics), Vuosikerta 14776 LNCS, Springer, Sivut 178-189, International Conference on Unconventional Computation and Natural Computation, Pohang, Etelä-Korea, 17/06/2024. https://doi.org/10.1007/978-3-031-63742-1_13

A General Design Method for Scaffold-Free DNA Wireframe Nanostructures. / Elonen, Antti; Mohammed, Abdulmelik; Orponen, Pekka.
Unconventional Computation and Natural Computation - 21st International Conference, UCNC 2024, Proceedings. toim. / Da-Jung Cho; Jongmin Kim. Springer, 2024. s. 178-189 (Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics); Vuosikerta 14776 LNCS).

Tutkimustuotos: Artikkeli kirjassa/konferenssijulkaisussa › Conference article in proceedings › Scientific › vertaisarvioitu

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T1 - A General Design Method for Scaffold-Free DNA Wireframe Nanostructures

AU - Elonen, Antti

AU - Mohammed, Abdulmelik

AU - Orponen, Pekka

N1 - Conference code: 21

PY - 2024

Y1 - 2024

N2 - 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.

AB - 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.

KW - cycle covers

KW - DNA origami

KW - DNA wireframes

KW - scaffold-free nanostructure design

KW - strong anti-parallel traces

KW - topological graph embeddings

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T3 - Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)

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Elonen A, Mohammed A, Orponen P. A General Design Method for Scaffold-Free DNA Wireframe Nanostructures. julkaisussa Cho DJ, Kim J, toimittajat, Unconventional Computation and Natural Computation - 21st International Conference, UCNC 2024, Proceedings. Springer. 2024. s. 178-189. (Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)). doi: 10.1007/978-3-031-63742-1_13