Designing 3D RNA Origami Nanostructures with a Minimum Number of Kissing Loops

Antti Elonen; Pekka Orponen

doi:10.4230/LIPIcs.DNA.30.4

Designing 3D RNA Origami Nanostructures with a Minimum Number of Kissing Loops

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

16 Lataukset (Pure)

Abstrakti

We present a general design technique for rendering any 3D wireframe model, that is any connected graph linearly embedded in 3D space, as an RNA origami nanostructure with a minimum number of kissing loops. The design algorithm, which applies some ideas and methods from topological graph theory, produces renderings that contain at most one kissing-loop pair for many interesting model families, including for instance all fully triangulated wireframes and the wireframes of all Platonic solids. The design method is already implemented and available for use in the design tool DNAforge (https://dnaforge.org).

Alkuperäiskieli	Englanti
Otsikko	30th International Conference on DNA Computing and Molecular Programming, DNA 30 2024
Toimittajat	Shinnosuke Seki, Jaimie Marie Stewart
Kustantaja	Schloss Dagstuhl - Leibniz-Zentrum für Informatik
Sivut	1-12
Sivumäärä	12
ISBN (elektroninen)	978-3-95977-344-7
DOI - pysyväislinkit	https://doi.org/10.4230/LIPIcs.DNA.30.4
Tila	Julkaistu - syysk. 2024
OKM-julkaisutyyppi	A4 Artikkeli konferenssijulkaisussa
Tapahtuma	International Conference on DNA Computing and Molecular Programming - Baltimore, Yhdysvallat Kesto: 16 syysk. 2024 → 20 syysk. 2024 Konferenssinumero: 30

Julkaisusarja

Nimi	Leibniz International Proceedings in Informatics, LIPIcs
Kustantaja	Schloss Dagstuhl - Leibniz-Zentrum für Informatik
Vuosikerta	314
ISSN (painettu)	1868-8969

Conference

Conference	International Conference on DNA Computing and Molecular Programming
Lyhennettä	DNA
Maa/Alue	Yhdysvallat
Kaupunki	Baltimore
Ajanjakso	16/09/2024 → 20/09/2024

Pääsy asiakirjaan

10.4230/LIPIcs.DNA.30.4

Designing 3D RNA Origami Nanostructures with a Minimum Number of Kissing LoopsFinal published version, 26,2 MBLisenssi: CC BY

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Elonen, A., & Orponen, P. (2024). Designing 3D RNA Origami Nanostructures with a Minimum Number of Kissing Loops. teoksessa S. Seki, & J. M. Stewart (Toimittajat), 30th International Conference on DNA Computing and Molecular Programming, DNA 30 2024 (Sivut 1-12). Artikkeli 4 (Leibniz International Proceedings in Informatics, LIPIcs; Vuosikerta 314). Schloss Dagstuhl - Leibniz-Zentrum für Informatik. https://doi.org/10.4230/LIPIcs.DNA.30.4

Elonen, Antti ; Orponen, Pekka. / Designing 3D RNA Origami Nanostructures with a Minimum Number of Kissing Loops. 30th International Conference on DNA Computing and Molecular Programming, DNA 30 2024. Toimittaja / Shinnosuke Seki ; Jaimie Marie Stewart. Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2024. Sivut 1-12 (Leibniz International Proceedings in Informatics, LIPIcs).

@inproceedings{7795698b4a824b5888b4610f86dc56de,

title = "Designing 3D RNA Origami Nanostructures with a Minimum Number of Kissing Loops",

abstract = "We present a general design technique for rendering any 3D wireframe model, that is any connected graph linearly embedded in 3D space, as an RNA origami nanostructure with a minimum number of kissing loops. The design algorithm, which applies some ideas and methods from topological graph theory, produces renderings that contain at most one kissing-loop pair for many interesting model families, including for instance all fully triangulated wireframes and the wireframes of all Platonic solids. The design method is already implemented and available for use in the design tool DNAforge (https://dnaforge.org).",

keywords = "kissing loops, polyhedra, RNA origami, self-assembly, topological graph embeddings, wireframe nanostructures",

author = "Antti Elonen and Pekka Orponen",

note = "Publisher Copyright: {\textcopyright} Antti Elonen and Pekka Orponen;; International Conference on DNA Computing and Molecular Programming, DNA ; Conference date: 16-09-2024 Through 20-09-2024",

year = "2024",

month = sep,

doi = "10.4230/LIPIcs.DNA.30.4",

language = "English",

series = "Leibniz International Proceedings in Informatics, LIPIcs",

publisher = "Schloss Dagstuhl - Leibniz-Zentrum f{\"u}r Informatik",

pages = "1--12",

editor = "Shinnosuke Seki and Stewart, {Jaimie Marie}",

booktitle = "30th International Conference on DNA Computing and Molecular Programming, DNA 30 2024",

address = "Germany",

}

Elonen, A & Orponen, P 2024, Designing 3D RNA Origami Nanostructures with a Minimum Number of Kissing Loops. julkaisussa S Seki & JM Stewart (toim), 30th International Conference on DNA Computing and Molecular Programming, DNA 30 2024., 4, Leibniz International Proceedings in Informatics, LIPIcs, Vuosikerta 314, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, Sivut 1-12, International Conference on DNA Computing and Molecular Programming, Baltimore, Maryland, Yhdysvallat, 16/09/2024. https://doi.org/10.4230/LIPIcs.DNA.30.4

Designing 3D RNA Origami Nanostructures with a Minimum Number of Kissing Loops. / Elonen, Antti ; Orponen, Pekka.
30th International Conference on DNA Computing and Molecular Programming, DNA 30 2024. toim. / Shinnosuke Seki; Jaimie Marie Stewart. Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2024. s. 1-12 4 (Leibniz International Proceedings in Informatics, LIPIcs; Vuosikerta 314).

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

TY - GEN

T1 - Designing 3D RNA Origami Nanostructures with a Minimum Number of Kissing Loops

AU - Elonen, Antti

AU - Orponen, Pekka

N1 - Conference code: 30

PY - 2024/9

Y1 - 2024/9

N2 - We present a general design technique for rendering any 3D wireframe model, that is any connected graph linearly embedded in 3D space, as an RNA origami nanostructure with a minimum number of kissing loops. The design algorithm, which applies some ideas and methods from topological graph theory, produces renderings that contain at most one kissing-loop pair for many interesting model families, including for instance all fully triangulated wireframes and the wireframes of all Platonic solids. The design method is already implemented and available for use in the design tool DNAforge (https://dnaforge.org).

AB - We present a general design technique for rendering any 3D wireframe model, that is any connected graph linearly embedded in 3D space, as an RNA origami nanostructure with a minimum number of kissing loops. The design algorithm, which applies some ideas and methods from topological graph theory, produces renderings that contain at most one kissing-loop pair for many interesting model families, including for instance all fully triangulated wireframes and the wireframes of all Platonic solids. The design method is already implemented and available for use in the design tool DNAforge (https://dnaforge.org).

KW - kissing loops

KW - polyhedra

KW - RNA origami

KW - self-assembly

KW - topological graph embeddings

KW - wireframe nanostructures

UR - http://www.scopus.com/inward/record.url?scp=85205013519&partnerID=8YFLogxK

U2 - 10.4230/LIPIcs.DNA.30.4

DO - 10.4230/LIPIcs.DNA.30.4

M3 - Conference article in proceedings

AN - SCOPUS:85205013519

T3 - Leibniz International Proceedings in Informatics, LIPIcs

SP - 1

EP - 12

BT - 30th International Conference on DNA Computing and Molecular Programming, DNA 30 2024

A2 - Seki, Shinnosuke

A2 - Stewart, Jaimie Marie

PB - Schloss Dagstuhl - Leibniz-Zentrum für Informatik

T2 - International Conference on DNA Computing and Molecular Programming

Y2 - 16 September 2024 through 20 September 2024

ER -

Elonen A , Orponen P. Designing 3D RNA Origami Nanostructures with a Minimum Number of Kissing Loops. julkaisussa Seki S, Stewart JM, toimittajat, 30th International Conference on DNA Computing and Molecular Programming, DNA 30 2024. Schloss Dagstuhl - Leibniz-Zentrum für Informatik. 2024. s. 1-12. 4. (Leibniz International Proceedings in Informatics, LIPIcs). doi: 10.4230/LIPIcs.DNA.30.4

Designing 3D RNA Origami Nanostructures with a Minimum Number of Kissing Loops

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