Algorithmic design of cotranscriptionally folding 2D RNA origami structures

Abdulmelik Mohammed; Pekka Orponen; Sachith Pai

doi:10.1007/978-3-319-92435-9_12

Algorithmic design of cotranscriptionally folding 2D RNA origami structures

Abdulmelik Mohammed, Pekka Orponen, Sachith Pai

Tutkimustuotos: Artikkeli kirjassa/konferenssijulkaisussa › Conference contribution › Scientific › vertaisarvioitu

188 Lataukset (Pure)

Abstrakti

We address a biochemical folding obstacle of “polymerase trapping” that arises in the remarkable RNA origami tile design framework of Geary, Rothemund and Andersen (Science 2014). We present a combinatorial formulation of this obstacle, together with an optimisation procedure that yields designs minimising the risk of encountering the corresponding topological trap in the tile folding phase. The procedure has been embedded in an automated software pipeline, and we provide examples of designs produced by the software, including an optimised version of the RNA smiley-face tile proposed by Geary and Andersen (DNA 2014).

Alkuperäiskieli	Englanti
Otsikko	Unconventional Computation and Natural Computation
Alaotsikko	17th International Conference, UCNC 2018, Fontainebleau, France, June 25-29, 2018, Proceedings
Toimittajat	Susan Stepney, Sergey Verlan
Sivut	159-172
ISBN (elektroninen)	978-3-319-92435-9
DOI - pysyväislinkit	https://doi.org/10.1007/978-3-319-92435-9_12
Tila	Julkaistu - 31 toukok. 2018
OKM-julkaisutyyppi	A4 Artikkeli konferenssijulkaisuussa
Tapahtuma	International Conference on Unconventional Computation and Natural Computation - Fontainebleau, Paris, Ranska Kesto: 25 kesäk. 2018 → 29 kesäk. 2018 Konferenssinumero: 17

Julkaisusarja

Nimi	Lecture Notes in Computer Science
Kustantaja	Springer
Vuosikerta	10867
ISSN (painettu)	0302-9743
ISSN (elektroninen)	1611-3349

Conference

Conference	International Conference on Unconventional Computation and Natural Computation
Lyhennettä	UCNC
Maa/Alue	Ranska
Kaupunki	Paris
Ajanjakso	25/06/2018 → 29/06/2018

Pääsy asiakirjaan

10.1007/978-3-319-92435-9_12

ucnc_2018Accepted author manuscript, 424 KB

SFX-saatavuus

Koko teksti

1 Päättynyt

ALBION: Algoritmisia menetelmiä biomolekulaaristen nanorakenteiden suunnitteluun (ALBION)
Mohammed, A., Orponen, P., Lohikko, A., Elonen, A., Korpela, D., Gautam, V., Saman Booy, M. & Vo, T.
01/09/2017 → 31/08/2021
Projekti: Academy of Finland: Other research funding

Science-IT
Mikko Hakala (Manager)
Perustieteiden korkeakoulu
Laitteistot/tilat: Facility

Siteeraa tätä

Mohammed, A., Orponen, P., & Pai, S. (2018). Algorithmic design of cotranscriptionally folding 2D RNA origami structures. teoksessa S. Stepney, & S. Verlan (Toimittajat), Unconventional Computation and Natural Computation: 17th International Conference, UCNC 2018, Fontainebleau, France, June 25-29, 2018, Proceedings (Sivut 159-172). (Lecture Notes in Computer Science; Vuosikerta 10867). https://doi.org/10.1007/978-3-319-92435-9_12

Mohammed, Abdulmelik ; Orponen, Pekka ; Pai, Sachith. / Algorithmic design of cotranscriptionally folding 2D RNA origami structures. Unconventional Computation and Natural Computation: 17th International Conference, UCNC 2018, Fontainebleau, France, June 25-29, 2018, Proceedings. Toimittaja / Susan Stepney ; Sergey Verlan. 2018. Sivut 159-172 (Lecture Notes in Computer Science).

@inproceedings{0edf573949cd442da29b7413e728e333,

title = "Algorithmic design of cotranscriptionally folding 2D RNA origami structures",

abstract = "We address a biochemical folding obstacle of “polymerase trapping” that arises in the remarkable RNA origami tile design framework of Geary, Rothemund and Andersen (Science 2014). We present a combinatorial formulation of this obstacle, together with an optimisation procedure that yields designs minimising the risk of encountering the corresponding topological trap in the tile folding phase. The procedure has been embedded in an automated software pipeline, and we provide examples of designs produced by the software, including an optimised version of the RNA smiley-face tile proposed by Geary and Andersen (DNA 2014).",

keywords = "RNA origami, RNA tiles, RNA nanotechnology, Rational design, Cotranscriptional folding, Grid graphs, Spanning trees, rna",

author = "Abdulmelik Mohammed and Pekka Orponen and Sachith Pai",

year = "2018",

month = may,

day = "31",

doi = "10.1007/978-3-319-92435-9_12",

language = "English",

isbn = "978-3-319-92434-2",

series = "Lecture Notes in Computer Science",

publisher = "Springer",

pages = "159--172",

editor = "Susan Stepney and Sergey Verlan",

booktitle = "Unconventional Computation and Natural Computation",

note = "International Conference on Unconventional Computation and Natural Computation, UCNC ; Conference date: 25-06-2018 Through 29-06-2018",

}

Mohammed, A , Orponen, P & Pai, S 2018, Algorithmic design of cotranscriptionally folding 2D RNA origami structures. julkaisussa S Stepney & S Verlan (toim), Unconventional Computation and Natural Computation: 17th International Conference, UCNC 2018, Fontainebleau, France, June 25-29, 2018, Proceedings. Lecture Notes in Computer Science, Vuosikerta 10867, Sivut 159-172, International Conference on Unconventional Computation and Natural Computation, Paris, Ranska, 25/06/2018. https://doi.org/10.1007/978-3-319-92435-9_12

Algorithmic design of cotranscriptionally folding 2D RNA origami structures. / Mohammed, Abdulmelik ; Orponen, Pekka; Pai, Sachith.

Unconventional Computation and Natural Computation: 17th International Conference, UCNC 2018, Fontainebleau, France, June 25-29, 2018, Proceedings. toim. / Susan Stepney; Sergey Verlan. 2018. s. 159-172 (Lecture Notes in Computer Science; Vuosikerta 10867).

Tutkimustuotos: Artikkeli kirjassa/konferenssijulkaisussa › Conference contribution › Scientific › vertaisarvioitu

TY - GEN

T1 - Algorithmic design of cotranscriptionally folding 2D RNA origami structures

AU - Mohammed, Abdulmelik

AU - Orponen, Pekka

AU - Pai, Sachith

N1 - Conference code: 17

PY - 2018/5/31

Y1 - 2018/5/31

N2 - We address a biochemical folding obstacle of “polymerase trapping” that arises in the remarkable RNA origami tile design framework of Geary, Rothemund and Andersen (Science 2014). We present a combinatorial formulation of this obstacle, together with an optimisation procedure that yields designs minimising the risk of encountering the corresponding topological trap in the tile folding phase. The procedure has been embedded in an automated software pipeline, and we provide examples of designs produced by the software, including an optimised version of the RNA smiley-face tile proposed by Geary and Andersen (DNA 2014).

AB - We address a biochemical folding obstacle of “polymerase trapping” that arises in the remarkable RNA origami tile design framework of Geary, Rothemund and Andersen (Science 2014). We present a combinatorial formulation of this obstacle, together with an optimisation procedure that yields designs minimising the risk of encountering the corresponding topological trap in the tile folding phase. The procedure has been embedded in an automated software pipeline, and we provide examples of designs produced by the software, including an optimised version of the RNA smiley-face tile proposed by Geary and Andersen (DNA 2014).

KW - RNA origami

KW - RNA tiles

KW - RNA nanotechnology

KW - Rational design

KW - Cotranscriptional folding

KW - Grid graphs

KW - Spanning trees

KW - rna

U2 - 10.1007/978-3-319-92435-9_12

DO - 10.1007/978-3-319-92435-9_12

M3 - Conference contribution

SN - 978-3-319-92434-2

T3 - Lecture Notes in Computer Science

SP - 159

EP - 172

BT - Unconventional Computation and Natural Computation

A2 - Stepney, Susan

A2 - Verlan, Sergey

T2 - International Conference on Unconventional Computation and Natural Computation

Y2 - 25 June 2018 through 29 June 2018

ER -

Mohammed A , Orponen P, Pai S. Algorithmic design of cotranscriptionally folding 2D RNA origami structures. julkaisussa Stepney S, Verlan S, toimittajat, Unconventional Computation and Natural Computation: 17th International Conference, UCNC 2018, Fontainebleau, France, June 25-29, 2018, Proceedings. 2018. s. 159-172. (Lecture Notes in Computer Science). https://doi.org/10.1007/978-3-319-92435-9_12

Algorithmic design of cotranscriptionally folding 2D RNA origami structures

Abstrakti

Julkaisusarja

Conference

Pääsy asiakirjaan

SFX-saatavuus

Sormenjälki

Projektit

ALBION: Algoritmisia menetelmiä biomolekulaaristen nanorakenteiden suunnitteluun (ALBION)

Laitteet

Science-IT

Siteeraa tätä