A nucleotide-level coarse-grained model of RNA

Petr Sulc, Flavio Romano, Thomas E. Ouldridge, Jonathan P.K. Doye, Ard A. Louis

Research output: Contribution to journalArticle

41 Citations (Scopus)

Abstract

We present a new, nucleotide-level model for RNA, oxRNA, based on the coarse-graining methodology recently developed for the oxDNA model of DNA. The model is designed to reproduce structural, mechanical, and thermodynamic properties of RNA, and the coarse-graining level aims to retain the relevant physics for RNA hybridization and the structure of single- and double-stranded RNA. In order to explore its strengths and weaknesses, we test the model in a range of nanotechnological and biological settings. Applications explored include the folding thermodynamics of a pseudoknot, the formation of a kissing loop complex, the structure of a hexagonal RNA nanoring, and the unzipping of a hairpin motif. We argue that the model can be used for efficient simulations of the structure of systems with thousands of base pairs, and for the assembly of systems of up to hundreds of base pairs. The source code implementing the model is released for public use.

Original languageEnglish (US)
Article number235102
JournalJournal of Chemical Physics
Volume140
Issue number23
DOIs
StatePublished - Jun 21 2014
Externally publishedYes

Fingerprint

nucleotides
Nucleotides
RNA
Nanorings
Double-Stranded RNA
folding
Structural properties
Thermodynamic properties
Physics
deoxyribonucleic acid
thermodynamic properties
assembly
Thermodynamics
mechanical properties
methodology
Mechanical properties
thermodynamics
physics
DNA
simulation

ASJC Scopus subject areas

  • Physics and Astronomy(all)
  • Physical and Theoretical Chemistry

Cite this

Sulc, P., Romano, F., Ouldridge, T. E., Doye, J. P. K., & Louis, A. A. (2014). A nucleotide-level coarse-grained model of RNA. Journal of Chemical Physics, 140(23), [235102]. https://doi.org/10.1063/1.4881424

A nucleotide-level coarse-grained model of RNA. / Sulc, Petr; Romano, Flavio; Ouldridge, Thomas E.; Doye, Jonathan P.K.; Louis, Ard A.

In: Journal of Chemical Physics, Vol. 140, No. 23, 235102, 21.06.2014.

Research output: Contribution to journalArticle

Sulc, P, Romano, F, Ouldridge, TE, Doye, JPK & Louis, AA 2014, 'A nucleotide-level coarse-grained model of RNA', Journal of Chemical Physics, vol. 140, no. 23, 235102. https://doi.org/10.1063/1.4881424
Sulc P, Romano F, Ouldridge TE, Doye JPK, Louis AA. A nucleotide-level coarse-grained model of RNA. Journal of Chemical Physics. 2014 Jun 21;140(23). 235102. https://doi.org/10.1063/1.4881424
Sulc, Petr ; Romano, Flavio ; Ouldridge, Thomas E. ; Doye, Jonathan P.K. ; Louis, Ard A. / A nucleotide-level coarse-grained model of RNA. In: Journal of Chemical Physics. 2014 ; Vol. 140, No. 23.
@article{832bc69dd988454893b82c8fd93f035d,
title = "A nucleotide-level coarse-grained model of RNA",
abstract = "We present a new, nucleotide-level model for RNA, oxRNA, based on the coarse-graining methodology recently developed for the oxDNA model of DNA. The model is designed to reproduce structural, mechanical, and thermodynamic properties of RNA, and the coarse-graining level aims to retain the relevant physics for RNA hybridization and the structure of single- and double-stranded RNA. In order to explore its strengths and weaknesses, we test the model in a range of nanotechnological and biological settings. Applications explored include the folding thermodynamics of a pseudoknot, the formation of a kissing loop complex, the structure of a hexagonal RNA nanoring, and the unzipping of a hairpin motif. We argue that the model can be used for efficient simulations of the structure of systems with thousands of base pairs, and for the assembly of systems of up to hundreds of base pairs. The source code implementing the model is released for public use.",
author = "Petr Sulc and Flavio Romano and Ouldridge, {Thomas E.} and Doye, {Jonathan P.K.} and Louis, {Ard A.}",
year = "2014",
month = "6",
day = "21",
doi = "10.1063/1.4881424",
language = "English (US)",
volume = "140",
journal = "Journal of Chemical Physics",
issn = "0021-9606",
publisher = "American Institute of Physics Publising LLC",
number = "23",

}

TY - JOUR

T1 - A nucleotide-level coarse-grained model of RNA

AU - Sulc, Petr

AU - Romano, Flavio

AU - Ouldridge, Thomas E.

AU - Doye, Jonathan P.K.

AU - Louis, Ard A.

PY - 2014/6/21

Y1 - 2014/6/21

N2 - We present a new, nucleotide-level model for RNA, oxRNA, based on the coarse-graining methodology recently developed for the oxDNA model of DNA. The model is designed to reproduce structural, mechanical, and thermodynamic properties of RNA, and the coarse-graining level aims to retain the relevant physics for RNA hybridization and the structure of single- and double-stranded RNA. In order to explore its strengths and weaknesses, we test the model in a range of nanotechnological and biological settings. Applications explored include the folding thermodynamics of a pseudoknot, the formation of a kissing loop complex, the structure of a hexagonal RNA nanoring, and the unzipping of a hairpin motif. We argue that the model can be used for efficient simulations of the structure of systems with thousands of base pairs, and for the assembly of systems of up to hundreds of base pairs. The source code implementing the model is released for public use.

AB - We present a new, nucleotide-level model for RNA, oxRNA, based on the coarse-graining methodology recently developed for the oxDNA model of DNA. The model is designed to reproduce structural, mechanical, and thermodynamic properties of RNA, and the coarse-graining level aims to retain the relevant physics for RNA hybridization and the structure of single- and double-stranded RNA. In order to explore its strengths and weaknesses, we test the model in a range of nanotechnological and biological settings. Applications explored include the folding thermodynamics of a pseudoknot, the formation of a kissing loop complex, the structure of a hexagonal RNA nanoring, and the unzipping of a hairpin motif. We argue that the model can be used for efficient simulations of the structure of systems with thousands of base pairs, and for the assembly of systems of up to hundreds of base pairs. The source code implementing the model is released for public use.

UR - http://www.scopus.com/inward/record.url?scp=84903139508&partnerID=8YFLogxK

UR - http://www.scopus.com/inward/citedby.url?scp=84903139508&partnerID=8YFLogxK

U2 - 10.1063/1.4881424

DO - 10.1063/1.4881424

M3 - Article

C2 - 24952569

AN - SCOPUS:84903139508

VL - 140

JO - Journal of Chemical Physics

JF - Journal of Chemical Physics

SN - 0021-9606

IS - 23

M1 - 235102

ER -