A nucleotide-level coarse-grained model of RNA
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 p...
| Main Authors: | , , , , |
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| Formato: | Journal article |
| Idioma: | English |
| Publicado: |
American Institute of Physics
2014
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| _version_ | 1826269439012634624 |
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| author | Šulc, P Romano, F Ouldridge, T Doye, J Louis, A |
| author_facet | Šulc, P Romano, F Ouldridge, T Doye, J Louis, A |
| author_sort | Šulc, P |
| collection | OXFORD |
| description | 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. |
| first_indexed | 2024-03-06T21:25:04Z |
| format | Journal article |
| id | oxford-uuid:42d0351a-1053-4fea-8764-b51a61aff7cd |
| institution | University of Oxford |
| language | English |
| last_indexed | 2024-03-06T21:25:04Z |
| publishDate | 2014 |
| publisher | American Institute of Physics |
| record_format | dspace |
| spelling | oxford-uuid:42d0351a-1053-4fea-8764-b51a61aff7cd2022-03-26T14:51:42ZA nucleotide-level coarse-grained model of RNAJournal articlehttp://purl.org/coar/resource_type/c_dcae04bcuuid:42d0351a-1053-4fea-8764-b51a61aff7cdEnglishSymplectic Elements at OxfordAmerican Institute of Physics2014Šulc, PRomano, FOuldridge, TDoye, JLouis, AWe 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. |
| spellingShingle | Šulc, P Romano, F Ouldridge, T Doye, J Louis, A A nucleotide-level coarse-grained model of RNA |
| title | A nucleotide-level coarse-grained model of RNA |
| title_full | A nucleotide-level coarse-grained model of RNA |
| title_fullStr | A nucleotide-level coarse-grained model of RNA |
| title_full_unstemmed | A nucleotide-level coarse-grained model of RNA |
| title_short | A nucleotide-level coarse-grained model of RNA |
| title_sort | nucleotide level coarse grained model of rna |
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