Coarse-grained modelling of DNA-RNA hybrids
We introduce oxNA, a new model for the simulation of DNA-RNA hybrids which is based on two previously developed coarse-grained models—oxDNA and oxRNA. The model naturally reproduces the physical properties of hybrid duplexes including their structure, persistence length and force-extension character...
Hauptverfasser: | , , , , |
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Format: | Internet publication |
Sprache: | English |
Veröffentlicht: |
2023
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_version_ | 1826312640229539840 |
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author | Ratajczyk, EJ Šulc, P Turberfield, AJ Doye, JPK Louis, AA |
author_facet | Ratajczyk, EJ Šulc, P Turberfield, AJ Doye, JPK Louis, AA |
author_sort | Ratajczyk, EJ |
collection | OXFORD |
description | We introduce oxNA, a new model for the simulation of DNA-RNA hybrids which is based on two previously developed coarse-grained models—oxDNA and oxRNA. The model naturally reproduces the physical properties of hybrid duplexes including their structure, persistence length and force-extension characteristics. By parameterising the DNA-RNA hydrogen bonding interaction we fit the model's thermodynamic properties to experimental data using both average-sequence and sequence-dependent parameters. To demonstrate the model's applicability we provide three examples of its use—calculating the free energy profiles of hybrid strand displacement reactions, studying the resolution of a short R-loop and simulating RNA-scaffolded wireframe origami. |
first_indexed | 2024-04-09T03:57:36Z |
format | Internet publication |
id | oxford-uuid:3d72022d-543c-49d8-8f39-82ab17c3a465 |
institution | University of Oxford |
language | English |
last_indexed | 2024-04-09T03:57:36Z |
publishDate | 2023 |
record_format | dspace |
spelling | oxford-uuid:3d72022d-543c-49d8-8f39-82ab17c3a4652024-04-04T14:27:18ZCoarse-grained modelling of DNA-RNA hybridsInternet publicationhttp://purl.org/coar/resource_type/c_7ad9uuid:3d72022d-543c-49d8-8f39-82ab17c3a465EnglishSymplectic Elements2023Ratajczyk, EJŠulc, PTurberfield, AJDoye, JPKLouis, AAWe introduce oxNA, a new model for the simulation of DNA-RNA hybrids which is based on two previously developed coarse-grained models—oxDNA and oxRNA. The model naturally reproduces the physical properties of hybrid duplexes including their structure, persistence length and force-extension characteristics. By parameterising the DNA-RNA hydrogen bonding interaction we fit the model's thermodynamic properties to experimental data using both average-sequence and sequence-dependent parameters. To demonstrate the model's applicability we provide three examples of its use—calculating the free energy profiles of hybrid strand displacement reactions, studying the resolution of a short R-loop and simulating RNA-scaffolded wireframe origami. |
spellingShingle | Ratajczyk, EJ Šulc, P Turberfield, AJ Doye, JPK Louis, AA Coarse-grained modelling of DNA-RNA hybrids |
title | Coarse-grained modelling of DNA-RNA hybrids |
title_full | Coarse-grained modelling of DNA-RNA hybrids |
title_fullStr | Coarse-grained modelling of DNA-RNA hybrids |
title_full_unstemmed | Coarse-grained modelling of DNA-RNA hybrids |
title_short | Coarse-grained modelling of DNA-RNA hybrids |
title_sort | coarse grained modelling of dna rna hybrids |
work_keys_str_mv | AT ratajczykej coarsegrainedmodellingofdnarnahybrids AT sulcp coarsegrainedmodellingofdnarnahybrids AT turberfieldaj coarsegrainedmodellingofdnarnahybrids AT doyejpk coarsegrainedmodellingofdnarnahybrids AT louisaa coarsegrainedmodellingofdnarnahybrids |