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...
| Main Authors: | , , , , |
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| Format: | Internet publication |
| Language: | English |
| Published: |
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 |