Coarse-grained modelling of DNA-RNA hybrids
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arXiv
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| Autori principali: | , , , , |
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| Natura: | Preprint |
| Pubblicazione: |
2023
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| _version_ | 1866914716811526144 |
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| author | Ratajczyk, Eryk J. Šulc, Petr Turberfield, Andrew J. Doye, Jonathan P. K. Louis, Ard A. |
| author_facet | Ratajczyk, Eryk J. Šulc, Petr Turberfield, Andrew J. Doye, Jonathan P. K. Louis, Ard A. |
| contents | We introduce oxNA, a new model for the simulation of DNA-RNA hybrids which is based on two previously developed coarse-grained models$\unicode{x2014}$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$\unicode{x2014}$calculating the free energy profiles of hybrid strand displacement reactions, studying the resolution of a short R-loop and simulating RNA-scaffolded wireframe origami. |
| format | Preprint |
| id |
arxiv_https___arxiv_org_abs_2311_07709 |
| institution | arXiv |
| publishDate | 2023 |
| record_format | arxiv |
| spellingShingle | Coarse-grained modelling of DNA-RNA hybrids Ratajczyk, Eryk J. Šulc, Petr Turberfield, Andrew J. Doye, Jonathan P. K. Louis, Ard A. Soft Condensed Matter Biological Physics Biomolecules We introduce oxNA, a new model for the simulation of DNA-RNA hybrids which is based on two previously developed coarse-grained models$\unicode{x2014}$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$\unicode{x2014}$calculating the free energy profiles of hybrid strand displacement reactions, studying the resolution of a short R-loop and simulating RNA-scaffolded wireframe origami. |
| title | Coarse-grained modelling of DNA-RNA hybrids |
| topic | Soft Condensed Matter Biological Physics Biomolecules |
| url | https://arxiv.org/abs/2311.07709 |