Internet publication
Coarse-grained modelling of DNA-RNA hybrids
- Abstract:
- 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.
- Publication status:
- Published
- Peer review status:
- Not peer reviewed
Actions
Access Document
- Files:
-
-
(Preview, Pre-print, pdf, 7.0MB, Terms of use)
-
- Publisher copy:
- 10.48550/arxiv.2311.07709
Authors
- Host title:
- arXiv
- Pages:
- 1-15
- Publication date:
- 2023-11-13
- DOI:
- Language:
-
English
- Keywords:
- Pubs id:
-
1565691
- Local pid:
-
pubs:1565691
- Deposit date:
-
2024-03-18
Terms of use
- Copyright holder:
- Ratajczyk et al.
- Copyright date:
- 2023
- Rights statement:
- © The Author(s) 2023. This article is licensed under an arXiv.org perpetual, non-exclusive license 1.0.
- Licence:
- Other
If you are the owner of this record, you can report an update to it here: Report update to this record