We introduce oxNA, a new model for the simulation of DNA-RNA hybrids that 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 parameterizing 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.
CITATION STYLE
Ratajczyk, E. J., Šulc, P., Turberfield, A. J., Doye, J. P. K., & Louis, A. A. (2024). Coarse-grained modeling of DNA-RNA hybrids. Journal of Chemical Physics, 160(11). https://doi.org/10.1063/5.0199558
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