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$\text{unicode}x2014$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$\text{unicode}x2014$calculating the free energy profiles of hybrid strand displacement reactions, studying the resolution of a short R-loop and simulating RNA-scaffolded wireframe origami.