Coarse-grained modeling of DNA–RNA hybrids

Abstract

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.