We introduce oxNA, a new model for the simulation of DNA-RNA hybrids which is based on two previously developed coarse-grained models\unicodex2014oxDNA 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\unicodex2014calculating the free energy profiles of hybrid strand displacement reactions, studying the resolution of a short R-loop and simulating RNA-scaffolded wireframe origami.
@article{arxiv.2311.07709,
title = {Coarse-grained modelling of DNA-RNA hybrids},
author = {Eryk J. Ratajczyk and Petr Šulc and Andrew J. Turberfield and Jonathan P. K. Doye and Ard A. Louis},
journal= {arXiv preprint arXiv:2311.07709},
year = {2024}
}