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Coarse-grained modelling of DNA-RNA hybridsEryk J. Ratajczyk, Petr Šulc, Andrew J. Turberfield, Jonathan P. K. Doye and Ard A. LouisAbstractWe 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.The full paper is available from arXiv.org. |