| Autor: |
Ratajczyk, Eryk J., Šulc, Petr, Turberfield, Andrew J., Doye, Jonathan P. K., Louis, Ard A. |
| Zdroj: |
Journal of Chemical Physics; 3/21/2024, Vol. 160 Issue 11, p1-14, 14p |
| Abstrakt: |
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. [ABSTRACT FROM AUTHOR] |
| Databáze: |
Complementary Index |
| Externí odkaz: |
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