Journal article
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.
- Publication status:
- Published
- Peer review status:
- Peer reviewed
Actions
Access Document
- Files:
-
-
(Preview, Version of record, pdf, 8.7MB, Terms of use)
-
- Publisher copy:
- 10.1063/5.0199558
Authors
- Publisher:
- American Institute of Physics
- Journal:
- Journal of Chemical Physics More from this journal
- Volume:
- 160
- Issue:
- 11
- Article number:
- 115101
- Publication date:
- 2024-03-18
- Acceptance date:
- 2024-01-26
- DOI:
- EISSN:
-
1089-7690
- ISSN:
-
0021-9606
- Language:
-
English
- Pubs id:
-
2120429
- Local pid:
-
pubs:2120429
- Deposit date:
-
2025-04-29
Terms of use
- Copyright holder:
- Ratajczyk et al
- Copyright date:
- 2024
- Rights statement:
- © 2024 Author(s). All article content, except where otherwise noted, is licensed under a Creative Commons Attribution (CC BY) license (http://creativecommons.org/licenses/by/4.0/).
- Licence:
- CC Attribution (CC BY)
If you are the owner of this record, you can report an update to it here: Report update to this record