Coarse-grained modeling of DNA-RNA hybrids.
J Chem Phys
; 160(11)2024 Mar 21.
Article
in En
| MEDLINE
| ID: mdl-38497475
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.
Full text:
1
Collection:
01-internacional
Database:
MEDLINE
Main subject:
DNA
/
RNA
Language:
En
Journal:
J Chem Phys
Year:
2024
Document type:
Article
Affiliation country:
United kingdom
Country of publication:
United States