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Title: Coarse-grained modeling of DNA–RNA hybrids
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.  more » « less
Award ID(s):
2211794
NSF-PAR ID:
10516693
Author(s) / Creator(s):
; ; ; ;
Publisher / Repository:
AIP
Date Published:
Journal Name:
The Journal of Chemical Physics
Volume:
160
Issue:
11
ISSN:
0021-9606
Format(s):
Medium: X
Sponsoring Org:
National Science Foundation
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