A coarse-grained DNA model to study protein-DNA interactions and liquid-liquid phase separation.

ABSTRACT: Recent advances in coarse-grained (CG) computational models for DNA have enabled molecular-level insights into the behavior of DNA in complex multiscale systems. However, most existing CG DNA models are not compatible with CG protein models, limiting their applications for emerging topics such as protein-nucleic acid assemblies. Here, we present a new computationally efficient CG DNA model. We first use experimental data to establish the model's ability to predict various aspects of DNA behavior, including melting thermodynamics and relevant local structural properties such as the major and minor grooves. We then employ an all-atom hydropathy scale to define non-bonded interactions between protein and DNA sites, to make our DNA model compatible with an existing CG protein model (HPS-Urry),

SUBMITTER: Kapoor U 

PROVIDER: S-EPMC10245785 | biostudies-literature | 2023 May

REPOSITORIES: biostudies-literature