DiSCO - Applications

Introduction
The chromatin fiber is a critical regulator of transcription and replication. In the chromatin fiber, each nucleosome core particle is represented as a DiSCO model with a few hundred discrete surface charges. The predicted chromatin model from Brownian dynamics simulation shows good agreement with the experimental diffusion coefficients and small angle X-ray scattering data.
More information
References
Beard D. A. & Schlick, T., Computational modeling predicts the structure and dynamics of chromatin fiber. Structure with Folding and Design, 9: 105-114, 2001.
Illustrations

From Fig. 1 of Beard & Schlick (Structure, 2001): Dinucleosome model with 277 charges per nucleosome core particle

From Daniel A. Beard: 48-nucleosome model for chromatin at different salt concentration C_S

Introduction
The 3-site juxtaposition of protein-bound supercoiled DNA is central to Hin-mediated inversion in S. typhimurium. (Two hix sites plus an enhancer must come together to form the invertasome.) Each Hin dimer and Fis dimer is represented as a DiSCO model respectively. This work aims to study the dependence of the rate of site juxtaposition on supercoiling, and the role of the proteins (Hin dimers and Fis dimers) on the juxtaposition kinetics.
More information
References
Huang, J. & Schlick, T., Macroscopic modeling and simulations of supercoiled DNA with bound proteins. J. Chem. Phys, 117: 8573-8586, 2002
Huang, J., Zhang, Q. & Schlick, T., Effect of DNA superhelicity and bound proteins on mechanistic aspects of the Hin-mediated and Fis-enhanced inversion. Biophys. J., 85: 804-817, 2003.
Illustrations

Provided by Jing Huang: Hin / Fis / DNA model